Starting phenix.real_space_refine on Sat May 17 18:03:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cli_16713/05_2025/8cli_16713.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cli_16713/05_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_16713/05_2025/8cli_16713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cli_16713/05_2025/8cli_16713.map" model { file = "/net/cci-nas-00/data/ceres_data/8cli_16713/05_2025/8cli_16713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cli_16713/05_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 9.87, per 1000 atoms: 0.62 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: 3.87 Conformation dependent library (CDL) restraints added in 1.8 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: 5.45 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: 6.57 Time building geometry restraints manager: 4.50 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: 7.250 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: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 43.570 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.450 ------------------------------------------------------------------------------- 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 : 1.802 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: 0.3494 time to fit residues: 94.3643 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 : 1.602 ------------------------------------------------------------------------------- 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 = 24806.888| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.10 r_work: 0.2965 rms_B_bonded: 3.05 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 1.86874 ( 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 : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ARG cc_start: 0.6583 (ttp80) cc_final: 0.6186 (mmm160) REVERT: A 238 HIS cc_start: 0.8521 (OUTLIER) cc_final: 0.8211 (t-90) REVERT: A 296 TYR cc_start: 0.7762 (m-80) cc_final: 0.7196 (m-80) REVERT: A 329 MET cc_start: 0.8641 (tpp) cc_final: 0.8050 (tpp) REVERT: A 623 GLU cc_start: 0.8770 (tt0) cc_final: 0.8453 (tt0) REVERT: A 627 ASN cc_start: 0.9096 (m-40) cc_final: 0.8843 (m110) REVERT: A 669 GLU cc_start: 0.8443 (tp30) cc_final: 0.7946 (tm-30) REVERT: A 686 LYS cc_start: 0.8975 (tptp) cc_final: 0.8406 (tptp) REVERT: B 725 ARG cc_start: 0.8572 (mmp-170) cc_final: 0.8285 (mmp-170) REVERT: C 683 LEU cc_start: 0.8748 (mp) cc_final: 0.8265 (tp) REVERT: C 811 ARG cc_start: 0.8739 (mtm180) cc_final: 0.8461 (ttp-110) outliers start: 12 outliers final: 7 residues processed: 140 average time/residue: 0.3184 time to fit residues: 65.7096 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 : 1.687 ------------------------------------------------------------------------------- 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: 7.9990 chunk 168 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 32 optimal weight: 0.0040 chunk 99 optimal weight: 0.6980 chunk 53 optimal weight: 8.9990 chunk 117 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.132483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.093208 restraints weight = 24640.236| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.06 r_work: 0.2932 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16475 Z= 0.175 Angle : 0.600 7.981 22609 Z= 0.322 Chirality : 0.044 0.158 2508 Planarity : 0.004 0.039 2640 Dihedral : 18.418 155.768 2733 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.19 % Allowed : 4.57 % Favored : 94.25 % 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: 0.70 (0.20), residues: 1790 helix: 1.25 (0.23), residues: 536 sheet: 0.18 (0.24), residues: 428 loop : 0.24 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 805 HIS 0.010 0.001 HIS B 733 PHE 0.040 0.002 PHE A 290 TYR 0.028 0.002 TYR A 296 ARG 0.006 0.000 ARG B 759 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 687) hydrogen bonds : angle 4.64442 ( 1889) metal coordination : bond 0.00726 ( 7) metal coordination : angle 2.34274 ( 3) covalent geometry : bond 0.00413 (16468) covalent geometry : angle 0.59986 (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 144 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ARG cc_start: 0.6493 (ttp80) cc_final: 0.6216 (mmm160) REVERT: A 238 HIS cc_start: 0.8582 (OUTLIER) cc_final: 0.8171 (t-90) REVERT: A 255 TYR cc_start: 0.8364 (m-10) cc_final: 0.8050 (m-10) REVERT: A 296 TYR cc_start: 0.7665 (m-80) cc_final: 0.7232 (m-80) REVERT: A 329 MET cc_start: 0.8734 (tpp) cc_final: 0.8268 (tpp) REVERT: A 417 MET cc_start: 0.8309 (mmm) cc_final: 0.8068 (mmm) REVERT: A 623 GLU cc_start: 0.8745 (tt0) cc_final: 0.8446 (tt0) REVERT: A 627 ASN cc_start: 0.9072 (m-40) cc_final: 0.8852 (m110) REVERT: A 686 LYS cc_start: 0.8978 (tptp) cc_final: 0.8512 (tptp) REVERT: B 328 MET cc_start: 0.7033 (mmt) cc_final: 0.6786 (mmp) REVERT: B 724 ASP cc_start: 0.8186 (t0) cc_final: 0.7980 (t0) REVERT: C 683 LEU cc_start: 0.8727 (mp) cc_final: 0.8212 (tp) outliers start: 19 outliers final: 11 residues processed: 138 average time/residue: 0.3267 time to fit residues: 66.0611 Evaluate side-chains 124 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 1.820 ------------------------------------------------------------------------------- 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 B residue 695 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 6 optimal weight: 0.0870 chunk 148 optimal weight: 0.0870 chunk 131 optimal weight: 0.9980 chunk 173 optimal weight: 0.9980 chunk 178 optimal weight: 0.9980 overall best weight: 0.5536 ------------------------------------------------------------------------------- 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 = 0.133540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.093781 restraints weight = 24734.118| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.09 r_work: 0.2942 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2271 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= 0.135 Angle : 0.565 9.428 22609 Z= 0.303 Chirality : 0.042 0.151 2508 Planarity : 0.004 0.042 2640 Dihedral : 18.329 154.835 2733 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.06 % Allowed : 6.44 % Favored : 92.50 % 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 (0.20), residues: 1790 helix: 1.45 (0.23), residues: 534 sheet: 0.11 (0.24), residues: 436 loop : 0.19 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 805 HIS 0.017 0.001 HIS B 733 PHE 0.032 0.002 PHE A 290 TYR 0.020 0.001 TYR A 296 ARG 0.011 0.000 ARG B 728 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 687) hydrogen bonds : angle 4.44184 ( 1889) metal coordination : bond 0.00471 ( 7) metal coordination : angle 2.21142 ( 3) covalent geometry : bond 0.00307 (16468) covalent geometry : angle 0.56411 (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 143 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7843 (pt) REVERT: A 238 HIS cc_start: 0.8591 (OUTLIER) cc_final: 0.8163 (t-90) REVERT: A 255 TYR cc_start: 0.8305 (m-10) cc_final: 0.7962 (m-10) REVERT: A 262 LEU cc_start: 0.8489 (mt) cc_final: 0.8220 (pp) REVERT: A 292 ARG cc_start: 0.8250 (mmm160) cc_final: 0.7796 (mmm160) REVERT: A 296 TYR cc_start: 0.7575 (m-80) cc_final: 0.7007 (m-80) REVERT: A 623 GLU cc_start: 0.8729 (tt0) cc_final: 0.8446 (tt0) REVERT: A 627 ASN cc_start: 0.9056 (m-40) cc_final: 0.8828 (m110) REVERT: A 635 PHE cc_start: 0.7603 (t80) cc_final: 0.7398 (t80) REVERT: A 669 GLU cc_start: 0.8288 (tp30) cc_final: 0.7905 (tm-30) REVERT: A 686 LYS cc_start: 0.9030 (tptp) cc_final: 0.8595 (tptp) REVERT: C 683 LEU cc_start: 0.8709 (mp) cc_final: 0.8216 (tp) REVERT: C 866 VAL cc_start: 0.8426 (OUTLIER) cc_final: 0.8125 (t) outliers start: 17 outliers final: 7 residues processed: 136 average time/residue: 0.3097 time to fit residues: 61.3267 Evaluate side-chains 124 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 1.585 ------------------------------------------------------------------------------- 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 366 MET Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain C residue 610 LEU 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: 1.9990 chunk 0 optimal weight: 3.9990 chunk 138 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 153 optimal weight: 6.9990 chunk 128 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN B 368 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 = 0.3762 r_free = 0.3762 target = 0.132655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.093419 restraints weight = 25165.446| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.07 r_work: 0.2934 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16475 Z= 0.150 Angle : 0.566 7.650 22609 Z= 0.302 Chirality : 0.042 0.152 2508 Planarity : 0.004 0.049 2640 Dihedral : 18.317 153.888 2733 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.31 % Allowed : 7.38 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.61 (0.23), residues: 537 sheet: 0.06 (0.23), residues: 442 loop : 0.15 (0.22), residues: 811 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 0.029 0.002 PHE A 290 TYR 0.016 0.001 TYR A 296 ARG 0.003 0.000 ARG B 759 Details of bonding type rmsd hydrogen bonds : bond 0.03765 ( 687) hydrogen bonds : angle 4.32505 ( 1889) metal coordination : bond 0.00628 ( 7) metal coordination : angle 2.28597 ( 3) covalent geometry : bond 0.00352 (16468) covalent geometry : angle 0.56501 (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 147 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 HIS cc_start: 0.8545 (OUTLIER) cc_final: 0.8195 (t-90) REVERT: A 239 SER cc_start: 0.7812 (m) cc_final: 0.7370 (p) REVERT: A 