Starting phenix.real_space_refine on Sat Jun 14 08:46:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cli_16713/06_2025/8cli_16713.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cli_16713/06_2025/8cli_16713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cli_16713/06_2025/8cli_16713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cli_16713/06_2025/8cli_16713.map" model { file = "/net/cci-nas-00/data/ceres_data/8cli_16713/06_2025/8cli_16713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cli_16713/06_2025/8cli_16713.cif" } resolution = 3.2 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= 0.004 sd= 0.093 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 70 5.49 5 S 93 5.16 5 C 9953 2.51 5 N 2816 2.21 5 O 3021 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15955 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4421 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 522} Chain breaks: 4 Chain: "B" Number of atoms: 5496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5496 Classifications: {'peptide': 689} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 653} Chain breaks: 2 Chain: "C" Number of atoms: 4601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4601 Classifications: {'peptide': 579} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 534} Chain breaks: 1 Chain: "D" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 721 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "E" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 714 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9303 SG CYS B 747 88.806 71.398 116.033 1.00122.97 S ATOM 9323 SG CYS B 750 86.680 73.366 118.400 1.00130.50 S ATOM 9437 SG CYS B 764 87.358 69.709 119.224 1.00132.00 S ATOM 9642 SG CYS B 788 93.860 53.177 98.783 1.00 64.43 S ATOM 9853 SG CYS B 814 96.413 52.371 101.828 1.00 81.43 S ATOM 9877 SG CYS B 817 94.743 50.771 99.424 1.00 79.12 S Time building chain proxies: 11.00, per 1000 atoms: 0.69 Number of scatterers: 15955 At special positions: 0 Unit cell: (138.918, 99.462, 135.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 93 16.00 P 70 15.00 O 3021 8.00 N 2816 7.00 C 9953 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: 4.05 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" ND1 HIS B 768 " pdb="ZN ZN B 901 " - pdb=" SG CYS B 750 " pdb="ZN ZN B 901 " - pdb=" SG CYS B 747 " pdb="ZN ZN B 901 " - pdb=" SG CYS B 764 " pdb=" ZN B 902 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 814 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 788 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 817 " Number of angles added : 3 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3412 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 22 sheets defined 31.1% alpha, 22.3% beta 35 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 5.92 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 3.690A pdb=" N GLU A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 30 Processing helix chain 'A' and resid 40 through 53 Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 154 through 164 Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 205 through 219 removed outlier: 4.521A pdb=" N ILE A 215 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU A 216 " --> pdb=" O HIS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 248 No H-bonds generated for 'chain 'A' and resid 246 through 248' Processing helix chain 'A' and resid 253 through 269 Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 286 through 300 removed outlier: 4.163A pdb=" N ARG A 292 " --> pdb=" O ARG A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 367 through 380 Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 386 through 394 Processing helix chain 'A' and resid 396 through 410 Processing helix chain 'A' and resid 431 through 435 removed outlier: 4.661A pdb=" N GLU A 435 " --> pdb=" O CYS A 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 431 through 435' Processing helix chain 'A' and resid 437 through 456 Processing helix chain 'A' and resid 611 through 628 Processing helix chain 'A' and resid 633 through 649 removed outlier: 3.582A pdb=" N ILE A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 669 Processing helix chain 'A' and resid 700 through 715 Processing helix chain 'B' and resid 122 through 135 removed outlier: 3.696A pdb=" N ALA B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 148 Processing helix chain 'B' and resid 208 through 219 Processing helix chain 'B' and resid 235 through 245 Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 467 through 473 removed outlier: 3.829A pdb=" N VAL B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 527 Processing helix chain 'B' and resid 532 through 535 Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.635A pdb=" N LEU B 542 " --> pdb=" O ASP B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 568 Processing helix chain 'B' and resid 570 through 588 removed outlier: 3.708A pdb=" N TRP B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 696 Processing helix chain 'B' and resid 708 through 716 Processing helix chain 'B' and resid 724 