Starting phenix.real_space_refine on Fri Feb 14 21:02:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t0w_10361/02_2025/6t0w_10361.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t0w_10361/02_2025/6t0w_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_10361/02_2025/6t0w_10361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t0w_10361/02_2025/6t0w_10361.map" model { file = "/net/cci-nas-00/data/ceres_data/6t0w_10361/02_2025/6t0w_10361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t0w_10361/02_2025/6t0w_10361.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.66, per 1000 atoms: 0.63 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: 2.55 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 3.45 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: 3.40 Time building geometry restraints manager: 2.95 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: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 28.370 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.340 ------------------------------------------------------------------------------- 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= 0.515 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.029 0.003 TRP B 437 HIS 0.006 0.001 HIS A 462 PHE 0.015 0.002 PHE B 181 TYR 0.020 0.003 TYR A 644 ARG 0.006 0.001 ARG B 233 *********************** 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 : 1.219 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: 0.7191 (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: 0.7499 (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: 0.2566 time to fit residues: 82.6173 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 : 1.301 ------------------------------------------------------------------------------- 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 108 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 306 ASN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.150277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.117893 restraints weight = 12949.831| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.68 r_work: 0.3054 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10821 Z= 0.183 Angle : 0.533 7.737 14715 Z= 0.286 Chirality : 0.041 0.184 1637 Planarity : 0.005 0.048 1796 Dihedral : 12.872 73.707 1810 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.78 % Favored : 97.14 % Rotamer: Outliers : 2.63 % Allowed : 12.52 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.21), residues: 1260 helix: -0.14 (0.21), residues: 557 sheet: -1.82 (0.38), residues: 146 loop : -2.20 (0.22), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 437 HIS 0.003 0.001 HIS B 663 PHE 0.012 0.001 PHE B 489 TYR 0.011 0.001 TYR B 556 ARG 0.004 0.000 ARG A 341 *********************** 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 168 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: A 261 ASP cc_start: 0.7997 (m-30) cc_final: 0.7770 (m-30) REVERT: A 271 ASN cc_start: 0.8941 (t0) cc_final: 0.8714 (t0) REVERT: A 424 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8546 (pt) REVERT: A 508 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7654 (mtp180) REVERT: A 599 MET cc_start: 0.4261 (mtp) cc_final: 0.4018 (mpp) REVERT: B 15 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.7877 (mp10) REVERT: B 124 GLN cc_start: 0.7617 (mm-40) cc_final: 0.7360 (mp10) REVERT: B 289 MET cc_start: 0.8483 (tpt) cc_final: 0.8253 (mmm) REVERT: B 570 LYS cc_start: 0.8374 (mttt) cc_final: 0.8008 (mtmm) REVERT: B 631 VAL cc_start: 0.7513 (t) cc_final: 0.7180 (m) REVERT: B 641 GLU cc_start: 0.3367 (OUTLIER) cc_final: 0.1823 (mp0) outliers start: 29 outliers final: 15 residues processed: 160 average time/residue: 0.2416 time to fit residues: 55.2038 Evaluate side-chains 147 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 424 ILE 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 84 optimal weight: 5.9990 chunk 53 optimal weight: 0.4980 chunk 71 optimal weight: 0.0000 chunk 70 optimal weight: 20.0000 chunk 87 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 overall best weight: 2.0990 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.149647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.117034 restraints weight = 13211.460| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.64 r_work: 0.3062 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10821 Z= 0.213 Angle : 0.507 7.609 14715 Z= 0.269 Chirality : 0.041 0.157 1637 Planarity : 0.004 0.042 1796 Dihedral : 12.007 73.794 1762 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.33 % Favored : 96.59 % Rotamer: Outliers : 2.72 % Allowed : 