255 TYR cc_start: 0.8336 (m-10) cc_final: 0.8095 (m-10) REVERT: A 262 LEU cc_start: 0.8526 (mt) cc_final: 0.8224 (pp) REVERT: A 296 TYR cc_start: 0.7538 (m-80) cc_final: 0.7335 (m-80) REVERT: A 329 MET cc_start: 0.8385 (tpp) cc_final: 0.7991 (tpp) REVERT: A 623 GLU cc_start: 0.8753 (tt0) cc_final: 0.8462 (tt0) REVERT: A 627 ASN cc_start: 0.9073 (m-40) cc_final: 0.8808 (m110) REVERT: A 631 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8464 (tt) REVERT: A 635 PHE cc_start: 0.7642 (t80) cc_final: 0.7424 (t80) REVERT: A 669 GLU cc_start: 0.8325 (tp30) cc_final: 0.7939 (tm-30) REVERT: B 75 ASP cc_start: 0.8316 (t70) cc_final: 0.8104 (t0) REVERT: C 683 LEU cc_start: 0.8712 (mp) cc_final: 0.8181 (tp) outliers start: 21 outliers final: 14 residues processed: 141 average time/residue: 0.3100 time to fit residues: 64.5461 Evaluate side-chains 132 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 1.662 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 84 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 68 optimal weight: 0.5980 chunk 164 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.137552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.094994 restraints weight = 25152.922| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.28 r_work: 0.3008 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2606 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= 0.164 Angle : 0.580 10.480 22609 Z= 0.305 Chirality : 0.042 0.162 2508 Planarity : 0.004 0.053 2640 Dihedral : 18.321 153.258 2733 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.44 % Allowed : 8.01 % Favored : 90.56 % 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: 0.71 (0.20), residues: 1790 helix: 1.58 (0.23), residues: 537 sheet: 0.03 (0.23), residues: 440 loop : 0.10 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 805 HIS 0.013 0.001 HIS B 733 PHE 0.029 0.002 PHE A 290 TYR 0.015 0.001 TYR A 294 ARG 0.008 0.000 ARG B 728 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 687) hydrogen bonds : angle 4.32160 ( 1889) metal coordination : bond 0.00706 ( 7) metal coordination : angle 2.25749 ( 3) covalent geometry : bond 0.00391 (16468) covalent geometry : angle 0.57913 (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 : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 HIS cc_start: 0.8606 (OUTLIER) cc_final: 0.8330 (t-90) REVERT: A 239 SER cc_start: 0.7861 (m) cc_final: 0.7404 (p) REVERT: A 623 GLU cc_start: 0.8837 (tt0) cc_final: 0.8541 (tt0) REVERT: A 627 ASN cc_start: 0.9119 (m-40) cc_final: 0.8899 (m110) REVERT: A 631 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8459 (tt) REVERT: A 635 PHE cc_start: 0.7621 (t80) cc_final: 0.7361 (t80) REVERT: A 669 GLU cc_start: 0.8439 (tp30) cc_final: 0.8085 (tm-30) REVERT: A 686 LYS cc_start: 0.9139 (tppt) cc_final: 0.8767 (mptt) REVERT: B 441 CYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8375 (t) REVERT: C 683 LEU cc_start: 0.8774 (mp) cc_final: 0.8159 (tp) outliers start: 23 outliers final: 17 residues processed: 137 average time/residue: 0.2759 time to fit residues: 56.8972 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 : 1.602 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 105 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 81 optimal weight: 0.6980 chunk 179 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 807 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.136861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.094278 restraints weight = 25107.293| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.27 r_work: 0.3003 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16475 Z= 0.178 Angle : 0.592 8.221 22609 Z= 0.311 Chirality : 0.043 0.161 2508 Planarity : 0.004 0.053 2640 Dihedral : 18.347 152.816 2733 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.56 % Allowed : 8.51 % Favored : 89.93 % 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: 0.64 (0.20), residues: 1790 helix: 1.54 (0.22), residues: 537 sheet: -0.01 (0.23), residues: 435 loop : 0.05 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 805 HIS 0.012 0.001 HIS B 733 PHE 0.037 0.002 PHE A 290 TYR 0.039 0.002 TYR A 296 ARG 0.004 0.000 ARG A 629 Details of bonding type rmsd hydrogen bonds : bond 0.03792 ( 687) hydrogen bonds : angle 4.36539 ( 1889) metal coordination : bond 0.00762 ( 7) metal coordination : angle 2.26711 ( 3) covalent geometry : bond 0.00426 (16468) covalent geometry : angle 0.59098 (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 151 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 HIS cc_start: 0.8616 (OUTLIER) cc_final: 0.8277 (t-90) REVERT: A 329 MET cc_start: 0.8336 (tpp) cc_final: 0.7891 (tpp) REVERT: A 623 GLU cc_start: 0.8827 (tt0) cc_final: 0.8548 (tt0) REVERT: A 627 ASN cc_start: 0.9121 (m-40) cc_final: 0.8889 (m110) REVERT: A 631 ILE cc_start: 