Starting phenix.real_space_refine on Thu Sep 18 10:14:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cli_16713/09_2025/8cli_16713.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cli_16713/09_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_16713/09_2025/8cli_16713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cli_16713/09_2025/8cli_16713.map" model { file = "/net/cci-nas-00/data/ceres_data/8cli_16713/09_2025/8cli_16713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cli_16713/09_2025/8cli_16713.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.97, per 1000 atoms: 0.25 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: 1.49 Conformation dependent library (CDL) restraints added in 749.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.97 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: 3.77 Time building geometry restraints manager: 2.03 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: 9.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.630 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.560 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.033 0.004 ARG B 796 TYR 0.025 0.005 TYR B 439 PHE 0.018 0.002 PHE C 700 TRP 0.030 0.002 TRP C 402 HIS 0.006 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00365 (16468) covalent geometry : angle 0.71726 (22606) hydrogen bonds : bond 0.16621 ( 687) hydrogen bonds : angle 7.12145 ( 1889) metal coordination : bond 0.01337 ( 7) metal coordination : angle 2.69155 ( 3) *********************** 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 : 0.622 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: 0.9237 (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: 0.1694 time to fit residues: 45.7040 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 : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.0770 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.0030 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 overall best weight: 0.3948 ------------------------------------------------------------------------------- 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 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN B 240 GLN C 687 HIS C 807 HIS C 857 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.134157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.094421 restraints weight = 24581.821| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.06 r_work: 0.2966 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16475 Z= 0.144 Angle : 0.623 8.117 22609 Z= 0.338 Chirality : 0.044 0.158 2508 Planarity : 0.004 0.054 2640 Dihedral : 18.447 156.874 2733 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.88 % Allowed : 3.31 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.20), residues: 1790 helix: 0.93 (0.22), residues: 535 sheet: 0.39 (0.24), residues: 432 loop : 0.18 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 288 TYR 0.044 0.002 TYR A 296 PHE 0.016 0.002 PHE C 391 TRP 0.019 0.001 TRP B 805 HIS 0.005 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00313 (16468) covalent geometry : angle 0.62226 (22606) hydrogen bonds : bond 0.04475 ( 687) hydrogen bonds : angle 4.98933 ( 1889) metal coordination : bond 0.00505 ( 7) metal coordination : angle 1.75728 ( 3) *********************** 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: 14 poor density : 133 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ARG cc_start: 0.6584 (ttp80) cc_final: 0.6110 (mmm160) REVERT: A 238 HIS cc_start: 0.8520 (OUTLIER) cc_final: 0.8220 (t-90) REVERT: A 296 TYR cc_start: 0.7783 (m-80) cc_final: 0.7219 (m-80) REVERT: A 329 MET cc_start: 0.8653 (tpp) cc_final: 0.8396 (tpp) REVERT: A 444 GLN cc_start: 0.8371 (mm-40) cc_final: 0.8143 (mt0) REVERT: A 623 GLU cc_start: 0.8763 (tt0) cc_final: 0.8449 (tt0) REVERT: A 627 ASN cc_start: 0.9042 (m110) cc_final: 0.8830 (m110) REVERT: A 669 GLU cc_start: 0.8461 (tp30) cc_final: 0.7978 (tm-30) REVERT: A 686 LYS cc_start: 0.8977 (tptp) cc_final: 0.8409 (tptp) REVERT: B 710 ARG cc_start: 0.8550 (ttm110) cc_final: 0.8279 (ptp-170) REVERT: C 683 LEU cc_start: 0.8744 (mp) cc_final: 0.8262 (tp) REVERT: C 811 ARG cc_start: 0.8732 (mtm180) cc_final: 0.8449 (ttp-110) outliers start: 14 outliers final: 8 residues processed: 140 average time/residue: 0.1550 time to fit residues: 31.8534 Evaluate side-chains 128 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 87 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 90 optimal weight: 0.4980 chunk 64 optimal weight: 0.0270 chunk 156 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 113 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 overall best weight: 0.