through 738 Processing helix chain 'B' and resid 803 through 810 Processing helix chain 'C' and resid 300 through 322 Proline residue: C 306 - end of helix removed outlier: 3.742A pdb=" N LEU C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N HIS C 312 " --> pdb=" O TRP C 308 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN C 320 " --> pdb=" O ASP C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 341 through 346 Processing helix chain 'C' and resid 515 through 523 removed outlier: 3.546A pdb=" N LEU C 519 " --> pdb=" O HIS C 515 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN C 522 " --> pdb=" O ALA C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 679 Processing helix chain 'C' and resid 740 through 744 removed outlier: 3.524A pdb=" N ASN C 743 " --> pdb=" O ASN C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 749 Processing helix chain 'C' and resid 786 through 792 Processing helix chain 'C' and resid 808 through 811 Processing helix chain 'C' and resid 812 through 822 Processing helix chain 'C' and resid 871 through 889 Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 122 Processing sheet with id=AA2, first strand: chain 'A' and resid 222 through 230 Processing sheet with id=AA3, first strand: chain 'A' and resid 273 through 275 Processing sheet with id=AA4, first strand: chain 'A' and resid 384 through 385 Processing sheet with id=AA5, first strand: chain 'A' and resid 582 through 583 Processing sheet with id=AA6, first strand: chain 'A' and resid 678 through 681 Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 59 removed outlier: 7.482A pdb=" N ARG B 54 " --> pdb=" O THR B 514 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N THR B 514 " --> pdb=" O ARG B 54 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N PHE B 512 " --> pdb=" O PRO B 56 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TYR B 488 " --> pdb=" O VAL B 482 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL B 482 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA B 490 " --> pdb=" O ILE B 480 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE B 480 " --> pdb=" O ALA B 490 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE B 492 " --> pdb=" O HIS B 478 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 70 through 72 removed outlier: 4.146A pdb=" N VAL B 103 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 164 through 169 removed outlier: 7.087A pdb=" N LEU B 191 " --> pdb=" O ASP B 207 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ASP B 207 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE B 193 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 248 through 257 removed outlier: 6.645A pdb=" N LEU B 279 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET B 251 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA B 277 " --> pdb=" O MET B 251 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TRP B 253 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU B 275 " --> pdb=" O TRP B 253 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY B 255 " --> pdb=" O SER B 273 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N SER B 273 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASN B 284 " --> pdb=" O PHE B 280 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLN B 291 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE B 300 " --> pdb=" O GLN B 291 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 313 through 323 removed outlier: 6.153A pdb=" N ILE B 340 " --> pdb=" O LEU B 362 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 371 through 381 removed outlier: 3.789A pdb=" N SER B 373 " --> pdb=" O ALA B 394 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS B 386 " --> pdb=" O HIS B 381 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N SER B 387 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ILE B 406 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 399 " --> pdb=" O VAL B 418 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 428 through 431 removed outlier: 3.637A pdb=" N SER B 428 " --> pdb=" O CYS B 441 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL B 447 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 761 through 763 Processing sheet with id=AB6, first strand: chain 'B' and resid 786 through 787 Processing sheet with id=AB7, first strand: chain 'C' and resid 337 through 339 removed outlier: 5.037A pdb=" N VAL C 535 " --> pdb=" O ALA C 464 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N PHE C 459 " --> pdb=" O GLY C 443 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY C 443 " --> pdb=" O PHE C 459 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR C 461 " --> pdb=" O LEU C 441 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LEU C 438 " --> pdb=" O SER C 419 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N SER C 419 " --> pdb=" O LEU C 438 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 358 through 362 removed outlier: 6.448A pdb=" N SER C 359 " --> pdb=" O PHE C 798 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ASP C 800 " --> pdb=" O SER C 359 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLN C 361 " --> pdb=" O ASP C 800 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU C 729 " --> pdb=" O ILE C 754 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU C 728 " --> pdb=" O ASP C 724 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER C 710 " --> pdb=" O GLY C 723 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 378 through 379 removed outlier: 3.927A pdb=" N SER C 378 " --> pdb=" O PHE C 392 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU C 860 " --> pdb=" O GLY C 856 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY C 856 " --> pdb=" O LEU C 860 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 470 through 475 removed outlier: 3.761A pdb=" N ASP C 472 " --> pdb=" O ALA C 502 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU C 513 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU C 498 " --> pdb=" O PHE C 511 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE C 511 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA C 500 " --> pdb=" O LEU C 509 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU C 509 " --> pdb=" O ALA C 500 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 539 " --> pdb=" O LEU C 510 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 557 through 562 removed outlier: 4.170A pdb=" N MET C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN C 607 " --> pdb=" O PHE C 582 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 618 through 621 removed outlier: 3.654A pdb=" N ASN C 651 " --> pdb=" O PHE C 640 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 658 through 662 removed outlier: 4.057A pdb=" N GLU C 660 " --> pdb=" O ALA C 673 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN C 674 " --> pdb=" O GLY C 685 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLY C 685 " --> pdb=" O GLN C 674 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE C 686 " --> pdb=" O THR C 701 " (cutoff:3.500A) 599 hydrogen bonds defined for protein. 1713 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 88 hydrogen bonds 176 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 6.95 Time building geometry restraints manager: 4.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4907 1.34 - 1.46: 3603 1.46 - 1.58: 7683 1.58 - 1.70: 138 1.70 - 1.83: 137 Bond restraints: 16468 Sorted by residual: bond pdb=" C4' DT D 10 " pdb=" O4' DT D 10 " ideal model delta sigma weight residual 1.450 1.418 0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" C3' DT D 10 " pdb=" C2' DT D 10 " ideal model delta sigma weight residual 1.525 1.556 -0.031 2.00e-02 2.50e+03 2.40e+00 bond pdb=" C3' DT D 7 " pdb=" C2' DT D 7 " ideal model delta sigma weight residual 1.525 1.554 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C4' DC E 58 " pdb=" O4' DC E 58 " ideal model delta sigma weight residual 1.450 1.422 0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" C4' DC D 16 " pdb=" O4' DC D 16 " ideal model delta sigma weight residual 1.450 1.424 0.026 2.00e-02 2.50e+03 1.75e+00 ... (remaining 16463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 21252 1.41 - 2.82: 1133 2.82 - 4.24: 183 4.24 - 5.65: 34 5.65 - 7.06: 4 Bond angle restraints: 22606 Sorted by residual: angle pdb=" C4' DG D 6 " pdb=" C3' DG D 6 " pdb=" O3' DG D 6 " ideal model delta sigma weight residual 110.00 115.61 -5.61 1.50e+00 4.44e-01 1.40e+01 angle pdb=" C3' DG D 6 " pdb=" O3' DG D 6 " pdb=" P DT D 7 " ideal model delta sigma weight residual 120.20 125.60 -5.40 1.50e+00 4.44e-01 1.29e+01 angle pdb=" O5' DG D 5 " pdb=" C5' DG D 5 " pdb=" C4' DG D 5 " ideal model delta sigma weight residual 110.80 116.07 -5.27 1.50e+00 4.44e-01 1.23e+01 angle pdb=" C2' DA D 18 " pdb=" C1' DA D 18 " pdb=" N9 DA D 18 " ideal model delta sigma weight residual 113.50 118.77 -5.27 1.50e+00 4.44e-01 1.23e+01 angle pdb=" N GLY B 338 " pdb=" CA GLY B 338 " pdb=" C GLY B 338 " ideal model delta sigma weight residual 112.34 119.40 -7.06 2.04e+00 2.40e-01 1.20e+01 ... (remaining 22601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.22: 9303 32.22 - 64.44: 410 64.44 - 96.66: 26 96.66 - 128.88: 0 128.88 - 161.10: 2 Dihedral angle restraints: 9741 sinusoidal: 4474 harmonic: 5267 Sorted by residual: dihedral pdb=" CA GLU B 68 " pdb=" C GLU B 68 " pdb=" N PRO B 69 " pdb=" CA PRO B 69 " ideal model delta harmonic sigma weight residual -180.00 -150.70 -29.30 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA ILE A 631 " pdb=" C ILE A 631 " pdb=" N GLU A 632 " pdb=" CA GLU A 632 " ideal model delta harmonic sigma weight residual -180.00 -151.28 -28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA SER B 85 " pdb=" C SER B 85 " pdb=" N ILE B 86 " pdb=" CA ILE B 86 " ideal model delta harmonic sigma weight residual 180.00 151.49 28.51 0 5.00e+00 4.00e-02 3.25e+01 ... (remaining 9738 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2062 0.065 - 0.129: 411 0.129 - 0.194: 33 0.194 - 0.259: 1 0.259 - 0.323: 1 Chirality restraints: 2508 Sorted by residual: chirality pdb=" C3' DG D 6 " pdb=" C4' DG D 6 " pdb=" O3' DG D 6 " pdb=" C2' DG D 6 " both_signs ideal model delta sigma weight residual False -2.66 -2.34 