13.07 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.22), residues: 1260 helix: 0.63 (0.22), residues: 557 sheet: -1.59 (0.39), residues: 146 loop : -1.93 (0.23), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 437 HIS 0.002 0.000 HIS B 663 PHE 0.011 0.001 PHE B 489 TYR 0.012 0.001 TYR B 554 ARG 0.003 0.000 ARG A 341 *********************** 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 161 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 1.310 Fit side-chains revert: symmetry clash REVERT: A 261 ASP cc_start: 0.8090 (m-30) cc_final: 0.7871 (m-30) REVERT: A 311 GLU cc_start: 0.8273 (tp30) cc_final: 0.7884 (tt0) REVERT: A 373 GLN cc_start: 0.8704 (pt0) cc_final: 0.8385 (pt0) REVERT: A 376 MET cc_start: 0.8436 (mmm) cc_final: 0.8148 (mmt) REVERT: A 424 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8535 (pt) REVERT: A 485 VAL cc_start: 0.9071 (OUTLIER) cc_final: 0.8862 (m) REVERT: A 508 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7612 (mtp180) REVERT: A 529 ASP cc_start: 0.8221 (t0) cc_final: 0.7851 (t0) REVERT: A 599 MET cc_start: 0.4262 (mtp) cc_final: 0.3976 (mpp) REVERT: A 712 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7789 (pt0) REVERT: B 15 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.7852 (mp10) REVERT: B 130 ASP cc_start: 0.8219 (t0) cc_final: 0.7776 (t70) REVERT: B 570 LYS cc_start: 0.8381 (mttt) cc_final: 0.8002 (mtmm) REVERT: B 631 VAL cc_start: 0.7557 (t) cc_final: 0.7126 (m) REVERT: B 641 GLU cc_start: 0.3532 (OUTLIER) cc_final: 0.1936 (mp0) REVERT: C 92 MET cc_start: 0.7946 (mmt) cc_final: 0.7454 (mmt) outliers start: 30 outliers final: 20 residues processed: 154 average time/residue: 0.2371 time to fit residues: 52.1018 Evaluate side-chains 148 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 424 ILE Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 502 LYS 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 684 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 141 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 440 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 4.9990 chunk 116 optimal weight: 20.0000 chunk 92 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 123 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 113 optimal weight: 0.0980 overall best weight: 1.4188 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.151102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.119035 restraints weight = 13055.005| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.56 r_work: 0.3107 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10821 Z= 0.159 Angle : 0.476 7.141 14715 Z= 0.250 Chirality : 0.039 0.147 1637 Planarity : 0.004 0.038 1796 Dihedral : 11.780 73.725 1759 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.45 % Allowed : 13.70 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.23), residues: 1260 helix: 1.12 (0.22), residues: 558 sheet: -1.38 (0.39), residues: 144 loop : -1.71 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 437 HIS 0.002 0.000 HIS A 506 PHE 0.008 0.001 PHE B 489 TYR 0.012 0.001 TYR B 554 ARG 0.002 0.000 ARG A 341 *********************** 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 153 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 1.149 Fit side-chains revert: symmetry clash REVERT: A 261 ASP cc_start: 0.8107 (m-30) cc_final: 0.7904 (m-30) REVERT: A 311 GLU cc_start: 0.8343 (tp30) cc_final: 0.7947 (tt0) REVERT: A 373 GLN cc_start: 0.8671 (pt0) cc_final: 0.8359 (pt0) REVERT: A 376 MET cc_start: 0.8308 (mmm) cc_final: 0.8044 (mmt) REVERT: A 424 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8470 (pt) REVERT: A 529 ASP cc_start: 0.8202 (t0) cc_final: 0.7849 (t0) REVERT: A 590 GLN cc_start: 0.7659 (mm110) cc_final: 0.6984 (mm110) REVERT: A 599 MET cc_start: 0.4478 (mtp) cc_final: 0.4047 (mpp) REVERT: A 712 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7826 (pt0) REVERT: B 15 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.7866 (mp10) REVERT: B 130 ASP cc_start: 0.8262 (t0) cc_final: 0.8002 (t70) REVERT: B 380 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8473 (mtm180) REVERT: B 570 LYS cc_start: 0.8350 (mttt) cc_final: 0.7990 (mtmm) REVERT: C 92 MET cc_start: 0.8022 (mmt) cc_final: 0.7340 (mmm) outliers start: 27 outliers final: 17 residues processed: 148 average time/residue: 0.2314 time to fit residues: 48.8283 Evaluate side-chains 140 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 424 ILE 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 314 ASN Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 380 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 10.0000 