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 797 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.133879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.094700 restraints weight = 25030.294| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.08 r_work: 0.2956 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16475 Z= 0.138 Angle : 0.573 6.779 22609 Z= 0.309 Chirality : 0.042 0.176 2508 Planarity : 0.004 0.040 2640 Dihedral : 18.373 155.931 2733 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.06 % Allowed : 4.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.20), residues: 1790 helix: 1.34 (0.23), residues: 534 sheet: 0.24 (0.24), residues: 428 loop : 0.27 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 728 TYR 0.029 0.001 TYR A 296 PHE 0.049 0.002 PHE A 290 TRP 0.022 0.001 TRP B 805 HIS 0.011 0.001 HIS B 733 Details of bonding type rmsd covalent geometry : bond 0.00314 (16468) covalent geometry : angle 0.57278 (22606) hydrogen bonds : bond 0.04017 ( 687) hydrogen bonds : angle 4.53581 ( 1889) metal coordination : bond 0.00474 ( 7) metal coordination : angle 2.15232 ( 3) *********************** 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 147 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 HIS cc_start: 0.8564 (OUTLIER) cc_final: 0.8132 (t-90) REVERT: A 255 TYR cc_start: 0.8328 (m-10) cc_final: 0.8025 (m-10) REVERT: A 296 TYR cc_start: 0.7667 (m-80) cc_final: 0.7284 (m-80) REVERT: A 329 MET cc_start: 0.8749 (tpp) cc_final: 0.8253 (tpp) REVERT: A 623 GLU cc_start: 0.8738 (tt0) cc_final: 0.8453 (tt0) REVERT: A 635 PHE cc_start: 0.7647 (t80) cc_final: 0.7421 (t80) REVERT: A 669 GLU cc_start: 0.8400 (tp30) cc_final: 0.7879 (tm-30) REVERT: A 686 LYS cc_start: 0.8933 (tptp) cc_final: 0.8470 (tptp) REVERT: B 328 MET cc_start: 0.7001 (mmt) cc_final: 0.6758 (mmp) REVERT: B 724 ASP cc_start: 0.8164 (t0) cc_final: 0.7875 (t0) REVERT: C 683 LEU cc_start: 0.8709 (mp) cc_final: 0.8218 (tp) REVERT: C 811 ARG cc_start: 0.8725 (mtm180) cc_final: 0.8474 (ttp-110) outliers start: 17 outliers final: 10 residues processed: 141 average time/residue: 0.1560 time to fit residues: 32.2544 Evaluate side-chains 127 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 691 VAL 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 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 147 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 171 optimal weight: 0.7980 chunk 156 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 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 = 0.3766 r_free = 0.3766 target = 0.133023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.093169 restraints weight = 24708.538| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.07 r_work: 0.2937 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16475 Z= 0.153 Angle : 0.570 9.744 22609 Z= 0.304 Chirality : 0.042 0.151 2508 Planarity : 0.004 0.049 2640 Dihedral : 18.336 154.499 2733 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.25 % Allowed : 6.44 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.20), residues: 1790 helix: 1.50 (0.23), residues: 536 sheet: 0.17 (0.24), residues: 431 loop : 0.19 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 759 TYR 0.020 0.001 TYR A 296 PHE 0.034 0.002 PHE A 290 TRP 0.013 0.001 TRP C 402 HIS 0.014 0.001 HIS B 733 Details of bonding type rmsd covalent geometry : bond 0.00358 (16468) covalent geometry : angle 0.56968 (22606) hydrogen bonds : bond 0.03809 ( 687) hydrogen bonds : angle 4.38985 ( 1889) metal coordination : bond 0.00618 ( 7) metal coordination : angle 2.35778 ( 3) *********************** 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 143 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.639 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: 0.8152 (t-90) REVERT: A 255 TYR cc_start: 0.8279 (m-10) cc_final: 0.7978 (m-10) REVERT: A 296 TYR cc_start: 0.7657 (m-80) cc_final: 0.7311 (m-80) REVERT: A 623 GLU cc_start: 0.8701 (tt0) cc_final: 0.8433 (tt0) REVERT: A 669 GLU cc_start: 0.8417 (tp30) cc_final: 0.7925 (tm-30) REVERT: B 724 ASP cc_start: 0.8183 (t0) cc_final: 0.7891 (t0) REVERT: C 683 LEU cc_start: 0.8711 (mp) cc_final: 0.8218 (tp) REVERT: C 811 ARG cc_start: 0.8757 (mtm180) cc_final: 0.8519 (ttp-110) REVERT: C 866 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8115 (t) outliers start: 20 outliers final: 12 residues processed: 135 average time/residue: 0.1533 time to fit residues: 30.4586 Evaluate side-chains 125 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 366 MET Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain C residue 520 LEU 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 724 ASP 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 102 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 145 optimal weight: 0.0270 chunk 107 optimal weight: 0.9980 chunk 133 optimal weight: 0.5980 chunk 132 optimal weight: 0.9990 chunk 135 optimal weight: 0.0970 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN B 733 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.133388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.093226 restraints weight = 24938.003| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.10 r_work: 0.2946 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16475 Z= 0.131 Angle : 0.551 7.160 22609 Z= 0.294 Chirality : 0.041 0.156 2508 Planarity : 0.004 0.053 2640 Dihedral : 18.293 154.048 2733 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.31 % Allowed : 7.07 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.20), residues: 1790 helix: 1.64 (0.23), residues: 535 sheet: 0.13 (0.23), residues: 440 loop : 0.20 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 629 TYR 0.017 0.001 TYR A 296 PHE 0.038 0.001 PHE A 290 TRP 0.014 0.001 TRP B 805 HIS 0.011 0.001 HIS B 733 Details of bonding type rmsd covalent geometry : bond 0.00300 (16468) covalent geometry : angle 0.55032 (22606) hydrogen bonds : bond 0.03635 ( 687) hydrogen bonds : angle 4.26902 ( 1889) metal coordination : bond 0.00475 ( 7) metal coordination : angle 2.15288 ( 3) *********************** 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 143 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7920 (pt) REVERT: A 238 HIS cc_start: 0.8556 (OUTLIER) cc_final: 0.8209 (t-90) REVERT: A 239 SER cc_start: 0.7736 (m) cc_final: 0.7327 (p) REVERT: A 329 MET cc_start: 0.8404 (tpp) cc_final: 0.7985 (tpp) REVERT: A 623 GLU cc_start: 0.8712 (tt0) cc_final: 0.8478 (tt0) REVERT: A 631 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8465 (tt) REVERT: A 635 PHE cc_start: 0.7577 (t80) cc_final: 0.7362 (t80) REVERT: A 669 GLU cc_start: 0.8376 (tp30) cc_final: 0.7953 (tm-30) REVERT: A 686 LYS cc_start: 0.9121 (tppt) cc_final: 0.8757 (mptt) REVERT: B 75 ASP cc_start: 0.8222 (t70) cc_final: 0.8009 (t0) REVERT: C 683 LEU cc_start: 0.8722 (mp) cc_final: 0.8216 (tp) REVERT: C 811 ARG cc_start: 0.8758 (mtm180) cc_final: 0.8429 (ttp-110) REVERT: C 866 VAL cc_start: 0.8443 (OUTLIER) cc_final: 0.8082 (t) outliers start: 21 outliers final: 10 residues processed: 136 average time/residue: 0.1491 time to fit residues: 30.1550 Evaluate side-chains 129 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 631 ILE 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 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 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 86 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 133 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 128 optimal weight: 0.0030 chunk 12 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.138733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.096788 restraints weight = 25149.734| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.19 r_work: 0.3048 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16475 Z= 0.141 Angle : 0.554 7.394 22609 Z= 0.294 Chirality : 0.042 0.165 2508 Planarity : 0.004 0.051 2640 Dihedral : 18.275 153.495 2733 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.44 % Allowed : 7.75 