Starting phenix.real_space_refine on Sat Jan 20 17:57:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cli_16713/01_2024/8cli_16713.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cli_16713/01_2024/8cli_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cli_16713/01_2024/8cli_16713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cli_16713/01_2024/8cli_16713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cli_16713/01_2024/8cli_16713.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cli_16713/01_2024/8cli_16713.pdb" } 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 Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 9.02, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 7.20 Conformation dependent library (CDL) restraints added in 2.7 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: 5.84 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: 6.90 Time building geometry restraints manager: 7.77 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: 98.31 - 105.47: 688 105.47 - 112.64: 8580 112.64 - 119.80: 5673 119.80 - 126.96: 7259 126.96 - 134.13: 406 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 2.440 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 ========== 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: 5.250 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: 0.010 Extract box with map and model: 22.270 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 53.750 Find NCS groups from input model: 0.430 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: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.850 ------------------------------------------------------------------------------- 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 16468 Z= 0.230 Angle : 0.717 7.058 22606 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 193 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 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: 0.3533 time to fit residues: 94.7747 Evaluate side-chains 120 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.630 ------------------------------------------------------------------------------- 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: 0.9980 chunk 47 optimal weight: 6.9990 chunk 94 optimal weight: 0.0980 chunk 74 optimal weight: 1.9990 chunk 145 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 88 optimal weight: 0.0670 chunk 107 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16468 Z= 0.212 Angle : 0.618 8.546 22606 Z= 0.334 Chirality : 0.043 0.148 2508 Planarity : 0.004 0.037 2640 Dihedral : 18.474 157.470 2733 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.94 % Allowed : 3.31 % Favored : 95.75 % 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: 0.56 (0.20), residues: 1790 helix: 0.90 (0.22), residues: 532 sheet: 0.37 (0.24), residues: 434 loop : 0.18 (0.22), residues: 824 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 0.015 0.002 PHE C 391 TYR 0.049 0.002 TYR A 296 ARG 0.004 0.000 ARG A 309 *********************** 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 145 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ARG cc_start: 0.6322 (ttp80) cc_final: 0.5927 (mmm160) REVERT: A 296 TYR cc_start: 0.7770 (m-80) cc_final: 0.7289 (m-80) REVERT: A 329 MET cc_start: 0.9220 (tpp) cc_final: 0.9004 (tpp) REVERT: A 444 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8301 (mt0) REVERT: A 623 GLU cc_start: 0.8838 (tt0) cc_final: 0.8490 (tt0) REVERT: A 627 ASN cc_start: 0.9192 (m-40) cc_final: 0.8923 (m110) REVERT: A 669 GLU cc_start: 0.8499 (tp30) cc_final: 0.7923 (tm-30) REVERT: B 75 ASP cc_start: 0.7677 (t0) cc_final: 0.7466 (t0) REVERT: B 681 MET cc_start: 0.8747 (tpt) cc_final: 0.8509 (tpt) REVERT: B 725 ARG cc_start: 0.8379 (mmp-170) cc_final: 0.8114 (mmp-170) REVERT: B 794 ILE cc_start: 0.8718 (mm) cc_final: 0.8384 (tp) REVERT: C 683 LEU cc_start: 0.8655 (mp) cc_final: 0.8022 (tp) outliers start: 15 outliers final: 8 residues processed: 138 average time/residue: 0.3148 time to fit residues: 64.5521 Evaluate side-chains 121 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 1.821 ------------------------------------------------------------------------------- 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 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 93 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 114 optimal weight: 0.0070 chunk 46 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 149 optimal weight: 0.1980 