Starting phenix.real_space_refine on Wed Mar 4 03:51:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t0w_10361/03_2026/6t0w_10361.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t0w_10361/03_2026/6t0w_10361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6t0w_10361/03_2026/6t0w_10361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t0w_10361/03_2026/6t0w_10361.map" model { file = "/net/cci-nas-00/data/ceres_data/6t0w_10361/03_2026/6t0w_10361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t0w_10361/03_2026/6t0w_10361.cif" } resolution = 3.18 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 25 5.49 5 S 79 5.16 5 C 6599 2.51 5 N 1806 2.21 5 O 2047 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10556 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4161 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 21, 'TRANS': 499} Chain: "B" Number of atoms: 5174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5174 Classifications: {'peptide': 661} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 627} Chain breaks: 1 Chain: "C" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 688 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "V" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 533 Classifications: {'RNA': 25} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 10, 'rna3p_pyr': 9} Link IDs: {'rna2p': 6, 'rna3p': 18} Chain breaks: 2 Time building chain proxies: 2.35, per 1000 atoms: 0.22 Number of scatterers: 10556 At special positions: 0 Unit cell: (104.009, 101.908, 113.465, 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 79 16.00 P 25 15.00 O 2047 8.00 N 1806 7.00 C 6599 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: 0.89 Conformation dependent library (CDL) restraints added in 469.6 milliseconds 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 11 sheets defined 47.4% alpha, 12.0% beta 6 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 206 through 214 Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.804A pdb=" N MET A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 245 removed outlier: 4.213A pdb=" N ARG A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 removed outlier: 3.564A pdb=" N ILE A 269 " --> pdb=" O GLY A 266 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR A 270 " --> pdb=" O PRO A 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 270' Processing helix chain 'A' and resid 301 through 313 Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.684A pdb=" N ARG A 317 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 318' Processing helix chain 'A' and resid 332 through 347 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 376 through 383 Processing helix chain 'A' and resid 401 through 410 removed outlier: 3.631A pdb=" N THR A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 447 removed outlier: 3.845A pdb=" N ASN A 444 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 472 removed outlier: 3.942A pdb=" N THR A 453 " --> pdb=" O CYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.566A pdb=" N TRP A 533 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 569 Processing helix chain 'A' and resid 574 through 592 removed outlier: 3.921A pdb=" N LEU A 578 " --> pdb=" O ARG A 574 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER A 580 " --> pdb=" O CYS A 576 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU A 591 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 605 Processing helix chain 'A' and resid 628 through 646 Processing helix chain 'A' and resid 648 through 670 removed outlier: 4.594A pdb=" N ARG A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 687 removed outlier: 3.598A pdb=" N MET A 682 " --> pdb=" O ASP A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 715 removed outlier: 3.687A pdb=" N LYS A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 12 removed outlier: 4.185A pdb=" N ASP B 11 " --> pdb=" O PHE B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.608A pdb=" N THR B 20 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 115 Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 138 through 151 Processing helix chain 'B' and resid 152 through 154 No H-bonds generated for 'chain 'B' and resid 152 through 154' Processing helix chain 'B' and resid 163 through 174 removed outlier: 3.805A pdb=" N LEU B 174 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 248 through 265 removed outlier: 3.840A pdb=" N VAL B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 291 Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.610A pdb=" N LEU B 313 