chunk 6 optimal weight: 0.0040 chunk 27 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 overall best weight: 4.0000 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.147414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.115330 restraints weight = 13138.111| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.49 r_work: 0.3015 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 10821 Z= 0.363 Angle : 0.575 7.813 14715 Z= 0.298 Chirality : 0.044 0.178 1637 Planarity : 0.004 0.037 1796 Dihedral : 11.715 73.810 1748 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.09 % Allowed : 14.79 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.23), residues: 1260 helix: 1.04 (0.22), residues: 555 sheet: -1.24 (0.39), residues: 144 loop : -1.72 (0.23), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 437 HIS 0.003 0.001 HIS A 506 PHE 0.011 0.001 PHE A 703 TYR 0.014 0.002 TYR B 554 ARG 0.003 0.000 ARG A 341 *********************** 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 162 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 1.260 Fit side-chains REVERT: A 261 ASP cc_start: 0.8079 (m-30) cc_final: 0.7850 (m-30) REVERT: A 311 GLU cc_start: 0.8276 (tp30) cc_final: 0.7916 (tt0) REVERT: A 424 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8571 (pt) REVERT: A 529 ASP cc_start: 0.8284 (t0) cc_final: 0.7927 (t0) REVERT: A 590 GLN cc_start: 0.7718 (mm110) cc_final: 0.7095 (mm110) REVERT: B 380 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8495 (mtm180) REVERT: B 570 LYS cc_start: 0.8342 (mttt) cc_final: 0.7963 (mtmm) outliers start: 34 outliers final: 24 residues processed: 156 average time/residue: 0.2264 time to fit residues: 50.2890 Evaluate side-chains 152 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 424 ILE 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 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 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 490 GLU Chi-restraints excluded: chain B residue 533 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 117 optimal weight: 20.0000 chunk 47 optimal weight: 0.0980 chunk 90 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 10 optimal weight: 0.0270 overall best weight: 0.5640 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.152325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.120175 restraints weight = 13218.583| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.46 r_work: 0.3109 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10821 Z= 0.118 Angle : 0.460 6.549 14715 Z= 0.243 Chirality : 0.038 0.141 1637 Planarity : 0.004 0.036 1796 Dihedral : 11.477 73.692 1748 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.27 % Allowed : 15.25 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.23), residues: 1260 helix: 1.51 (0.22), residues: 554 sheet: -0.95 (0.42), residues: 132 loop : -1.55 (0.23), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 437 HIS 0.002 0.000 HIS A 643 PHE 0.008 0.001 PHE A 223 TYR 0.012 0.001 TYR B 554 ARG 0.002 0.000 ARG B 666 *********************** 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 156 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 1.208 Fit side-chains revert: symmetry clash REVERT: A 311 GLU cc_start: 0.8330 (tp30) cc_final: 0.7952 (tt0) REVERT: A 373 GLN cc_start: 0.8689 (pt0) cc_final: 0.8368 (pt0) REVERT: A 590 GLN cc_start: 0.7668 (mm110) cc_final: 0.7040 (mm110) REVERT: A 599 MET cc_start: 0.4239 (mtp) cc_final: 0.3886 (mpp) REVERT: A 712 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7738 (pt0) REVERT: B 15 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.7825 (mp10) REVERT: B 570 LYS cc_start: 0.8321 (mttt) cc_final: 0.7963 (mtmm) REVERT: C 92 MET cc_start: 0.8032 (mmt) cc_final: 0.7687 (mmt) outliers start: 25 outliers final: 19 residues processed: 152 average time/residue: 0.2407 time to fit residues: 51.7232 Evaluate side-chains 140 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 546 VAL Chi-restraints excluded: chain A residue 557 CYS 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 141 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 533 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 84 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 117 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.150248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.118439 restraints weight = 13348.193| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.57 r_work: 0.3068 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10821 Z= 0.216 Angle : 0.504 9.313 14715 Z= 0.260 Chirality : 0.040 0.158 1637 Planarity : 0.004 0.036 1796 Dihedral : 11.544 73.758 1748 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.45 % Allowed : 15.