Starting phenix.real_space_refine on Fri Mar 6 14:32:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8clj_16714/03_2026/8clj_16714.cif Found real_map, /net/cci-nas-00/data/ceres_data/8clj_16714/03_2026/8clj_16714.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/8clj_16714/03_2026/8clj_16714.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8clj_16714/03_2026/8clj_16714.map" model { file = "/net/cci-nas-00/data/ceres_data/8clj_16714/03_2026/8clj_16714.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8clj_16714/03_2026/8clj_16714.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.115 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 4 6.06 5 P 140 5.49 5 S 186 5.16 5 C 19906 2.51 5 N 5632 2.21 5 O 6042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31910 Number of models: 1 Model: "" Number of chains: 12 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: "F" 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: "G" 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: "H" 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: "I" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 721 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "J" 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} Chain: "G" 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 9642 SG CYS B 788 93.819 78.621 216.226 1.00 68.29 S ATOM 9853 SG CYS B 814 96.389 77.902 219.327 1.00 84.20 S ATOM 9877 SG CYS B 817 94.711 76.018 216.955 1.00 83.95 S ATOM 9303 SG CYS B 747 88.947 96.857 233.639 1.00126.91 S ATOM 9323 SG CYS B 750 86.904 98.774 236.189 1.00135.84 S ATOM 9437 SG CYS B 764 87.452 94.969 236.718 1.00133.44 S ATOM 25256 SG CYS G 747 56.843 32.837 60.069 1.00127.96 S ATOM 25276 SG CYS G 750 54.710 32.357 57.158 1.00122.81 S ATOM 25390 SG CYS G 764 58.424 31.537 56.896 1.00133.14 S ATOM 25595 SG CYS G 788 75.439 43.289 73.790 1.00 56.86 S ATOM 25806 SG CYS G 814 76.641 40.226 74.422 1.00 88.24 S ATOM 25830 SG CYS G 817 78.819 42.226 73.485 1.00 79.03 S Time building chain proxies: 6.81, per 1000 atoms: 0.21 Number of scatterers: 31910 At special positions: 0 Unit cell: (138.096, 139.74, 253.998, 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 4 29.99 S 186 16.00 P 140 15.00 O 6042 8.00 N 5632 7.00 C 19906 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" SG CYS B 814 " pdb="ZN ZN B 901 " - pdb=" SG CYS B 788 " pdb="ZN ZN B 901 " - pdb=" SG CYS B 817 " pdb=" ZN B 902 " pdb="ZN ZN B 902 " - pdb=" ND1 HIS B 768 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 750 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 747 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 764 " pdb=" ZN G 901 " pdb="ZN ZN G 901 " - pdb=" ND1 HIS G 768 " pdb="ZN ZN G 901 " - pdb=" SG CYS G 750 " pdb="ZN ZN G 901 " - pdb=" SG CYS G 747 " pdb="ZN ZN G 901 " - pdb=" SG CYS G 764 " pdb=" ZN G 902 " pdb="ZN ZN G 902 " - pdb=" SG CYS G 814 " pdb="ZN ZN G 902 " - pdb=" SG CYS G 788 " pdb="ZN ZN G 902 " - pdb=" SG CYS G 817 " Number of angles added : 6 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6824 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 45 sheets defined 31.0% alpha, 23.0% beta 70 base pairs and 125 stacking pairs defined. Time for finding SS restraints: 4.00 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 3.613A 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: 4.470A pdb=" N ILE A 215 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 4.556A 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: 4.095A 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 437 through 456 Processing helix chain 'A' and resid 611 through 628 Processing helix chain 'A' and resid 633 through 649 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: 3.577A 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 218 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: 3.826A 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 533 through 535 No H-bonds generated for 'chain 'B' and resid 533 through 535' Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.659A 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: 3.703A 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 718 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: 3.712A pdb=" N LEU C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N HIS C 312 " --> pdb=" O TRP C 308 " (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: 3.554A pdb=" N LEU C 519 " --> pdb=" O HIS C 515 " (cutoff:3.500A) removed outlier: 3.528A 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: 3.547A 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 helix chain 'F' and resid 2 through 13 removed outlier: 3.634A pdb=" N LEU F 8 " --> pdb=" O LEU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 30 Processing helix chain 'F' and resid 40 through 53 Processing helix chain 'F' and resid 123 through 128 Processing helix chain 'F' and resid 137 through 146 Processing helix chain 'F' and resid 154 through 164 Processing helix chain 'F' and resid 174 through 187 Processing helix chain 'F' and resid 193 through 200 Processing helix chain 'F' and resid 205 through 219 removed outlier: 4.508A pdb=" N ILE F 215 " --> pdb=" O TYR F 211 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU F 216 " --> pdb=" O HIS F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 248 No H-bonds generated for 'chain 'F' and resid 246 through 248' Processing helix chain 'F' and resid 253 through 269 Processing helix chain 'F' and resid 276 through 282 Processing helix chain 'F' and resid 286 through 300 removed outlier: 4.075A pdb=" N ARG F 292 " --> pdb=" O ARG F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 314 Processing helix chain 'F' and