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" C1' DA D 18 " pdb=" O4' DA D 18 " pdb=" C2' DA D 18 " pdb=" N9 DA D 18 " both_signs ideal model delta sigma weight residual False 2.42 2.18 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C4' DC D 16 " pdb=" C5' DC D 16 " pdb=" O4' DC D 16 " pdb=" C3' DC D 16 " both_signs ideal model delta sigma weight residual False -2.53 -2.35 -0.18 2.00e-01 2.50e+01 8.07e-01 ... (remaining 2505 not shown) Planarity restraints: 2640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 796 " 0.303 9.50e-02 1.11e+02 1.37e-01 1.49e+01 pdb=" NE ARG B 796 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 796 " 0.029 2.00e-02 2.50e+03 pdb=" NH1 ARG B 796 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG B 796 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 186 " -0.295 9.50e-02 1.11e+02 1.33e-01 1.40e+01 pdb=" NE ARG A 186 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG A 186 " -0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG A 186 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 186 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 841 " 0.289 9.50e-02 1.11e+02 1.31e-01 1.38e+01 pdb=" NE ARG C 841 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG C 841 " 0.029 2.00e-02 2.50e+03 pdb=" NH1 ARG C 841 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG C 841 " -0.000 2.00e-02 2.50e+03 ... (remaining 2637 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 72 2.56 - 3.14: 12588 3.14 - 3.73: 24998 3.73 - 4.31: 36290 4.31 - 4.90: 59180 Nonbonded interactions: 133128 Sorted by model distance: nonbonded pdb=" OD1 ASP B 792 " pdb="ZN ZN B 902 " model vdw 1.973 2.230 nonbonded pdb=" OD2 ASP B 792 " pdb="ZN ZN B 902 " model vdw 2.034 2.230 nonbonded pdb=" OG SER B 793 " pdb="ZN ZN B 902 " model vdw 2.125 2.230 nonbonded pdb=" OH TYR B 321 " pdb=" O SER B 387 " model vdw 2.170 3.040 nonbonded pdb=" CG ASP B 792 " pdb="ZN ZN B 902 " model vdw 2.197 2.460 ... (remaining 133123 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: 7.700 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: 0.720 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 48.030 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16475 Z= 0.160 Angle : 0.718 7.058 22609 Z= 0.418 Chirality : 0.049 0.323 2508 Planarity : 0.010 0.137 2640 Dihedral : 16.633 161.096 6329 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: -0.73 (0.18), residues: 1790 helix: -0.88 (0.19), residues: 525 sheet: 0.25 (0.24), residues: 440 loop : -0.46 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 402 HIS 0.006 0.001 HIS A 198 PHE 0.018 0.002 PHE C 700 TYR 0.025 0.005 TYR B 439 ARG 0.033 0.004 ARG B 796 Details of bonding type rmsd hydrogen bonds : bond 0.16621 ( 687) hydrogen bonds : angle 7.12145 ( 1889) metal coordination : bond 0.01337 ( 7) metal coordination : angle 2.69155 ( 3) covalent geometry : bond 0.00365 (16468) covalent geometry : angle 0.71726 (22606) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ARG cc_start: 0.6451 (ttp80) cc_final: 0.5908 (mmm160) REVERT: A 255 TYR cc_start: 0.8216 (m-10) cc_final: 0.7935 (m-10) REVERT: A 627 ASN cc_start: 0.9149 (m110) cc_final: 0.8942 (m110) REVERT: A 708 GLU cc_start: 0.9472 (mm-30) cc_final: 0.9256 (mm-30) REVERT: B 681 MET cc_start: 0.8762 (tpt) cc_final: 0.8481 (tpt) REVERT: B 710 ARG cc_start: 0.8176 (ttm110) cc_final: 0.7875 (ptp-170) REVERT: B 733 HIS cc_start: 0.8948 (m170) cc_final: 0.8712 (m-70) REVERT: C 683 LEU cc_start: 0.8636 (mp) cc_final: 0.8145 (tp) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.3647 time to fit residues: 98.5648 Evaluate side-chains 120 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 145 optimal weight: 0.0010 chunk 56 optimal weight: 0.7980 chunk 88 optimal weight: 0.1980 chunk 107 optimal weight: 0.0770 chunk 168 optimal weight: 1.9990 overall best weight: 0.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS A 272 HIS ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 627 ASN B 152 ASN B 240 GLN B 797 HIS C 687 HIS C 807 HIS C 857 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.134640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.094210 restraints weight = 24806.856| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.10 r_work: 0.2965 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16475 Z= 0.140 Angle : 0.626 7.876 22609 Z= 0.340 Chirality : 0.044 0.158 2508 Planarity : 0.004 0.055 2640 Dihedral : 18.442 156.658 2733 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.75 % Allowed : 3.38 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: 0.60 (0.20), residues: 1790 helix: 0.92 (0.22), residues: 535 sheet: 0.42 (0.24), residues: 427 loop : 0.19 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 805 HIS 0.005 0.001 HIS A 198 PHE 0.016 0.002 PHE C 391 TYR 0.046 0.002 TYR A 296 ARG 0.007 0.001 ARG A 713 Details of bonding type rmsd hydrogen bonds : bond 0.04481 ( 687) hydrogen bonds : angle 4.99473 ( 1889) metal coordination : bond 0.00449 ( 7) metal coordination : angle 1.86873 ( 3) covalent geometry : bond 0.00305 (16468) covalent geometry : angle 0.62526 (22606) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ARG