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 337 Processing helix chain 'B' and resid 339 through 345 Processing helix chain 'B' and resid 370 through 375 removed outlier: 3.528A pdb=" N LEU B 373 " --> pdb=" O CYS B 370 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE B 374 " --> pdb=" O PRO B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.507A pdb=" N TYR B 381 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 415 through 426 Processing helix chain 'B' and resid 454 through 471 removed outlier: 3.746A pdb=" N LEU B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 536 Processing helix chain 'B' and resid 539 through 558 Processing helix chain 'B' and resid 571 through 582 Processing helix chain 'B' and resid 584 through 588 removed outlier: 3.924A pdb=" N GLY B 587 " --> pdb=" O GLY B 584 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 588 " --> pdb=" O ARG B 585 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 584 through 588' Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 606 through 612 Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing helix chain 'B' and resid 616 through 624 Processing helix chain 'C' and resid 45 through 55 Processing helix chain 'C' and resid 65 through 70 Processing helix chain 'C' and resid 94 through 105 removed outlier: 3.655A pdb=" N VAL C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 128 removed outlier: 3.602A pdb=" N PHE C 121 " --> pdb=" O TYR C 117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 255 through 256 removed outlier: 3.550A pdb=" N GLY B 304 " --> pdb=" O PHE B 446 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE B 446 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 291 through 294 removed outlier: 7.325A pdb=" N TYR A 497 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU A 555 " --> pdb=" O ARG A 540 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ARG A 540 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N CYS A 557 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N VAL A 538 " --> pdb=" O CYS A 557 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 538 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 294 removed outlier: 5.290A pdb=" N ASP A 494 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL A 485 " --> pdb=" O ASP A 494 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LEU A 496 " --> pdb=" O ASN A 483 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASN A 483 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 498 " --> pdb=" O ILE A 481 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 477 " --> pdb=" O LYS A 502 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR A 476 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 373 through 374 removed outlier: 5.966A pdb=" N GLN A 373 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N GLN B 367 " --> pdb=" O GLN A 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 625 through 627 removed outlier: 7.066A pdb=" N VAL A 625 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN B 2 " --> pdb=" O THR A 619 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA7, first strand: chain 'B' and resid 128 through 130 removed outlier: 3.564A pdb=" N ARG B 135 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 179 through 184 Processing sheet with id=AA9, first strand: chain 'B' and resid 240 through 244 removed outlier: 6.938A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 488 through 491 Processing sheet with id=AB2, first strand: chain 'B' and resid 641 through 642 removed outlier: 4.101A pdb=" N ALA B 642 " --> pdb=" O MET B 654 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET B 654 " --> pdb=" O ALA B 642 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 455 hydrogen bonds defined for protein. 1290 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 32 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 1.89 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2394 1.33 - 1.45: 2340 1.45 - 1.57: 5907 1.57 - 1.69: 47 1.69 - 1.81: 133 Bond restraints: 10821 Sorted by residual: bond pdb=" N ASP B 445 " pdb=" CA ASP B 445 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.21e-02 6.83e+03 8.55e+00 bond pdb=" N LYS A 300 " pdb=" CA LYS A 300 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.16e-02 7.43e+03 6.84e+00 bond pdb=" N PHE B 446 " pdb=" CA PHE B 446 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.75e+00 bond pdb=" N ASP B 444 " pdb=" CA ASP B 444 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.27e-02 6.20e+03 6.49e+00 bond pdb=" N LYS A 301 " pdb=" CA LYS A 301 " ideal model