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.23), residues: 1260 helix: 1.39 (0.22), residues: 563 sheet: -0.81 (0.42), residues: 128 loop : -1.53 (0.24), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 437 HIS 0.002 0.000 HIS A 506 PHE 0.007 0.001 PHE B 489 TYR 0.013 0.001 TYR B 554 ARG 0.005 0.000 ARG B 151 *********************** 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 151 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 1.194 Fit side-chains REVERT: A 311 GLU cc_start: 0.8310 (tp30) cc_final: 0.7949 (tt0) REVERT: A 373 GLN cc_start: 0.8734 (pt0) cc_final: 0.8404 (pt0) REVERT: A 590 GLN cc_start: 0.7686 (mm110) cc_final: 0.7102 (mm110) REVERT: A 599 MET cc_start: 0.4295 (mtp) cc_final: 0.3756 (mpp) REVERT: A 712 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7932 (pt0) REVERT: B 15 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.7851 (mp10) REVERT: B 494 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7829 (ptp) REVERT: B 570 LYS cc_start: 0.8357 (mttt) cc_final: 0.7981 (mtmm) REVERT: C 92 MET cc_start: 0.8027 (mmt) cc_final: 0.7628 (mmt) outliers start: 27 outliers final: 23 residues processed: 144 average time/residue: 0.2145 time to fit residues: 45.1507 Evaluate side-chains 145 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 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 141 THR 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 436 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 533 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 111 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 0.0030 chunk 68 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.150374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.118968 restraints weight = 13097.088| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.59 r_work: 0.3089 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10821 Z= 0.190 Angle : 0.499 11.225 14715 Z= 0.258 Chirality : 0.040 0.154 1637 Planarity : 0.004 0.036 1796 Dihedral : 11.527 73.736 1748 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.36 % Allowed : 15.79 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.23), residues: 1260 helix: 1.45 (0.22), residues: 563 sheet: -0.67 (0.41), residues: 137 loop : -1.53 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 437 HIS 0.001 0.000 HIS B 32 PHE 0.007 0.001 PHE B 181 TYR 0.013 0.001 TYR B 554 ARG 0.004 0.000 ARG B 151 *********************** 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 150 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 1.136 Fit side-chains revert: symmetry clash REVERT: A 311 GLU cc_start: 0.8317 (tp30) cc_final: 0.7941 (tt0) REVERT: A 373 GLN cc_start: 0.8710 (pt0) cc_final: 0.8380 (pt0) REVERT: A 590 GLN cc_start: 0.7658 (mm110) cc_final: 0.7103 (mm110) REVERT: A 599 MET cc_start: 0.4295 (mtp) cc_final: 0.3658 (mpp) REVERT: A 712 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7903 (pt0) REVERT: B 15 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.7849 (mp10) REVERT: B 494 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7722 (ptp) REVERT: B 570 LYS cc_start: 0.8351 (mttt) cc_final: 0.7968 (mtmm) REVERT: C 92 MET cc_start: 0.8052 (mmt) cc_final: 0.7634 (mmt) outliers start: 26 outliers final: 22 residues processed: 144 average time/residue: 0.2346 time to fit residues: 49.3682 Evaluate side-chains 142 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 320 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 141 THR 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 436 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 538 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 106 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 59 optimal weight: 0.3980 chunk 81 optimal weight: 0.0030 chunk 9 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 overall best weight: 1.4594 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.151051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.118581 restraints weight = 13294.257| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.72 r_work: 0.3100 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10821 Z= 0.167 Angle : 0.496 12.284 14715 Z= 0.256 Chirality : 0.040 0.179 1637 Planarity : 0.004 0.036 1796 Dihedral : 11.502 73.633 1747 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.09 % Allowed : 16.