cc_start: 0.6586 (ttp80) cc_final: 0.6182 (mmm160) REVERT: A 238 HIS cc_start: 0.8521 (OUTLIER) cc_final: 0.8211 (t-90) REVERT: A 296 TYR cc_start: 0.7764 (m-80) cc_final: 0.7207 (m-80) REVERT: A 329 MET cc_start: 0.8594 (tpp) cc_final: 0.7997 (tpp) REVERT: A 623 GLU cc_start: 0.8771 (tt0) cc_final: 0.8453 (tt0) REVERT: A 627 ASN cc_start: 0.9096 (m-40) cc_final: 0.8842 (m110) REVERT: A 669 GLU cc_start: 0.8443 (tp30) cc_final: 0.7945 (tm-30) REVERT: A 686 LYS cc_start: 0.8977 (tptp) cc_final: 0.8408 (tptp) REVERT: B 725 ARG cc_start: 0.8577 (mmp-170) cc_final: 0.8288 (mmp-170) REVERT: C 683 LEU cc_start: 0.8747 (mp) cc_final: 0.8265 (tp) REVERT: C 811 ARG cc_start: 0.8735 (mtm180) cc_final: 0.8458 (ttp-110) outliers start: 12 outliers final: 7 residues processed: 140 average time/residue: 0.3052 time to fit residues: 63.1220 Evaluate side-chains 126 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 707 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 50 optimal weight: 0.0010 chunk 168 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 55 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 53 optimal weight: 9.9990 chunk 117 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.133655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.094446 restraints weight = 24598.147| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.07 r_work: 0.2958 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16475 Z= 0.146 Angle : 0.577 7.951 22609 Z= 0.311 Chirality : 0.043 0.159 2508 Planarity : 0.004 0.039 2640 Dihedral : 18.383 156.025 2733 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.13 % Allowed : 4.69 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: 0.78 (0.20), residues: 1790 helix: 1.31 (0.23), residues: 536 sheet: 0.25 (0.24), residues: 428 loop : 0.29 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 805 HIS 0.009 0.001 HIS B 733 PHE 0.035 0.002 PHE A 290 TYR 0.027 0.001 TYR A 296 ARG 0.006 0.000 ARG B 759 Details of bonding type rmsd hydrogen bonds : bond 0.04105 ( 687) hydrogen bonds : angle 4.59606 ( 1889) metal coordination : bond 0.00510 ( 7) metal coordination : angle 2.09711 ( 3) covalent geometry : bond 0.00330 (16468) covalent geometry : angle 0.57641 (22606) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ARG cc_start: 0.6514 (ttp80) cc_final: 0.6257 (mmm160) REVERT: A 238 HIS cc_start: 0.8582 (OUTLIER) cc_final: 0.8166 (t-90) REVERT: A 296 TYR cc_start: 0.7639 (m-80) cc_final: 0.7345 (m-80) REVERT: A 329 MET cc_start: 0.8710 (tpp) cc_final: 0.8235 (tpp) REVERT: A 417 MET cc_start: 0.8305 (mmm) cc_final: 0.8051 (mmm) REVERT: A 623 GLU cc_start: 0.8734 (tt0) cc_final: 0.8441 (tt0) REVERT: A 627 ASN cc_start: 0.9057 (m-40) cc_final: 0.8825 (m110) REVERT: A 686 LYS cc_start: 0.8968 (tptp) cc_final: 0.8500 (tptp) REVERT: B 328 MET cc_start: 0.7001 (mmt) cc_final: 0.6762 (mmp) REVERT: B 724 ASP cc_start: 0.8153 (t0) cc_final: 0.7953 (t0) REVERT: C 683 LEU cc_start: 0.8716 (mp) cc_final: 0.8218 (tp) REVERT: C 811 ARG cc_start: 0.8731 (mtm180) cc_final: 0.8483 (ttp-110) outliers start: 18 outliers final: 11 residues processed: 135 average time/residue: 0.3117 time to fit residues: 61.8150 Evaluate side-chains 125 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 707 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 3 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 148 optimal weight: 0.1980 chunk 131 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.133532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.094250 restraints weight = 24740.731| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.11 r_work: 0.2951 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16475 Z= 0.142 Angle : 0.568 10.017 22609 Z= 0.304 Chirality : 0.042 0.152 2508 Planarity : 0.004 0.043 2640 Dihedral : 18.331 154.849 2733 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.00 % Allowed : 6.13 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: 0.79 (0.20), residues: 1790 helix: 1.48 (0.23), residues: 534 sheet: 0.17 (0.24), residues: 442 loop : 0.23 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 805 HIS 0.015 0.001 HIS B 733 PHE 0.030 0.002 PHE A 290 TYR 0.020 0.001 TYR A 296 ARG 0.010 0.000 ARG B 728 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 687) hydrogen bonds : angle 4.43904 ( 1889) metal coordination : bond 0.00520 ( 7) metal coordination : angle 2.24058 ( 3) covalent geometry : bond 0.00329 (16468) covalent geometry : angle 0.56729 (22606) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 HIS cc_start: 0.8577 (OUTLIER) cc_final: 0.8152 (t-90) REVERT: A 255 TYR cc_start: 0.8312 (m-10) cc_final: 0.7934 (m-10) REVERT: A 262 LEU cc_start: 0.8491 (mt) cc_final: 0.8118 (pp) REVERT: A 296 TYR cc_start: 0.7567 (m-80) cc_final: 0.7282 (m-80) REVERT: A 623 GLU cc_start: 0.8750 (tt0) cc_final: 0.8452 (tt0) REVERT: A 627 ASN cc_start: 0.9083 (m-40) cc_final: 0.8845 (m110) REVERT: A 635 PHE cc_start: 0.7561 (t80) cc_final: 0.7357 (t80) REVERT: A 669 GLU cc_start: 0.8287 (tp30) cc_final: 0.7880 (tm-30) REVERT: A 686 LYS cc_start: 0.9031 (tptp) cc_final: 0.8598 (tptp) REVERT: C 683 LEU cc_start: 