delta sigma weight residual 1.452 1.487 -0.035 1.41e-02 5.03e+03 6.28e+00 ... (remaining 10816 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 14228 1.95 - 3.91: 432 3.91 - 5.86: 42 5.86 - 7.81: 11 7.81 - 9.77: 2 Bond angle restraints: 14715 Sorted by residual: angle pdb=" N LYS B 393 " pdb=" CA LYS B 393 " pdb=" C LYS B 393 " ideal model delta sigma weight residual 109.81 119.58 -9.77 2.21e+00 2.05e-01 1.95e+01 angle pdb=" N ILE B 339 " pdb=" CA ILE B 339 " pdb=" C ILE B 339 " ideal model delta sigma weight residual 112.12 108.89 3.23 8.40e-01 1.42e+00 1.48e+01 angle pdb=" CA TRP B 437 " pdb=" CB TRP B 437 " pdb=" CG TRP B 437 " ideal model delta sigma weight residual 113.60 120.80 -7.20 1.90e+00 2.77e-01 1.44e+01 angle pdb=" C ILE B 427 " pdb=" N LYS B 428 " pdb=" CA LYS B 428 " ideal model delta sigma weight residual 121.54 128.59 -7.05 1.91e+00 2.74e-01 1.36e+01 angle pdb=" N GLY A 542 " pdb=" CA GLY A 542 " pdb=" C GLY A 542 " ideal model delta sigma weight residual 110.58 115.27 -4.69 1.35e+00 5.49e-01 1.21e+01 ... (remaining 14710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 5859 17.31 - 34.61: 538 34.61 - 51.92: 128 51.92 - 69.22: 59 69.22 - 86.53: 16 Dihedral angle restraints: 6600 sinusoidal: 2943 harmonic: 3657 Sorted by residual: dihedral pdb=" CA MET B 409 " pdb=" C MET B 409 " pdb=" N MET B 410 " pdb=" CA MET B 410 " ideal model delta harmonic sigma weight residual 180.00 157.35 22.65 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA MET B 408 " pdb=" C MET B 408 " pdb=" N MET B 409 " pdb=" CA MET B 409 " ideal model delta harmonic sigma weight residual 180.00 159.03 20.97 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA THR B 303 " pdb=" C THR B 303 " pdb=" N GLY B 304 " pdb=" CA GLY B 304 " ideal model delta harmonic sigma weight residual -180.00 -161.33 -18.67 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 6597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1100 0.050 - 0.101: 450 0.101 - 0.151: 78 0.151 - 0.201: 7 0.201 - 0.252: 2 Chirality restraints: 1637 Sorted by residual: chirality pdb=" CB VAL A 485 " pdb=" CA VAL A 485 " pdb=" CG1 VAL A 485 " pdb=" CG2 VAL A 485 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB VAL A 277 " pdb=" CA VAL A 277 " pdb=" CG1 VAL A 277 " pdb=" CG2 VAL A 277 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA LYS B 393 " pdb=" N LYS B 393 " pdb=" C LYS B 393 " pdb=" CB LYS B 393 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.93e-01 ... (remaining 1634 not shown) Planarity restraints: 1796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " 0.034 2.00e-02 2.50e+03 1.53e-02 6.40e+00 pdb=" N9 A V 4 " -0.035 2.00e-02 2.50e+03 pdb=" C8 A V 4 " -0.006 2.00e-02 2.50e+03 pdb=" N7 A V 4 " 0.006 2.00e-02 2.50e+03 pdb=" C5 A V 4 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A V 4 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A V 4 " 0.005 2.00e-02 2.50e+03 pdb=" C2 A V 4 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A V 4 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A V 4 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 137 " 0.041 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO B 138 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 138 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 138 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 314 " 0.037 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PRO B 315 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 315 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 315 " 0.031 5.00e-02 4.00e+02 ... (remaining 1793 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2449 2.78 - 3.31: 8765 3.31 - 3.84: 17233 3.84 - 4.37: 20970 4.37 - 4.90: 36206 Nonbonded interactions: 85623 Sorted by model distance: nonbonded pdb=" OD2 ASP B 521 " pdb=" OH TYR B 558 " model vdw 2.251 3.040 nonbonded pdb=" O ILE B 18 " pdb=" OG1 THR B 21 " model vdw 2.283 3.040 nonbonded pdb=" O LEU A 211 " pdb=" OG SER A 215 " model vdw 2.286 3.040 nonbonded pdb=" O SER B 291 " pdb=" OG SER B 291 " model vdw 2.305 3.040 nonbonded pdb=" O ALA A 362 " pdb=" OG1 THR A 366 " model vdw 2.311 3.040 ... (remaining 85618 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.320 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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 : 0.008 0.072 10821 Z= 0.352 Angle : 0.803 9.768 14715 Z= 0.459 Chirality : 0.052 0.252 1637 Planarity : 0.007 0.063 1796 Dihedral : 15.458 86.528 4248 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.63 % Favored : 94.29 % Rotamer: Outliers : 6.26 % Allowed : 8.17 