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.20), residues: 1790 helix: 1.66 (0.23), residues: 537 sheet: 0.09 (0.23), residues: 440 loop : 0.18 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 629 TYR 0.038 0.001 TYR A 296 PHE 0.037 0.002 PHE A 290 TRP 0.014 0.001 TRP B 805 HIS 0.005 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00330 (16468) covalent geometry : angle 0.55358 (22606) hydrogen bonds : bond 0.03608 ( 687) hydrogen bonds : angle 4.24923 ( 1889) metal coordination : bond 0.00541 ( 7) metal coordination : angle 2.02199 ( 3) *********************** 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 146 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 HIS cc_start: 0.8591 (OUTLIER) cc_final: 0.8306 (t-90) REVERT: A 239 SER cc_start: 0.7791 (m) cc_final: 0.7367 (p) REVERT: A 623 GLU cc_start: 0.8784 (tt0) cc_final: 0.8536 (tt0) REVERT: A 635 PHE cc_start: 0.7612 (t80) cc_final: 0.7398 (t80) REVERT: A 669 GLU cc_start: 0.8455 (tp30) cc_final: 0.8049 (tm-30) REVERT: A 686 LYS cc_start: 0.8981 (tppt) cc_final: 0.8566 (tptp) REVERT: B 441 CYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8368 (t) REVERT: C 811 ARG cc_start: 0.8782 (mtm180) cc_final: 0.8463 (ttp-110) outliers start: 23 outliers final: 16 residues processed: 139 average time/residue: 0.1414 time to fit residues: 29.6238 Evaluate side-chains 130 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain C residue 813 GLU Chi-restraints excluded: chain C residue 866 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 23 optimal weight: 0.0980 chunk 100 optimal weight: 0.4980 chunk 131 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 169 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 79 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: B 733 HIS C 614 GLN C 807 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.138790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.096448 restraints weight = 25149.221| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.28 r_work: 0.3034 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2756 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= 0.132 Angle : 0.548 8.072 22609 Z= 0.291 Chirality : 0.041 0.164 2508 Planarity : 0.004 0.053 2640 Dihedral : 18.268 152.823 2733 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.31 % Allowed : 8.44 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.20), residues: 1790 helix: 1.68 (0.22), residues: 537 sheet: 0.09 (0.24), residues: 440 loop : 0.17 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 288 TYR 0.042 0.001 TYR A 296 PHE 0.033 0.001 PHE A 290 TRP 0.014 0.001 TRP B 805 HIS 0.013 0.001 HIS B 733 Details of bonding type rmsd covalent geometry : bond 0.00307 (16468) covalent geometry : angle 0.54802 (22606) hydrogen bonds : bond 0.03504 ( 687) hydrogen bonds : angle 4.19657 ( 1889) metal coordination : bond 0.00449 ( 7) metal coordination : angle 1.95919 ( 3) *********************** 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 141 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 HIS cc_start: 0.8586 (OUTLIER) cc_final: 0.8317 (t-90) REVERT: A 239 SER cc_start: 0.7844 (m) cc_final: 0.7382 (p) REVERT: A 296 TYR cc_start: 0.7309 (m-80) cc_final: 0.7057 (m-80) REVERT: A 329 MET cc_start: 0.8323 (tpp) cc_final: 0.7879 (tpp) REVERT: A 623 GLU cc_start: 0.8797 (tt0) cc_final: 0.8566 (tt0) REVERT: A 631 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8359 (tt) REVERT: A 669 GLU cc_start: 0.8457 (tp30) cc_final: 0.8039 (tm-30) REVERT: A 686 LYS cc_start: 0.8953 (tppt) cc_final: 0.8555 (tptp) REVERT: B 441 CYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8413 (t) REVERT: C 811 ARG cc_start: 0.8793 (mtm180) cc_final: 0.8435 (ttp-110) outliers start: 21 outliers final: 16 residues processed: 135 average time/residue: 0.1341 time to fit residues: 27.6612 Evaluate side-chains 135 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 631 ILE 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 491 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 Chi-restraints excluded: chain C residue 813 GLU Chi-restraints excluded: chain C residue 866 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 0.0020 chunk 159 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 