0.8707 (mp) cc_final: 0.8196 (tp) REVERT: C 811 ARG cc_start: 0.8724 (mtm180) cc_final: 0.8494 (ttp-110) REVERT: C 866 VAL cc_start: 0.8446 (OUTLIER) cc_final: 0.8183 (t) outliers start: 16 outliers final: 8 residues processed: 136 average time/residue: 0.3082 time to fit residues: 61.9187 Evaluate side-chains 121 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 866 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 99 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 43 optimal weight: 0.0470 chunk 159 optimal weight: 0.0970 chunk 67 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 153 optimal weight: 6.9990 chunk 128 optimal weight: 0.3980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN C 807 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.133930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.095317 restraints weight = 25149.477| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.04 r_work: 0.2971 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16475 Z= 0.123 Angle : 0.552 12.327 22609 Z= 0.293 Chirality : 0.041 0.152 2508 Planarity : 0.004 0.048 2640 Dihedral : 18.274 154.144 2733 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.06 % Allowed : 7.19 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: 0.83 (0.20), residues: 1790 helix: 1.63 (0.23), residues: 535 sheet: 0.13 (0.24), residues: 441 loop : 0.20 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 805 HIS 0.011 0.001 HIS B 733 PHE 0.036 0.001 PHE A 290 TYR 0.014 0.001 TYR A 296 ARG 0.004 0.000 ARG A 629 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 687) hydrogen bonds : angle 4.29057 ( 1889) metal coordination : bond 0.00410 ( 7) metal coordination : angle 2.04579 ( 3) covalent geometry : bond 0.00279 (16468) covalent geometry : angle 0.55128 (22606) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 HIS cc_start: 0.8547 (OUTLIER) cc_final: 0.8237 (t-90) REVERT: A 239 SER cc_start: 0.7747 (m) cc_final: 0.7383 (p) REVERT: A 296 TYR cc_start: 0.7494 (m-80) cc_final: 0.7195 (m-80) REVERT: A 329 MET cc_start: 0.8436 (tpp) cc_final: 0.8039 (tpp) REVERT: A 623 GLU cc_start: 0.8763 (tt0) cc_final: 0.8459 (tt0) REVERT: A 627 ASN cc_start: 0.9032 (m-40) cc_final: 0.8799 (m110) REVERT: A 631 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8487 (tt) REVERT: A 635 PHE cc_start: 0.7679 (t80) cc_final: 0.7462 (t80) REVERT: A 669 GLU cc_start: 0.8285 (tp30) cc_final: 0.7931 (tm-30) REVERT: C 683 LEU cc_start: 0.8716 (mp) cc_final: 0.8226 (tp) REVERT: C 811 ARG cc_start: 0.8760 (mtm180) cc_final: 0.8461 (ttp-110) REVERT: C 866 VAL cc_start: 0.8403 (OUTLIER) cc_final: 0.8075 (t) outliers start: 17 outliers final: 10 residues processed: 131 average time/residue: 0.2864 time to fit residues: 55.9421 Evaluate side-chains 125 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 866 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 84 optimal weight: 0.5980 chunk 115 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 68 optimal weight: 0.3980 chunk 164 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 178 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.138424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.096045 restraints weight = 25062.462| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.26 r_work: 0.3026 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16475 Z= 0.150 Angle : 0.564 8.626 22609 Z= 0.298 Chirality : 0.042 0.147 2508 Planarity : 0.004 0.050 2640 Dihedral : 18.289 153.213 2733 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.44 % Allowed : 7.69 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: 0.83 (0.20), residues: 1790 helix: 1.65 (0.23), residues: 537 sheet: 0.10 (0.23), residues: 440 loop : 0.19 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 805 HIS 0.012 0.001 HIS B 733 PHE 0.023 0.002 PHE A 290 TYR 0.013 0.001 TYR A 294 ARG 0.005 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 687) hydrogen bonds : angle 4.25527 ( 1889) metal coordination : bond 0.00590 ( 7) metal coordination : angle 2.06374 ( 3) covalent geometry : bond 0.00353 (16468) covalent geometry : angle 0.56382 (22606) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 HIS cc_start: 0.8570 (OUTLIER) cc_final: 0.8295 (t-90) REVERT: A 239 SER cc_start: 0.7828 (m) cc_final: 0.7391 (p) REVERT: A 623 GLU cc_start: 0.8860 (tt0) cc_final: 0.8547 (tt0) REVERT: A 627 ASN cc_start: 0.9120 (m-40) cc_final: 0.8862 (m110) REVERT: A 635 PHE cc_start: 0.7596 (t80) cc_final: 0.7357 (t80) REVERT: A 669 GLU cc_start: 0.8439 (tp30) cc_final: 0.8057 (tm-30) REVERT: B 441 CYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8364 (t) REVERT: C 683 LEU cc_start: 0.8755 (mp) cc_final: 0.8141 (tp) REVERT: C 811 ARG cc_start: 0.8825 (mtm180) cc_final: 0.8497 (ttp-110) outliers start: 23 outliers final: 15 residues processed: 137 average time/residue: 0.2962 time to fit residues: 61.4268 Evaluate side-chains 130 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 707 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 105 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 179 optimal weight: 10.0000 chunk 32 optimal weight: 0.0270 chunk 50 optimal weight: 8.9990 chunk 10 optimal weight: 0.0000 chunk 111 optimal weight: 0.0770 chunk 71 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 overall best weight: 0.