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -3.70 (0.18), residues: 1260 helix: -2.29 (0.16), residues: 548 sheet: -1.83 (0.37), residues: 151 loop : -2.71 (0.22), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 233 TYR 0.020 0.003 TYR A 644 PHE 0.015 0.002 PHE B 181 TRP 0.029 0.003 TRP B 437 HIS 0.006 0.001 HIS A 462 Details of bonding type rmsd covalent geometry : bond 0.00804 (10821) covalent geometry : angle 0.80324 (14715) hydrogen bonds : bond 0.15516 ( 467) hydrogen bonds : angle 6.45765 ( 1322) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 171 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 231 ASP cc_start: 0.7665 (m-30) cc_final: 0.7438 (t0) REVERT: A 261 ASP cc_start: 0.7393 (m-30) cc_final: 0.7192 (m-30) REVERT: A 373 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.8007 (pt0) REVERT: A 437 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: A 508 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7500 (mtp180) REVERT: B 196 ARG cc_start: 0.2403 (OUTLIER) cc_final: 0.1864 (mtt180) REVERT: B 273 VAL cc_start: 0.5345 (OUTLIER) cc_final: 0.5137 (p) REVERT: B 279 LYS cc_start: 0.6822 (mttt) cc_final: 0.6569 (mptt) REVERT: B 314 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7876 (m-40) REVERT: B 380 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8274 (mtm180) REVERT: B 570 LYS cc_start: 0.8100 (mttt) cc_final: 0.7782 (mtmm) REVERT: B 641 GLU cc_start: 0.3486 (OUTLIER) cc_final: 0.1952 (mp0) REVERT: C 120 PHE cc_start: 0.4881 (OUTLIER) cc_final: 0.4622 (m-80) outliers start: 69 outliers final: 31 residues processed: 233 average time/residue: 0.1062 time to fit residues: 34.7870 Evaluate side-chains 169 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 483 CYS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain C residue 120 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN A 666 GLN B 47 HIS B 70 ASN B 99 HIS B 104 GLN B 268 GLN B 314 ASN B 367 GLN ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.152837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.120954 restraints weight = 13024.894| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.53 r_work: 0.3091 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10821 Z= 0.102 Angle : 0.510 7.454 14715 Z= 0.274 Chirality : 0.040 0.173 1637 Planarity : 0.005 0.047 1796 Dihedral : 12.732 73.673 1810 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.78 % Favored : 97.14 % Rotamer: Outliers : 2.63 % Allowed : 12.25 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -1.80 (0.21), residues: 1260 helix: -0.10 (0.21), residues: 557 sheet: -1.86 (0.38), residues: 146 loop : -2.13 (0.23), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 341 TYR 0.014 0.001 TYR B 556 PHE 0.011 0.001 PHE B 489 TRP 0.019 0.001 TRP B 437 HIS 0.002 0.001 HIS B 604 Details of bonding type rmsd covalent geometry : bond 0.00214 (10821) covalent geometry : angle 0.51031 (14715) hydrogen bonds : bond 0.03932 ( 467) hydrogen bonds : angle 4.49624 ( 1322) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 271 ASN cc_start: 0.8928 (t0) cc_final: 0.8680 (t0) REVERT: A 311 GLU cc_start: 0.8154 (tp30) cc_final: 0.7907 (tt0) REVERT: A 508 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7631 (mtp180) REVERT: B 15 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.7821 (mp10) REVERT: B 124 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7359 (mp10) REVERT: B 289 MET cc_start: 0.8445 (tpt) cc_final: 0.8241 (mmm) REVERT: B 323 GLU cc_start: 0.7829 (tp30) cc_final: 0.7609 (tp30) REVERT: B 570 LYS cc_start: 0.8332 (mttt) cc_final: 0.7972 (mtmm) REVERT: B 631 VAL cc_start: 0.7587 (t) cc_final: 0.7142 (m) REVERT: B 641 GLU cc_start: 0.3632 (OUTLIER) cc_final: 0.2097 (mp0) outliers start: 29 outliers final: 14 residues processed: 158 average time/residue: 0.1078 time to fit residues: 24.0959 Evaluate side-chains 143 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 483 CYS Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain C residue 125 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 126 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN B 306 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.147296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.114180 restraints weight = 13228.752| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.70 r_work: 0.3042 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10821 Z= 0.246 Angle : 0.594 8.094 14715 Z= 0.310 Chirality : 0.044 0.180 1637 Planarity : 0.005 0.043 1796 Dihedral : 12.160 73.889 1762 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.37 % Favored : 95.56 % Rotamer: Outliers : 2.72 % Allowed : 13.79 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -1.29 (0.22), residues: 1260 helix: 0.46 (0.21), residues: 557 sheet: -1.63 (0.39), residues: 146 loop : -2.02 (0.23), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 439 TYR 0.013 0.002 TYR B 554 PHE 0.013 0.002 PHE A 703 TRP 0.022 0.002 TRP B 437 HIS 0.003 0.001 HIS B 663 Details of bonding type rmsd covalent geometry : bond 0.00593 (10821) covalent geometry : angle 0.59400 (14715) hydrogen bonds : bond 0.05152 ( 467) hydrogen bonds : angle 4.50374 ( 1322) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.397 Fit side-chains REVERT: A 261 ASP cc_start: 0.8051 (m-30) cc_final: 0.7815 (m-30) REVERT: A 273 GLU cc_start: 0.8213 (mp0) cc_final: 0.7866 (mp0) REVERT: A 311 GLU cc_start: 0.8353 (tp30) cc_final: 0.8000 (tt0) REVERT: A 376 MET cc_start: 0.8382 (mmm) cc_final: 0.8146 (mmt) REVERT: A 508 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7568 (mtp180) REVERT: A 599 MET cc_start: 0.4871 (mpp) cc_final: 0.4183 (mtp) REVERT: A 623 LYS cc_start: 0.8390 (tttt) cc_final: 0.8187 (ttpt) REVERT: B 273 VAL cc_start: 0.5078 (OUTLIER) cc_final: 0.4872 (p) REVERT: B 279 LYS cc_start: 0.6971 (mttt) cc_final: 0.6344 (mptt) REVERT: B 570 LYS cc_start: 0.8408 (mttt) cc_final: 0.8039 (mtmm) REVERT: C 92 MET cc_start: 0.7966 (mmt) cc_final: 0.7508 (mmt) outliers start: 30 outliers final: 22 residues processed: 157 average time/residue: 0.1106 time to fit residues: 24.5640 Evaluate side-chains 150 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain C residue 125 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 66 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.150086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.117274 restraints weight = 13338.996| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.63 r_work: 0.3088 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10821 Z= 0.115 Angle : 0.485 7.213 14715 Z= 0.257 Chirality : 0.040 0.157 1637 Planarity : 0.004 0.039 1796 Dihedral : 11.806 73.729 1758 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.00 % Allowed : 15.06 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -0.73 (0.23), residues: 1260 helix: 1.03 (0.22), residues: 557 sheet: -1.46 (0.39), residues: 144 loop : -1.80 (0.23), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 439 TYR 0.012 0.001 TYR B 554 PHE 0.009 0.001 PHE B 489 TRP 0.017 0.001 TRP B 437 HIS 0.001 0.000 HIS B 663 Details of bonding type rmsd covalent geometry : bond 0.00262 (10821) covalent geometry : angle 0.48451 (14715) hydrogen bonds : bond 0.03883 ( 467) hydrogen bonds : angle 4.20482 ( 1322) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 261 ASP cc_start: 0.8035 (m-30) cc_final: 0.7806 (m-30) REVERT: A 311 GLU cc_start: 0.8311 (tp30) cc_final: 0.7911 (tt0) REVERT: A 373 GLN cc_start: 0.8724 (pt0) cc_final: 0.8393 (pt0) REVERT: A 376 MET cc_start: 0.8401 (mmm) cc_final: 0.8101 (mmt) REVERT: A 529 ASP cc_start: 0.8241 (t0) cc_final: 0.7863 (t0) REVERT: A 599 MET cc_start: 0.4896 (mpp) cc_final: 0.4263 (mtp) REVERT: A 712 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7922 (pt0) REVERT: B 15 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.7849 (mp10) REVERT: B 130 ASP cc_start: 0.8290 (t0) cc_final: 0.7855 (t70) REVERT: B 282 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7430 (mp) REVERT: B 570 LYS cc_start: 0.8368 (mttt) cc_final: 0.7990 (mtmm) REVERT: B 641 GLU cc_start: 0.3313 (OUTLIER) cc_final: 0.1774 (mp0) REVERT: C 92 MET cc_start: 0.7994 (mmt) cc_final: 0.7487 (mmt) outliers start: 22 outliers final: 15 residues processed: 144 average time/residue: 0.0940 time to fit residues: 19.8990 Evaluate side-chains 142 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 641 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 101 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.147491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.114989 restraints weight = 13257.176| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.68 r_work: 0.3033 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10821 Z= 0.211 Angle : 0.555 7.743 14715 Z= 0.288 Chirality : 0.043 0.178 1637 Planarity : 0.004 0.038 1796 Dihedral : 11.755 73.780 1751 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.18 % Allowed : 15.06 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -0.66 (0.23), residues: 1260 helix: 1.08 (0.22), residues: 552 sheet: -1.32 (0.39), residues: 144 loop : -1.77 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 341 TYR 0.014 0.002 TYR B 554 PHE 0.010 0.001 PHE B 181 TRP 0.019 