0.8642 (tt) cc_final: 0.8394 (tt) REVERT: A 635 PHE cc_start: 0.7621 (t80) cc_final: 0.7368 (t80) REVERT: A 669 GLU cc_start: 0.8458 (tp30) cc_final: 0.8107 (tm-30) REVERT: B 441 CYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8375 (t) REVERT: C 683 LEU cc_start: 0.8768 (mp) cc_final: 0.8176 (tp) outliers start: 25 outliers final: 17 residues processed: 140 average time/residue: 0.2855 time to fit residues: 60.7223 Evaluate side-chains 134 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 1.696 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 10 optimal weight: 1.9990 chunk 92 optimal weight: 0.0770 chunk 30 optimal weight: 8.9990 chunk 174 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 68 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 153 optimal weight: 0.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 807 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.137554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.095098 restraints weight = 24939.509| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.27 r_work: 0.3019 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2824 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= 0.148 Angle : 0.567 10.092 22609 Z= 0.300 Chirality : 0.042 0.162 2508 Planarity : 0.004 0.052 2640 Dihedral : 18.325 152.509 2733 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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 (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: 1.61 (0.23), residues: 539 sheet: -0.03 (0.23), residues: 440 loop : 0.06 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 805 HIS 0.015 0.001 HIS B 733 PHE 0.033 0.002 PHE B 715 TYR 0.031 0.001 TYR A 296 ARG 0.005 0.000 ARG A 629 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 687) hydrogen bonds : angle 4.29661 ( 1889) metal coordination : bond 0.00565 ( 7) metal coordination : angle 2.12371 ( 3) covalent geometry : bond 0.00348 (16468) covalent geometry : angle 0.56650 (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 142 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 1.827 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: 0.8317 (t-90) REVERT: A 329 MET cc_start: 0.8386 (tpp) cc_final: 0.7957 (tpp) REVERT: A 623 GLU cc_start: 0.8812 (tt0) cc_final: 0.8591 (tt0) REVERT: A 627 ASN cc_start: 0.9086 (m-40) cc_final: 0.8829 (m110) REVERT: A 631 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8369 (tt) REVERT: A 669 GLU cc_start: 0.8472 (tp30) cc_final: 0.8101 (tm-30) REVERT: A 673 ARG cc_start: 0.7860 (mmt90) cc_final: 0.7632 (mmt90) REVERT: A 686 LYS cc_start: 0.8979 (tppt) cc_final: 0.8531 (tptp) REVERT: B 441 CYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8388 (t) outliers start: 21 outliers final: 17 residues processed: 133 average time/residue: 0.2944 time to fit residues: 59.0191 Evaluate side-chains 135 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 1.723 ------------------------------------------------------------------------------- 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 712 LEU 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 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: 0.7980 chunk 73 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 118 optimal weight: 0.1980 chunk 110 optimal weight: 3.9990 chunk 184 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 120 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.137499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.095079 restraints weight = 25026.805| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.28 r_work: 0.3017 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16475 Z= 0.153 Angle : 0.574 7.694 22609 Z= 0.305 Chirality : 0.042 0.194 2508 Planarity : 0.004 0.053 2640 Dihedral : 18.329 152.071 2733 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.50 % Allowed : 8.94 % 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: 0.71 (0.20), residues: 1790 helix: 1.69 (0.22), residues: 539 sheet: -0.05 (0.24), residues: 440 loop : 0.05 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 805 HIS 0.017 0.001 HIS B 733 PHE 0.038 0.002 PHE A 635 TYR 0.047 0.001 TYR A 296 ARG 0.004 0.000 ARG A 629 Details of bonding type rmsd hydrogen bonds : bond 0.03640 ( 687) hydrogen bonds : angle 4.28382 ( 1889) metal coordination : bond 0.00520 ( 7) metal coordination : angle 2.03291 ( 3) covalent geometry : bond 0.00360 (16468) covalent geometry : angle 0.57392 (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 147 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 HIS cc_start: 0.8615 (OUTLIER) cc_final: 0.8350 (t-90) REVERT: A 329 MET cc_start: 0.8470 (tpp) cc_final: 0.8068 (tpp) REVERT: A 627 ASN cc_start: 0.9080 (m-40) cc_final: 0.8840 (m110) REVERT: A 631 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8365 (tt) REVERT: A 669 GLU cc_start: 