chunk 175 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 179 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 overall best weight: 0.8390 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.137944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.095379 restraints weight = 25117.897| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.27 r_work: 0.3017 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16475 Z= 0.158 Angle : 0.561 6.732 22609 Z= 0.298 Chirality : 0.042 0.164 2508 Planarity : 0.004 0.052 2640 Dihedral : 18.303 152.139 2733 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.31 % Allowed : 8.94 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.20), residues: 1790 helix: 1.66 (0.22), residues: 539 sheet: 0.05 (0.24), residues: 440 loop : 0.12 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 215 TYR 0.039 0.001 TYR A 296 PHE 0.041 0.002 PHE A 290 TRP 0.014 0.001 TRP B 805 HIS 0.005 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00374 (16468) covalent geometry : angle 0.56073 (22606) hydrogen bonds : bond 0.03632 ( 687) hydrogen bonds : angle 4.22573 ( 1889) metal coordination : bond 0.00594 ( 7) metal coordination : angle 2.07744 ( 3) *********************** 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: 21 poor density : 125 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 HIS cc_start: 0.8620 (OUTLIER) cc_final: 0.8361 (t-90) REVERT: A 296 TYR cc_start: 0.7325 (m-80) cc_final: 0.7048 (m-80) REVERT: A 329 MET cc_start: 0.8452 (tpp) cc_final: 0.8024 (tpp) REVERT: A 623 GLU cc_start: 0.8789 (tt0) cc_final: 0.8568 (tt0) REVERT: A 631 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8283 (tt) REVERT: A 635 PHE cc_start: 0.7275 (t80) cc_final: 0.7002 (t80) REVERT: A 669 GLU cc_start: 0.8546 (tp30) cc_final: 0.8064 (tm-30) REVERT: A 686 LYS cc_start: 0.8932 (tppt) cc_final: 0.8546 (tptp) REVERT: B 441 CYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8414 (t) REVERT: C 683 LEU cc_start: 0.8593 (mp) cc_final: 0.8043 (tp) REVERT: C 811 ARG cc_start: 0.8781 (mtm180) cc_final: 0.8428 (ttp-110) outliers start: 21 outliers final: 17 residues processed: 139 average time/residue: 0.1287 time to fit residues: 27.5501 Evaluate side-chains 136 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 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 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 618 THR Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 866 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 70 optimal weight: 2.9990 chunk 31 optimal weight: 50.0000 chunk 1 optimal weight: 0.7980 chunk 111 optimal weight: 0.0270 chunk 10 optimal weight: 0.3980 chunk 52 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 = 0.3880 r_free = 0.3880 target = 0.138568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.096200 restraints weight = 24905.791| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.28 r_work: 0.3029 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16475 Z= 0.136 Angle : 0.556 6.707 22609 Z= 0.296 Chirality : 0.041 0.181 2508 Planarity : 0.004 0.053 2640 Dihedral : 18.280 151.954 2733 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.31 % Allowed : 9.01 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.20), residues: 1790 helix: 1.70 (0.22), residues: 539 sheet: 0.02 (0.24), residues: 440 loop : 0.10 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 808 TYR 0.037 0.001 TYR A 296 PHE 0.033 0.001 PHE A 635 TRP 0.016 0.001 TRP B 805 HIS 0.005 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00317 (16468) covalent geometry : angle 0.55591 (22606) hydrogen bonds : bond 0.03496 ( 687) hydrogen bonds : angle 4.21301 ( 1889) metal coordination : bond 0.00414 ( 7) metal coordination : angle 1.92712 ( 3) *********************** 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: 21 poor density : 123 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 MET cc_start: 0.8476 (tpp) cc_final: 0.8070 (tpp) REVERT: A 631 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8305 (tt) REVERT: A 669 GLU cc_start: 0.8550 (tp30) cc_final: 0.8037 (tm-30) REVERT: A 686 LYS cc_start: 0.8933 (tppt) cc_final: 0.8565 (tptp) REVERT: C 811 ARG cc_start: 