0.002 TRP B 437 HIS 0.003 0.001 HIS A 506 Details of bonding type rmsd covalent geometry : bond 0.00509 (10821) covalent geometry : angle 0.55460 (14715) hydrogen bonds : bond 0.04624 ( 467) hydrogen bonds : angle 4.33433 ( 1322) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 261 ASP cc_start: 0.8085 (m-30) cc_final: 0.7842 (m-30) REVERT: A 311 GLU cc_start: 0.8291 (tp30) cc_final: 0.7949 (tt0) REVERT: A 508 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7519 (mtp180) REVERT: A 529 ASP cc_start: 0.8286 (t0) cc_final: 0.7898 (t0) REVERT: A 590 GLN cc_start: 0.7662 (mm110) cc_final: 0.7050 (mm110) REVERT: A 599 MET cc_start: 0.4799 (mpp) cc_final: 0.4313 (mtp) REVERT: B 15 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.7967 (mp10) REVERT: B 279 LYS cc_start: 0.6855 (mttt) cc_final: 0.6154 (mptt) REVERT: B 282 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7520 (mp) REVERT: B 380 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8467 (mtm180) REVERT: B 570 LYS cc_start: 0.8364 (mttt) cc_final: 0.7982 (mtmm) REVERT: B 641 GLU cc_start: 0.3270 (OUTLIER) cc_final: 0.1647 (mp0) outliers start: 35 outliers final: 25 residues processed: 156 average time/residue: 0.0999 time to fit residues: 22.3192 Evaluate side-chains 158 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 483 CYS Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 641 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 93 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 29 optimal weight: 0.0370 chunk 91 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.149520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.116098 restraints weight = 13229.007| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.65 r_work: 0.3033 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10821 Z= 0.110 Angle : 0.481 9.552 14715 Z= 0.251 Chirality : 0.040 0.155 1637 Planarity : 0.004 0.037 1796 Dihedral : 11.580 73.671 1751 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.27 % Allowed : 15.70 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -0.32 (0.23), residues: 1260 helix: 1.35 (0.22), residues: 560 sheet: -1.02 (0.41), residues: 132 loop : -1.66 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 439 TYR 0.012 0.001 TYR B 554 PHE 0.008 0.001 PHE B 489 TRP 0.017 0.001 TRP B 437 HIS 0.001 0.000 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00254 (10821) covalent geometry : angle 0.48097 (14715) hydrogen bonds : bond 0.03652 ( 467) hydrogen bonds : angle 4.07314 ( 1322) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 261 ASP cc_start: 0.8138 (m-30) cc_final: 0.7918 (m-30) REVERT: A 311 GLU cc_start: 0.8390 (tp30) cc_final: 0.7982 (tt0) REVERT: A 373 GLN cc_start: 0.8768 (pt0) cc_final: 0.8431 (pt0) REVERT: A 376 MET cc_start: 0.8412 (mmm) cc_final: 0.8108 (mmp) REVERT: A 529 ASP cc_start: 0.8256 (t0) cc_final: 0.7737 (t0) REVERT: A 590 GLN cc_start: 0.7737 (mm110) cc_final: 0.7133 (mm110) REVERT: A 599 MET cc_start: 0.4806 (mpp) cc_final: 0.4315 (mtp) REVERT: A 712 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7809 (pt0) REVERT: B 15 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.7786 (mp10) REVERT: B 130 ASP cc_start: 0.8279 (t0) cc_final: 0.7780 (t70) REVERT: B 282 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7439 (mp) REVERT: B 380 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8506 (mtm180) REVERT: B 570 LYS cc_start: 0.8373 (mttt) cc_final: 0.8002 (mtmm) REVERT: B 641 GLU cc_start: 0.3172 (OUTLIER) cc_final: 0.1601 (mp0) REVERT: C 92 MET cc_start: 0.8010 (mmt) cc_final: 0.7626 (mmt) outliers start: 25 outliers final: 18 residues processed: 147 average time/residue: 0.1071 time to fit residues: 22.3822 Evaluate side-chains 146 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 641 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 6 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 45 optimal weight: 0.0570 chunk 110 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.152153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.119863 restraints weight = 13159.021| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.50 r_work: 0.3106 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10821 Z= 0.087 Angle : 0.459 7.223 14715 Z= 0.240 Chirality : 0.038 0.142 1637 Planarity : 0.003 0.036 1796 Dihedral : 11.490 73.707 1749 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.91 % Allowed : 16.33 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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 (0.23), residues: 1260 helix: 1.62 (0.22), residues: 556 sheet: -1.06 (0.39), residues: 144 loop : -1.46 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 135 TYR 0.012 0.001 TYR B 554 PHE 0.008 0.001 PHE B 489 TRP 0.017 0.001 TRP B 437 HIS 0.001 0.000 HIS A 643 Details of bonding type rmsd covalent geometry : bond 0.00190 (10821) covalent geometry : angle 0.45870 (14715) hydrogen bonds : bond 0.03299 ( 467) hydrogen bonds : angle 3.93401 ( 1322) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 261 ASP cc_start: 0.8142 (m-30) cc_final: 0.7938 (m-30) REVERT: A 311 GLU cc_start: 0.8385 (tp30) cc_final: 0.7999 (tt0) REVERT: A 373 GLN cc_start: 0.8737 (pt0) cc_final: 0.8413 (pt0) REVERT: A 590 GLN cc_start: 0.7704 (mm110) cc_final: 0.7107 (mm110) REVERT: A 599 MET cc_start: 0.4822 (mpp) cc_final: 0.4261 (mtp) REVERT: A 712 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7878 (pt0) REVERT: B 15 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.7769 (mp10) REVERT: B 282 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7396 (mp) REVERT: B 570 LYS cc_start: 0.8377 (mttt) cc_final: 0.8001 (mtmm) REVERT: B 641 GLU cc_start: 0.3272 (OUTLIER) cc_final: 0.1840 (mp0) REVERT: C 92 MET cc_start: 0.8063 (mmt) cc_final: 0.7712 (mmt) outliers start: 21 outliers final: 15 residues processed: 144 average time/residue: 0.0995 time to fit residues: 20.6798 Evaluate side-chains 139 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 641 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 24 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 119 optimal weight: 0.0770 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.150820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.118873 restraints weight = 13052.055| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.54 r_work: 0.3071 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10821 Z= 0.126 Angle : 0.496 11.426 14715 Z= 0.255 Chirality : 0.040 0.172 1637 Planarity : 0.004 0.036 1796 Dihedral : 11.504 73.761 1747 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.09 % Allowed : 16.42 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.23), residues: 1260 helix: 1.49 (0.22), residues: 564 sheet: -0.75 (0.42), residues: 132 loop : -1.56 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 135 TYR 0.012 0.001 TYR B 554 PHE 0.009 0.001 PHE B 489 TRP 0.020 0.001 TRP B 437 HIS 0.002 0.000 HIS A 506 Details of bonding type rmsd covalent geometry : bond 0.00297 (10821) covalent geometry : angle 0.49597 (14715) hydrogen bonds : bond 0.03726 ( 467) hydrogen bonds : angle 3.97678 ( 1322) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 261 ASP cc_start: 0.8087 (m-30) cc_final: 0.7881 (m-30) REVERT: A 311 GLU cc_start: 0.8404 (tp30) cc_final: 0.8015 (tt0) REVERT: A 590 GLN cc_start: 0.7746 (mm110) cc_final: 0.7164 (mm110) REVERT: A 599 MET cc_start: 0.4826 (mpp) cc_final: 0.4304 (mtp) REVERT: A 712 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7800 (pt0) REVERT: B 15 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.7819 (mp10) REVERT: B 282 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7513 (mp) REVERT: B 570 LYS cc_start: 0.8344 (mttt) cc_final: 0.7983 (mtmm) REVERT: B 641 GLU cc_start: 0.2992 (OUTLIER) cc_final: 0.1688 (mp0) REVERT: C 92 MET cc_start: 0.8048 (mmt) cc_final: 0.7733 (mmt) outliers start: 23 outliers final: 18 residues processed: 143 average time/residue: 0.0941 time to fit residues: 19.7237 Evaluate side-chains 144 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 641 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 51 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.149354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.116898 restraints weight = 13239.032| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.59 r_work: 0.3066 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10821 Z= 0.164 Angle : 0.532 12.330 14715 Z= 0.273 Chirality : 0.042 0.171 1637 Planarity : 0.004 0.036 1796 Dihedral : 11.553 73.742 1747 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.45 % Allowed : 16.33 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -0.18 (0.23), residues: 1260 helix: 1.38 (0.22), residues: 558 sheet: -0.62 (0.41), residues: 137 loop : -1.58 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 341 TYR 0.015 0.001 TYR B 30 PHE 0.017 0.001 PHE A 442 TRP 0.020 0.001 TRP B 437 HIS 0.002 0.001 HIS A 506 Details of bonding type rmsd covalent geometry : bond 0.00390 (10821) covalent geometry : angle 0.53225 (14715) hydrogen bonds : bond 0.04082 ( 467) hydrogen bonds : angle 4.07630 ( 1322) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.402 Fit side-chains REVERT: A 261 ASP