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 733 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.139847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.098750 restraints weight = 25115.858| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.37 r_work: 0.3067 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16475 Z= 0.115 Angle : 0.543 8.090 22609 Z= 0.288 Chirality : 0.041 0.165 2508 Planarity : 0.004 0.051 2640 Dihedral : 18.244 153.015 2733 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.25 % Allowed : 8.38 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: 0.86 (0.20), residues: 1790 helix: 1.72 (0.23), residues: 537 sheet: 0.12 (0.24), residues: 440 loop : 0.18 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 805 HIS 0.010 0.001 HIS B 733 PHE 0.029 0.001 PHE A 290 TYR 0.039 0.001 TYR A 296 ARG 0.003 0.000 ARG A 292 Details of bonding type rmsd hydrogen bonds : bond 0.03379 ( 687) hydrogen bonds : angle 4.18036 ( 1889) metal coordination : bond 0.00322 ( 7) metal coordination : angle 1.82697 ( 3) covalent geometry : bond 0.00258 (16468) covalent geometry : angle 0.54251 (22606) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 HIS cc_start: 0.8578 (OUTLIER) cc_final: 0.8308 (t-90) REVERT: A 239 SER cc_start: 0.7786 (m) cc_final: 0.7358 (p) REVERT: A 329 MET cc_start: 0.8298 (tpp) cc_final: 0.7842 (tpp) REVERT: A 623 GLU cc_start: 0.8827 (tt0) cc_final: 0.8554 (tt0) REVERT: A 627 ASN cc_start: 0.9107 (m-40) cc_final: 0.8853 (m110) REVERT: A 631 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8318 (tt) REVERT: A 669 GLU cc_start: 0.8401 (tp30) cc_final: 0.8057 (tm-30) REVERT: C 811 ARG cc_start: 0.8803 (mtm180) cc_final: 0.8449 (ttp-110) outliers start: 20 outliers final: 15 residues processed: 139 average time/residue: 0.2916 time to fit residues: 61.3187 Evaluate side-chains 137 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 707 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 10 optimal weight: 0.3980 chunk 92 optimal weight: 2.9990 chunk 30 optimal weight: 20.0000 chunk 174 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 109 optimal weight: 0.0980 chunk 153 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 614 GLN C 794 HIS C 807 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.136597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.093857 restraints weight = 24926.026| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.27 r_work: 0.2991 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 16475 Z= 0.212 Angle : 0.614 9.279 22609 Z= 0.323 Chirality : 0.044 0.166 2508 Planarity : 0.004 0.050 2640 Dihedral : 18.367 151.785 2733 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.38 % Allowed : 8.63 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: 0.68 (0.20), residues: 1790 helix: 1.59 (0.22), residues: 539 sheet: -0.02 (0.24), residues: 434 loop : 0.06 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 805 HIS 0.005 0.001 HIS A 198 PHE 0.029 0.002 PHE A 635 TYR 0.050 0.002 TYR A 296 ARG 0.006 0.000 ARG B 215 Details of bonding type rmsd hydrogen bonds : bond 0.03983 ( 687) hydrogen bonds : angle 4.37728 ( 1889) metal coordination : bond 0.00924 ( 7) metal coordination : angle 2.47868 ( 3) covalent geometry : bond 0.00510 (16468) covalent geometry : angle 0.61351 (22606) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ARG cc_start: 0.8196 (mmm160) cc_final: 0.7788 (mmm160) REVERT: A 329 MET cc_start: 0.8491 (tpp) cc_final: 0.8062 (tpp) REVERT: A 623 GLU cc_start: 0.8852 (tt0) cc_final: 0.8599 (tt0) REVERT: A 627 ASN cc_start: 0.9131 (m-40) cc_final: 0.8871 (m110) REVERT: A 631 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8334 (tt) REVERT: A 635 PHE cc_start: 0.7368 (t80) cc_final: 0.7093 (t80) REVERT: A 669 GLU cc_start: 0.8467 (tp30) cc_final: 0.8106 (tm-30) REVERT: A 673 ARG cc_start: 0.7878 (mmt90) cc_final: 0.7643 (mmt90) REVERT: A 686 LYS cc_start: 0.8980 (tppt) cc_final: 0.8534 (tptp) REVERT: B 441 CYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8351 (t) REVERT: C 683 LEU cc_start: 0.8584 (mp) cc_final: 0.8031 (tp) REVERT: C 811 ARG cc_start: 0.8783 (mtm180) cc_final: 0.8419 (ttp-110) outliers start: 22 outliers final: 19 residues processed: 138 average time/residue: 0.3979 time to fit residues: 84.9258 Evaluate side-chains 140 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 707 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 1 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 118 optimal weight: 0.0050 chunk 110 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 120 optimal weight: 0.0870 chunk 164 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 overall best weight: 0.5772 ------------------------------------------------------------------------------- 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 = 0.3878 r_free = 0.3878 target = 0.138371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.095991 restraints weight = 