chunk 166 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 807 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16468 Z= 0.231 Angle : 0.578 8.604 22606 Z= 0.310 Chirality : 0.043 0.155 2508 Planarity : 0.004 0.038 2640 Dihedral : 18.389 156.156 2733 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.13 % Allowed : 4.82 % Favored : 94.06 % 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: 0.72 (0.20), residues: 1790 helix: 1.33 (0.23), residues: 534 sheet: 0.25 (0.24), residues: 425 loop : 0.18 (0.22), residues: 831 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 0.049 0.002 PHE A 290 TYR 0.029 0.001 TYR A 296 ARG 0.006 0.000 ARG B 728 *********************** 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 140 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7765 (pt) REVERT: A 255 TYR cc_start: 0.8309 (m-10) cc_final: 0.7975 (m-10) REVERT: A 296 TYR cc_start: 0.7700 (m-80) cc_final: 0.7257 (m-80) REVERT: A 297 MET cc_start: 0.8644 (tpp) cc_final: 0.8424 (tpp) REVERT: A 444 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8295 (mt0) REVERT: A 623 GLU cc_start: 0.8854 (tt0) cc_final: 0.8537 (tt0) REVERT: A 627 ASN cc_start: 0.9189 (m-40) cc_final: 0.8953 (m110) REVERT: B 328 MET cc_start: 0.6853 (mmt) cc_final: 0.6577 (mmp) REVERT: C 683 LEU cc_start: 0.8602 (mp) cc_final: 0.7991 (tp) outliers start: 18 outliers final: 9 residues processed: 135 average time/residue: 0.3309 time to fit residues: 65.8068 Evaluate side-chains 121 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 1.771 ------------------------------------------------------------------------------- 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 691 VAL Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 707 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 0.0040 chunk 126 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 178 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16468 Z= 0.204 Angle : 0.558 10.007 22606 Z= 0.296 Chirality : 0.042 0.148 2508 Planarity : 0.004 0.039 2640 Dihedral : 18.318 155.038 2733 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.88 % Allowed : 6.75 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.20), residues: 1790 helix: 1.55 (0.23), residues: 535 sheet: 0.23 (0.24), residues: 426 loop : 0.13 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 805 HIS 0.011 0.001 HIS B 733 PHE 0.034 0.002 PHE A 290 TYR 0.021 0.001 TYR A 296 ARG 0.009 0.000 ARG B 725 *********************** 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 137 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 TYR cc_start: 0.8287 (m-10) cc_final: 0.7968 (m-10) REVERT: A 296 TYR cc_start: 0.7727 (m-80) cc_final: 0.7306 (m-80) REVERT: A 329 MET cc_start: 0.9065 (tpp) cc_final: 0.8739 (tpp) REVERT: A 444 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8282 (mt0) REVERT: A 623 GLU cc_start: 0.8851 (tt0) cc_final: 0.8535 (tt0) REVERT: A 627 ASN cc_start: 0.9160 (m-40) cc_final: 0.8924 (m110) REVERT: A 669 GLU cc_start: 0.8328 (tp30) cc_final: 0.7851 (tm-30) REVERT: B 759 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7580 (ptt180) REVERT: C 683 LEU cc_start: 0.8621 (mp) cc_final: 0.7996 (tp) REVERT: C 811 ARG cc_start: 0.8388 (mtm180) cc_final: 0.8013 (ttp-110) REVERT: C 866 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8337 (t) outliers start: 14 outliers final: 11 residues processed: 132 average time/residue: 0.2998 time to fit residues: 59.2017 Evaluate side-chains 127 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 759 ARG 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 866 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN C 584 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16468 Z= 0.277 Angle : 0.577 7.174 22606 Z= 0.307 Chirality : 0.043 0.162 2508 Planarity : 0.004 0.044 2640 Dihedral : 18.347 153.807 2733 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.44 % Allowed : 7.25 % 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: 0.75 (0.20), residues: 1790 helix: 1.64 (0.23), residues: 533 sheet: 0.08 (0.23), residues: 437 loop : 0.09 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 402 HIS 0.010 0.001 HIS B 733 PHE 0.038 0.002 PHE A 290 TYR 0.018 0.001 TYR A 296 ARG 0.003 0.000 ARG A 213 *********************** 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 146 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 SER cc_start: 0.7737 (m) cc_final: 0.7309 (p) REVERT: A 255 TYR cc_start: 0.8289 (m-10) cc_final: 0.7911 (m-10) REVERT: A 262 LEU cc_start: 0.8449 (mt) cc_final: 0.8139 (pp) REVERT: A 292 ARG cc_start: 0.8534 (mmm160) cc_final: 0.8221 (mmm160) REVERT: A 296 TYR cc_start: 0.7628 (m-80) cc_final: 0.7129 (m-80) REVERT: A 444 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8306 (mt0) REVERT: A 623 GLU cc_start: 0.8831 (tt0) cc_final: 0.8542 (tt0) REVERT: A 627 ASN cc_start: 0.9135 (m-40) cc_final: 0.8884 (m110) REVERT: A 669 GLU cc_start: 0.8380 (tp30) cc_final: 0.7918 (tm-30) REVERT: A 686 LYS cc_start: 0.8936 (tppt) cc_final: 0.8530 (tptp) REVERT: B 759 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7610 (ptt180) REVERT: C 683 LEU cc_start: 0.8593 (mp) cc_final: 0.7952 (tp) REVERT: C 811 ARG cc_start: 0.8454 (mtm180) cc_final: 0.8069 (ttp-110) outliers start: 23 outliers final: 17 residues processed: 140 average time/residue: 0.3195 time to fit residues: 65.6174 Evaluate side-chains 131 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 1.889 ------------------------------------------------------------------------------- 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 B residue 50 MET Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 759 ARG 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 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 60 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 178 optimal weight: 0.8980 chunk 148 optimal weight: 0.0870 chunk 82 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 93 optimal weight: 0.2980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16468 Z= 0.193 Angle : 0.545 7.255 22606 Z= 0.289 Chirality : 0.041 0.166 2508 Planarity : 0.004 0.044 2640 Dihedral : 18.283 153.504 2733 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.44 % Allowed : 8.07 % Favored : 90.49 % 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: 0.80 (0.20), residues: 1790 helix: 1.68 (0.23), residues: 535 sheet: 0.17 (0.23), residues: 430 loop : 0.08 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 402 HIS 0.013 0.001 HIS B 733 PHE 0.031 0.001 PHE A 290 TYR 0.014 0.001 TYR A 296 ARG 0.007 0.000 ARG A 629 *********************** 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 fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 TYR cc_start: 0.7666 (m-80) cc_final: 0.7418 (m-80) REVERT: A 329 MET cc_start: 0.8926 (tpp) cc_final: 0.8547 (tpp) REVERT: A 444 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8290 (mt0) REVERT: A 623 GLU cc_start: 0.8853 (tt0) cc_final: 0.8559 (tt0) REVERT: A 627 ASN cc_start: 0.9104 (m-40) cc_final: 0.8847 (m110) REVERT: A 669 GLU cc_start: 0.8365 (tp30) cc_final: 0.7934 (tm-30) REVERT: A 686 LYS cc_start: 0.8808 (tppt) cc_final: 0.8404 (tptp) REVERT: B 441 CYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8183 (t) REVERT: B 759 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7686 (ptt180) REVERT: C 683 LEU cc_start: 0.8585 (mp) cc_final: 0.7972 (tp) REVERT: C 811 ARG cc_start: 0.8454 (mtm180) cc_final: 0.8082 (ttp-110) outliers start: 23 outliers final: 15 residues processed: 137 average time/residue: 0.2773 time to fit residues: 57.9395 Evaluate side-chains 131 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 1.808 ------------------------------------------------------------------------------- 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 628 LEU 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 B residue 759 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 0.0870 chunk 20 optimal weight: 0.0170 chunk 101 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 178 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16468 Z= 0.228 Angle : 0.555 9.567 22606 Z= 0.293 Chirality : 0.042 0.161 2508 Planarity : 0.004 0.048 2640 Dihedral : 18.293 152.687 2733 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.56 % Allowed : 8.57 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.20), residues: 1790 helix: 1.75 (0.23), residues: 533 sheet: 0.15 (0.24), residues: 430 loop : 0.04 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 402 HIS 0.013 0.001 HIS B 733 PHE 0.025 0.002 PHE A 635 TYR 0.011 0.001 TYR A 294 ARG 0.006 0.000 ARG B 215 *********************** 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 fitting. rotamer outliers: 25 poor density : 126 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8295 (mt0) REVERT: A 623 GLU cc_start: 0.8829 (tt0) cc_final: 0.8545 (tt0) REVERT: A 627 ASN cc_start: 0.9095 (m-40) cc_final: 0.8840 (m110) REVERT: A 631 ILE cc_start: 0.8341 (tt) cc_final: 0.8101 (tt) REVERT: A 669 GLU cc_start: 0.8400 (tp30) cc_final: 0.7987 (tm-30) REVERT: A 673 ARG cc_start: 0.7817 (mmt90) cc_final: 0.7572 (mmt90) REVERT: B 441 CYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8253 (t) REVERT: B 733 HIS cc_start: 0.8838 (m170) cc_final: 0.8543 (m90) REVERT: B 759 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7676 (ptt180) REVERT: C 469 CYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7672 (m) REVERT: C 683 LEU cc_start: 0.8571 (mp) cc_final: 0.7953 (tp) REVERT: C 811 ARG cc_start: 0.8434 (mtm180) cc_final: 0.8058 (ttp-110) outliers start: 25 outliers final: 19 residues processed: 142 average time/residue: 0.2951 time to fit residues: 62.4859 Evaluate side-chains 139 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 1.735 ------------------------------------------------------------------------------- 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 B residue 80 VAL Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 759 ARG 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 0.0670 chunk 106 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16468 Z= 0.222 Angle : 0.558 8.169 22606 Z= 0.294 Chirality : 0.041 0.174 2508 Planarity : 0.004 0.046 2640 Dihedral : 18.279 152.440 2733 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.44 % Allowed : 8.88 % 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: 0.81 (0.20), residues: 1790 helix: 1.77 (0.23), residues: 535 sheet: 0.10 (0.23), residues: 438 loop : 0.07 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 805 HIS 0.010 0.001 HIS B 733 PHE 0.025 0.001 PHE A 635 TYR 0.028 0.001 TYR A 296 ARG 0.003 0.000 ARG A 629 *********************** 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 143 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 MET cc_start: 0.8836 (tpp) cc_final: 0.8459 (tpp) REVERT: A 623 GLU cc_start: 0.8840 (tt0) cc_final: 0.8570 (tt0) REVERT: A 627 ASN cc_start: 0.9115 (m-40) cc_final: 0.8855 (m110) REVERT: A 631 ILE cc_start: 0.8303 (tt) cc_final: 0.8060 (tt) REVERT: A 669 GLU cc_start: 0.8391 (tp30) cc_final: 0.7993 (tm-30) REVERT: A 673 ARG cc_start: 0.7862 (mmt90) cc_final: 0.7632 (mmt90) REVERT: B 441 CYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8225 (t) REVERT: B 759 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7677 (ptt180) REVERT: B 794 ILE cc_start: 0.8610 (mm) cc_final: 0.8268 (tp) REVERT: C 469 CYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7658 (m) REVERT: C 683 LEU cc_start: 0.8553 (mp) cc_final: 0.7933 (tp) REVERT: C 811 ARG cc_start: 0.8424 (mtm180) cc_final: 0.7968 (ttp-110) outliers start: 23 outliers final: 19 residues processed: 135 average time/residue: 0.3044 time to fit residues: 62.4935 Evaluate side-chains 139 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 1.633 ------------------------------------------------------------------------------- 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 690 LEU Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 759 ARG 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 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 170 optimal weight: 0.5980 chunk 155 optimal weight: 0.7980 chunk 166 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 150 optimal weight: 1.9990 chunk 157 optimal weight: 0.6980 chunk 165 optimal weight: 0.4980 chunk 109 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16468 Z= 0.203 Angle : 0.547 7.506 22606 Z= 0.289 Chirality : 0.041 0.163 2508 Planarity : 0.004 0.047 2640 Dihedral : 18.252 152.062 2733 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.44 % Allowed : 9.19 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.20), residues: 1790 helix: 1.87 (0.23), residues: 535 sheet: 0.12 (0.24), residues: 435 loop : 0.06 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 805 HIS 0.014 0.001 HIS B 733 PHE 0.028 0.001 PHE A 635 TYR 0.043 0.001 TYR A 296 ARG 0.005 0.000 ARG A 292 *********************** 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 145 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 MET cc_start: 0.8841 (tpp) cc_final: 0.8463 (tpp) REVERT: A 623 GLU cc_start: 0.8836 (tt0) cc_final: 0.8609 (tt0) REVERT: A 627 ASN cc_start: 0.9119 (m-40) cc_final: 0.8848 (m110) REVERT: A 631 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.8037 (tt) REVERT: A 669 GLU cc_start: 0.8408 (tp30) cc_final: 0.7973 (tm-30) REVERT: A 673 ARG cc_start: 0.7896 (mmt90) cc_final: 0.7687 (mmt90) REVERT: B 441 CYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8225 (t) REVERT: B 725 ARG cc_start: 0.8628 (mmp-170) cc_final: 0.8334 (mmp-170) REVERT: B 733 HIS cc_start: 0.8845 (m170) cc_final: 0.8633 (m90) REVERT: B 759 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7788 (ptt180) REVERT: C 469 CYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7709 (m) REVERT: C 683 LEU cc_start: 0.8573 (mp) cc_final: 0.8054 (tt) REVERT: C 811 ARG cc_start: 0.8430 (mtm180) cc_final: 0.7986 (ttp-110) outliers start: 23 outliers final: 17 residues processed: 135 average time/residue: 0.2985 time to fit residues: 60.7139 Evaluate side-chains 140 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 1.813 ------------------------------------------------------------------------------- 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 690 LEU 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 738 MET Chi-restraints excluded: chain B residue 759 ARG Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 469 CYS 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 175 optimal weight: 0.9980 chunk 107 optimal weight: 0.2980 chunk 83 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 184 optimal weight: 4.9990 chunk 169 optimal weight: 0.7980 chunk 146 optimal weight: 0.3980 chunk 15 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 HIS C 807 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16468 Z= 0.205 Angle : 0.555 7.986 22606 Z= 0.291 Chirality : 0.041 0.163 2508 Planarity : 0.004 0.047 2640 Dihedral : 18.235 151.710 2733 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.63 % Allowed : 9.32 % Favored : 89.06 % 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: 0.87 (0.20), residues: 1790 helix: 1.89 (0.23), residues: 535 sheet: 0.09 (0.24), residues: 435 loop : 0.07 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 805 HIS 0.014 0.001 HIS B 733 PHE 0.028 0.001 PHE A 635 TYR 0.037 0.001 TYR A 296 ARG 0.003 0.000 ARG A 629 ********************** 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 148 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 122 time to evaluate : 2.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 MET cc_start: 0.8803 (tpp) cc_final: 0.8431 (tpp) REVERT: A 623 GLU cc_start: 0.8818 (tt0) cc_final: 0.8616 (tt0) REVERT: A 627 ASN cc_start: 0.9121 (m-40) cc_final: 0.8863 (m110) REVERT: A 631 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.8043 (tt) REVERT: A 669 GLU cc_start: 0.8416 (tp30) cc_final: 0.7959 (tm-30) REVERT: B 441 CYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8235 (t) REVERT: B 759 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7931 (ttp-170) REVERT: C 469 CYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7702 (m) REVERT: C 683 LEU cc_start: 0.8563 (mp) cc_final: 0.8052 (tt) REVERT: C 811 ARG cc_start: 0.8416 (mtm180) cc_final: 0.8022 (ttp-110) outliers start: 26 outliers final: 20 residues processed: 136 average time/residue: 0.3058 time to fit residues: 62.0315 Evaluate side-chains 144 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 120 time to evaluate : 1.719 ------------------------------------------------------------------------------- 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 262 LEU Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 759 ARG 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 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 156 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 135 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.137321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.095031 restraints weight = 25190.709| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.26 r_work: 0.3003 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16468 Z= 0.269 Angle : 0.586 8.467 22606 Z= 0.305 Chirality : 0.042 0.186 2508 Planarity : 0.004 0.047 2640 Dihedral : 18.263 151.183 2733 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.69 % Allowed : 9.26 % Favored : 89.06 % 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: 0.81 (0.20), residues: 1790 helix: 1.87 (0.23), residues: 537 sheet: 0.04 (0.24), residues: 434 loop : 0.02 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 805 HIS 0.005 0.001 HIS A 198 PHE 0.035 0.002 PHE B 715 TYR 0.039 0.001 TYR A 296 ARG 0.009 0.000 ARG A 713 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3211.41 seconds wall clock time: 60 minutes 21.86 seconds (3621.86 seconds total)