cc_start: 0.8026 (m-30) cc_final: 0.7800 (m-30) REVERT: A 273 GLU cc_start: 0.8182 (mp0) cc_final: 0.7917 (mp0) REVERT: A 311 GLU cc_start: 0.8360 (tp30) cc_final: 0.8003 (tt0) REVERT: A 590 GLN cc_start: 0.7727 (mm110) cc_final: 0.7199 (mm110) REVERT: A 599 MET cc_start: 0.4834 (mpp) cc_final: 0.4317 (mtp) REVERT: A 712 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7771 (pt0) REVERT: B 15 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.7821 (mp10) REVERT: B 282 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7521 (mp) REVERT: B 570 LYS cc_start: 0.8355 (mttt) cc_final: 0.7993 (mtmm) REVERT: B 641 GLU cc_start: 0.3429 (OUTLIER) cc_final: 0.1938 (mp0) REVERT: C 92 MET cc_start: 0.8030 (mmt) cc_final: 0.7635 (mmt) outliers start: 27 outliers final: 22 residues processed: 143 average time/residue: 0.0950 time to fit residues: 19.7942 Evaluate side-chains 144 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain C residue 125 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 111 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 85 optimal weight: 0.0670 chunk 112 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.151655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.119870 restraints weight = 13045.456| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.55 r_work: 0.3111 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10821 Z= 0.103 Angle : 0.495 12.789 14715 Z= 0.254 Chirality : 0.040 0.179 1637 Planarity : 0.003 0.036 1796 Dihedral : 11.484 73.669 1747 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.36 % Allowed : 16.52 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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 (0.23), residues: 1260 helix: 1.58 (0.22), residues: 559 sheet: -0.52 (0.41), residues: 137 loop : -1.45 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 439 TYR 0.013 0.001 TYR B 554 PHE 0.007 0.001 PHE B 489 TRP 0.019 0.001 TRP B 437 HIS 0.001 0.000 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00236 (10821) covalent geometry : angle 0.49533 (14715) hydrogen bonds : bond 0.03548 ( 467) hydrogen bonds : angle 3.95217 ( 1322) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 261 ASP cc_start: 0.8056 (m-30) cc_final: 0.7851 (m-30) REVERT: A 273 GLU cc_start: 0.8091 (mp0) cc_final: 0.7819 (mp0) REVERT: A 311 GLU cc_start: 0.8378 (tp30) cc_final: 0.8004 (tt0) REVERT: A 590 GLN cc_start: 0.7729 (mm110) cc_final: 0.7199 (mm110) REVERT: A 599 MET cc_start: 0.4831 (mpp) cc_final: 0.4290 (mtp) REVERT: A 712 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7943 (pt0) REVERT: B 15 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.7873 (mp10) REVERT: B 282 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7479 (mp) REVERT: B 534 ILE cc_start: 0.8519 (mm) cc_final: 0.8318 (mt) REVERT: B 570 LYS cc_start: 0.8336 (mttt) cc_final: 0.7969 (mtmm) REVERT: C 92 MET cc_start: 0.8076 (mmt) cc_final: 0.7756 (mmt) outliers start: 26 outliers final: 22 residues processed: 141 average time/residue: 0.0979 time to fit residues: 20.2273 Evaluate side-chains 145 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 526 MET Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain C residue 125 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 15 optimal weight: 0.0010 chunk 100 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 122 optimal weight: 0.0570 chunk 24 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 4 optimal weight: 0.0270 chunk 115 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.154724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.123791 restraints weight = 13118.000| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.43 r_work: 0.3127 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10821 Z= 0.082 Angle : 0.470 12.977 14715 Z= 0.241 Chirality : 0.038 0.163 1637 Planarity : 0.003 0.036 1796 Dihedral : 11.414 74.406 1747 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.54 % Allowed : 17.06 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 0.31 (0.24), residues: 1260 helix: 1.80 (0.22), residues: 557 sheet: -0.41 (0.42), residues: 137 loop : -1.32 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 439 TYR 0.012 0.001 TYR B 554 PHE 0.008 0.001 PHE B 251 TRP 0.014 0.001 TRP B 437 HIS 0.001 0.000 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00173 (10821) covalent geometry : angle 0.46979 (14715) hydrogen bonds : bond 0.03033 ( 467) hydrogen bonds : angle 3.77212 ( 1322) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2614.91 seconds wall clock time: 45 minutes 30.00 seconds (2730.00 seconds total)