0.8476 (tp30) cc_final: 0.8113 (tm-30) REVERT: A 673 ARG cc_start: 0.7927 (mmt90) cc_final: 0.7717 (mmt90) REVERT: A 686 LYS cc_start: 0.8954 (tppt) cc_final: 0.8525 (tptp) REVERT: B 441 CYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8402 (t) REVERT: C 469 CYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8205 (m) outliers start: 24 outliers final: 18 residues processed: 137 average time/residue: 0.2742 time to fit residues: 56.3791 Evaluate side-chains 139 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 1.619 ------------------------------------------------------------------------------- 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 B residue 712 LEU Chi-restraints excluded: chain B residue 733 HIS Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 469 CYS 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 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: 0.9980 chunk 183 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 174 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 124 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 100 optimal weight: 0.0010 chunk 109 optimal weight: 1.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.137955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.095508 restraints weight = 25042.584| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.29 r_work: 0.3023 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2958 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= 0.137 Angle : 0.568 8.029 22609 Z= 0.300 Chirality : 0.041 0.162 2508 Planarity : 0.004 0.053 2640 Dihedral : 18.303 151.842 2733 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.38 % Allowed : 8.94 % 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 (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 (0.20), residues: 1790 helix: 1.76 (0.23), residues: 539 sheet: -0.07 (0.24), residues: 440 loop : 0.06 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 805 HIS 0.021 0.001 HIS B 733 PHE 0.041 0.002 PHE A 635 TYR 0.044 0.001 TYR A 296 ARG 0.004 0.000 ARG A 629 Details of bonding type rmsd hydrogen bonds : bond 0.03590 ( 687) hydrogen bonds : angle 4.24192 ( 1889) metal coordination : bond 0.00407 ( 7) metal coordination : angle 1.96408 ( 3) covalent geometry : bond 0.00318 (16468) covalent geometry : angle 0.56768 (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: 22 poor density : 120 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 MET cc_start: 0.8381 (tpp) cc_final: 0.7979 (tpp) REVERT: A 631 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8357 (tt) REVERT: A 669 GLU cc_start: 0.8477 (tp30) cc_final: 0.8084 (tm-30) REVERT: A 673 ARG cc_start: 0.7913 (mmt90) cc_final: 0.7706 (mmt90) REVERT: A 686 LYS cc_start: 0.8958 (tppt) cc_final: 0.8530 (tptp) REVERT: C 469 CYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8198 (m) outliers start: 22 outliers final: 18 residues processed: 132 average time/residue: 0.2854 time to fit residues: 56.9960 Evaluate side-chains 138 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 1.804 ------------------------------------------------------------------------------- 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 B residue 712 LEU Chi-restraints excluded: chain B residue 733 HIS Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 469 CYS 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 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: 1.9990 chunk 120 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 101 optimal weight: 0.4980 chunk 145 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.137770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.095310 restraints weight = 25029.411| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.29 r_work: 0.3019 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2991 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= 0.143 Angle : 0.568 8.117 22609 Z= 0.300 Chirality : 0.042 0.163 2508 Planarity : 0.004 0.053 2640 Dihedral : 18.295 151.606 2733 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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 (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: 0.69 (0.20), residues: 1790 helix: 1.77 (0.23), residues: 539 sheet: -0.13 (0.23), residues: 447 loop : 0.03 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 805 HIS 0.017 0.001 HIS B 733 PHE 0.040 0.002 PHE A 635 TYR 0.045 0.001 TYR A 296 ARG 0.004 0.000 ARG A 629 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 687) hydrogen bonds : angle 4.23811 ( 1889) metal coordination : bond 0.00440 ( 7) metal coordination : angle 1.94349 ( 3) covalent geometry : bond 0.00335 (16468) covalent geometry : angle 0.56763 (22606) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8950.54 seconds wall clock time: 156 minutes 53.12 seconds (9413.12 seconds total)