0.8768 (mtm180) cc_final: 0.8426 (ttp-110) outliers start: 21 outliers final: 16 residues processed: 137 average time/residue: 0.1260 time to fit residues: 26.4820 Evaluate side-chains 134 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 366 MET Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 491 ILE 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 618 THR Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 866 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 143 optimal weight: 0.3980 chunk 156 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 14 optimal weight: 0.1980 chunk 124 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3886 r_free = 0.3886 target = 0.139089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.098389 restraints weight = 25038.494| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.27 r_work: 0.3038 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3018 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= 0.127 Angle : 0.555 7.038 22609 Z= 0.294 Chirality : 0.041 0.166 2508 Planarity : 0.004 0.053 2640 Dihedral : 18.247 151.629 2733 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.06 % Allowed : 9.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.20), residues: 1790 helix: 1.80 (0.22), residues: 539 sheet: 0.02 (0.24), residues: 440 loop : 0.11 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 808 TYR 0.055 0.001 TYR A 296 PHE 0.033 0.001 PHE A 635 TRP 0.013 0.001 TRP C 402 HIS 0.005 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00291 (16468) covalent geometry : angle 0.55508 (22606) hydrogen bonds : bond 0.03450 ( 687) hydrogen bonds : angle 4.19663 ( 1889) metal coordination : bond 0.00316 ( 7) metal coordination : angle 1.81182 ( 3) ********************** 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: 17 poor density : 125 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 MET cc_start: 0.8330 (tpp) cc_final: 0.7933 (tpp) REVERT: A 631 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8313 (tt) REVERT: A 669 GLU cc_start: 0.8459 (tp30) cc_final: 0.8006 (tm-30) REVERT: A 686 LYS cc_start: 0.8937 (tppt) cc_final: 0.8573 (tptp) REVERT: C 811 ARG cc_start: 0.8583 (mtm180) cc_final: 0.8241 (ttp-110) REVERT: C 818 MET cc_start: 0.8109 (ttp) cc_final: 0.7721 (ttp) outliers start: 17 outliers final: 16 residues processed: 136 average time/residue: 0.1208 time to fit residues: 25.2273 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 : 0.590 ------------------------------------------------------------------------------- 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 366 MET Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 491 ILE 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 618 THR Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 866 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 99 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 124 optimal weight: 0.5980 chunk 129 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 170 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 28 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.138074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.095802 restraints weight = 24984.697| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.28 r_work: 0.3024 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16475 Z= 0.152 Angle : 0.573 8.658 22609 Z= 0.302 Chirality : 0.042 0.164 2508 Planarity : 0.004 0.053 2640 Dihedral : 18.263 151.121 2733 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.13 % Allowed : 9.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.20), residues: 1790 helix: 1.81 (0.22), residues: 536 sheet: -0.02 (0.24), residues: 440 loop : 0.09 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 215 TYR 0.049 0.001 TYR A 296 PHE 0.037 0.001 PHE A 635 TRP 0.013 0.001 TRP B 805 HIS 0.005 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00357 (16468) covalent geometry : angle 0.57256 (22606) hydrogen bonds : bond 0.03542 ( 687) hydrogen bonds : angle 4.22800 ( 1889) metal coordination : bond 0.00461 ( 7) metal coordination : angle 1.92903 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4584.87 seconds wall clock time: 79 minutes 13.53 seconds (4753.53 seconds total)