25015.310| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.29 r_work: 0.3031 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16475 Z= 0.136 Angle : 0.562 8.426 22609 Z= 0.299 Chirality : 0.041 0.189 2508 Planarity : 0.004 0.051 2640 Dihedral : 18.298 151.929 2733 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.19 % Allowed : 9.19 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: 0.74 (0.20), residues: 1790 helix: 1.71 (0.22), residues: 539 sheet: -0.02 (0.24), residues: 440 loop : 0.08 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 805 HIS 0.007 0.001 HIS B 733 PHE 0.033 0.001 PHE A 635 TYR 0.044 0.001 TYR A 296 ARG 0.003 0.000 ARG A 292 Details of bonding type rmsd hydrogen bonds : bond 0.03520 ( 687) hydrogen bonds : angle 4.27480 ( 1889) metal coordination : bond 0.00426 ( 7) metal coordination : angle 2.02680 ( 3) covalent geometry : bond 0.00314 (16468) covalent geometry : angle 0.56136 (22606) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ARG cc_start: 0.8287 (mmm160) cc_final: 0.8049 (mmm160) REVERT: A 329 MET cc_start: 0.8450 (tpp) cc_final: 0.8032 (tpp) REVERT: A 627 ASN cc_start: 0.9107 (m-40) cc_final: 0.8858 (m110) REVERT: A 631 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8363 (tt) REVERT: A 669 GLU cc_start: 0.8444 (tp30) cc_final: 0.8083 (tm-30) REVERT: A 673 ARG cc_start: 0.7877 (mmt90) cc_final: 0.7668 (mmt90) REVERT: A 686 LYS cc_start: 0.8917 (tppt) cc_final: 0.8500 (tptp) REVERT: C 683 LEU cc_start: 0.8638 (mp) cc_final: 0.8042 (tp) REVERT: C 811 ARG cc_start: 0.8776 (mtm180) cc_final: 0.8414 (ttp-110) outliers start: 19 outliers final: 16 residues processed: 137 average time/residue: 0.2967 time to fit residues: 61.0418 Evaluate side-chains 135 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 707 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 158 optimal weight: 0.0970 chunk 183 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.138063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.095594 restraints weight = 25044.222| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.28 r_work: 0.3020 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16475 Z= 0.148 Angle : 0.570 8.697 22609 Z= 0.301 Chirality : 0.042 0.167 2508 Planarity : 0.004 0.051 2640 Dihedral : 18.278 151.369 2733 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.13 % Allowed : 9.01 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: 0.77 (0.20), residues: 1790 helix: 1.76 (0.23), residues: 539 sheet: -0.03 (0.24), residues: 440 loop : 0.09 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 805 HIS 0.005 0.001 HIS A 198 PHE 0.031 0.002 PHE A 635 TYR 0.045 0.001 TYR A 296 ARG 0.003 0.000 ARG A 292 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 687) hydrogen bonds : angle 4.27062 ( 1889) metal coordination : bond 0.00488 ( 7) metal coordination : angle 1.96370 ( 3) covalent geometry : bond 0.00348 (16468) covalent geometry : angle 0.56991 (22606) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ARG cc_start: 0.8303 (mmm160) cc_final: 0.8080 (mmm160) REVERT: A 329 MET cc_start: 0.8490 (tpp) cc_final: 0.8088 (tpp) REVERT: A 631 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8240 (tt) REVERT: A 669 GLU cc_start: 0.8421 (tp30) cc_final: 0.8040 (tm-30) REVERT: A 673 ARG cc_start: 0.7859 (mmt90) cc_final: 0.7652 (mmt90) REVERT: A 686 LYS cc_start: 0.8934 (tppt) cc_final: 0.8522 (tptp) REVERT: C 683 LEU cc_start: 0.8569 (mp) cc_final: 0.7991 (tp) REVERT: C 811 ARG cc_start: 0.8577 (mtm180) cc_final: 0.8247 (ttp-110) outliers start: 18 outliers final: 16 residues processed: 134 average time/residue: 0.3654 time to fit residues: 73.5471 Evaluate side-chains 138 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 707 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 162 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 145 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 13 optimal weight: 0.0980 chunk 67 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.138555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.096244 restraints weight = 25032.424| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.29 r_work: 0.3035 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16475 Z= 0.133 Angle : 0.565 9.275 22609 Z= 0.297 Chirality : 0.041 0.171 2508 Planarity : 0.004 0.051 2640 Dihedral : 18.248 151.063 2733 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.06 % Allowed : 9.38 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: 0.82 (0.20), residues: 1790 helix: 1.84 (0.23), residues: 538 sheet: -0.02 (0.24), residues: 440 loop : 0.10 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 805 HIS 0.005 0.001 HIS A 198 PHE 0.038 0.002 PHE A 635 TYR 0.044 0.001 TYR A 296 ARG 0.005 0.000 ARG B 215 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 687) hydrogen bonds : angle 4.23757 ( 1889) metal coordination : bond 0.00377 ( 7) metal coordination : angle 1.87431 ( 3) covalent geometry : bond 0.00308 (16468) covalent geometry : angle 0.56471 (22606) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9918.85 seconds wall clock time: 175 minutes 25.46 seconds (10525.46 seconds total)