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.23), residues: 1260 helix: 1.48 (0.22), residues: 564 sheet: -0.58 (0.41), residues: 137 loop : -1.48 (0.24), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 437 HIS 0.002 0.000 HIS A 272 PHE 0.007 0.001 PHE B 489 TYR 0.013 0.001 TYR B 554 ARG 0.004 0.000 ARG B 135 *********************** 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 148 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 1.278 Fit side-chains revert: symmetry clash REVERT: A 273 GLU cc_start: 0.8056 (mp0) cc_final: 0.7794 (mp0) REVERT: A 311 GLU cc_start: 0.8353 (tp30) cc_final: 0.7967 (tt0) REVERT: A 373 GLN cc_start: 0.8715 (pt0) cc_final: 0.8383 (pt0) REVERT: A 590 GLN cc_start: 0.7698 (mm110) cc_final: 0.7150 (mm110) REVERT: A 712 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7907 (pt0) REVERT: B 15 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.7793 (mp10) REVERT: B 494 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7711 (ptp) REVERT: B 570 LYS cc_start: 0.8347 (mttt) cc_final: 0.7975 (mtmm) REVERT: C 92 MET cc_start: 0.8065 (mmt) cc_final: 0.7739 (mmt) outliers start: 23 outliers final: 20 residues processed: 142 average time/residue: 0.2355 time to fit residues: 49.0096 Evaluate side-chains 144 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 320 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 141 THR 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 440 LEU Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 494 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 37 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 58 optimal weight: 0.4980 chunk 124 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 92 optimal weight: 0.0010 chunk 57 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 overall best weight: 1.4390 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.151376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.119891 restraints weight = 13179.813| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.54 r_work: 0.3124 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10821 Z= 0.166 Angle : 0.499 12.711 14715 Z= 0.256 Chirality : 0.040 0.163 1637 Planarity : 0.004 0.036 1796 Dihedral : 11.494 73.714 1747 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.18 % Allowed : 16.24 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.23), residues: 1260 helix: 1.50 (0.22), residues: 564 sheet: -0.52 (0.42), residues: 137 loop : -1.44 (0.24), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 437 HIS 0.002 0.000 HIS A 272 PHE 0.007 0.001 PHE B 489 TYR 0.012 0.001 TYR B 554 ARG 0.004 0.000 ARG B 135 ********************** 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 149 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: A 311 GLU cc_start: 0.8327 (tp30) cc_final: 0.7959 (tt0) REVERT: A 373 GLN cc_start: 0.8710 (pt0) cc_final: 0.8373 (pt0) REVERT: A 590 GLN cc_start: 0.7751 (mm110) cc_final: 0.7212 (mm110) REVERT: A 599 MET cc_start: 0.4145 (mtp) cc_final: 0.3276 (mpp) REVERT: A 712 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7913 (pt0) REVERT: B 15 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.7884 (mp10) REVERT: B 570 LYS cc_start: 0.8339 (mttt) cc_final: 0.7964 (mtmm) REVERT: C 92 MET cc_start: 0.8011 (mmt) cc_final: 0.7677 (mmt) outliers start: 24 outliers final: 21 residues processed: 144 average time/residue: 0.2173 time to fit residues: 46.0667 Evaluate side-chains 144 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL 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 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 141 THR 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 436 LEU Chi-restraints excluded: chain B residue 490 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 33 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 47 optimal weight: 0.0050 chunk 81 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.150366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.118390 restraints weight = 13159.145| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.60 r_work: 0.3084 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10821 Z= 0.207 Angle : 0.516 12.922 14715 Z= 0.264 Chirality : 0.041 0.173 1637 Planarity : 0.004 0.035 1796 Dihedral : 11.524 73.742 1747 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.00 % Allowed : 16.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.23), residues: 1260 helix: 1.51 (0.22), residues: 559 sheet: -0.53 (0.41), residues: 137 loop : -1.46 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 437 HIS 0.002 0.000 HIS A 506 PHE 0.007 0.001 PHE B 181 TYR 0.013 0.001 TYR B 30 ARG 0.004 0.000 ARG B 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5564.82 seconds wall clock time: 99 minutes 27.44 seconds (5967.44 seconds total)