resid 367 through 380 Processing helix chain 'F' and resid 381 through 383 No H-bonds generated for 'chain 'F' and resid 381 through 383' Processing helix chain 'F' and resid 386 through 394 Processing helix chain 'F' and resid 396 through 410 Processing helix chain 'F' and resid 437 through 457 Processing helix chain 'F' and resid 611 through 628 Processing helix chain 'F' and resid 633 through 649 removed outlier: 3.566A pdb=" N ILE F 637 " --> pdb=" O SER F 633 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 669 Processing helix chain 'F' and resid 700 through 715 Processing helix chain 'G' and resid 122 through 136 removed outlier: 3.945A pdb=" N ALA G 127 " --> pdb=" O LYS G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 148 removed outlier: 3.505A pdb=" N ASP G 148 " --> pdb=" O THR G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 218 Processing helix chain 'G' and resid 235 through 245 Processing helix chain 'G' and resid 296 through 298 No H-bonds generated for 'chain 'G' and resid 296 through 298' Processing helix chain 'G' and resid 468 through 473 Processing helix chain 'G' and resid 517 through 527 Processing helix chain 'G' and resid 536 through 551 Processing helix chain 'G' and resid 554 through 568 Processing helix chain 'G' and resid 570 through 588 removed outlier: 3.609A pdb=" N TRP G 574 " --> pdb=" O VAL G 570 " (cutoff:3.500A) Processing helix chain 'G' and resid 664 through 698 Processing helix chain 'G' and resid 701 through 707 Processing helix chain 'G' and resid 708 through 718 Processing helix chain 'G' and resid 724 through 738 Processing helix chain 'G' and resid 803 through 810 removed outlier: 3.674A pdb=" N LEU G 809 " --> pdb=" O TRP G 805 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 322 Proline residue: H 306 - end of helix removed outlier: 3.590A pdb=" N LEU H 311 " --> pdb=" O VAL H 307 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS H 312 " --> pdb=" O TRP H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 333 through 335 No H-bonds generated for 'chain 'H' and resid 333 through 335' Processing helix chain 'H' and resid 341 through 346 Processing helix chain 'H' and resid 515 through 523 Processing helix chain 'H' and resid 676 through 679 Processing helix chain 'H' and resid 740 through 744 Processing helix chain 'H' and resid 746 through 749 removed outlier: 3.628A pdb=" N GLU H 749 " --> pdb=" O ARG H 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 746 through 749' Processing helix chain 'H' and resid 786 through 792 Processing helix chain 'H' and resid 808 through 811 Processing helix chain 'H' and resid 812 through 822 Processing helix chain 'H' 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: 7.503A pdb=" N ARG B 54 " --> pdb=" O THR B 514 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR B 514 " --> pdb=" O ARG B 54 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N PHE B 512 " --> pdb=" O PRO B 56 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TYR B 488 " --> pdb=" O VAL B 482 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL B 482 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA B 490 " --> pdb=" O ILE B 480 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ILE B 480 " --> pdb=" O ALA B 490 " (cutoff:3.500A) removed outlier: 6.184A 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: 4.168A 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: 7.093A pdb=" N LEU B 191 " --> pdb=" O ASP B 207 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASP B 207 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 6.806A 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: 6.715A pdb=" N LEU B 279 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N MET B 251 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA B 277 " --> pdb=" O MET B 251 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TRP B 253 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU B 275 " --> pdb=" O TRP B 253 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY B 255 " --> pdb=" O SER B 273 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N SER B 273 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN B 284 " --> pdb=" O PHE B 280 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLN B 291 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 5.979A 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: 6.143A 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: 3.784A pdb=" N SER B 373 " --> pdb=" O ALA B 394 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS B 386 " --> pdb=" O HIS B 381 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N SER B 387 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ILE B 406 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 3.545A 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: 3.621A pdb=" N SER B 428 " --> pdb=" O CYS B 441 " (cutoff:3.500A) removed outlier: 4.237A 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: 5.016A pdb=" N VAL C 535 " --> pdb=" O ALA C 464 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N PHE C 459 " --> pdb=" O GLY C 443 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY C 443 " --> pdb=" O PHE C 459 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR C 461 " --> pdb=" O LEU C 441 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU C 438 " --> pdb=" O SER C 419 " (cutoff:3.500A) removed outlier: 4.647A 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: 6.740A pdb=" N LEU C 729 " --> pdb=" O ILE C 754 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU C 728 " --> pdb=" O ASP C 724 " (cutoff:3.500A) removed outlier: 3.775A 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: 3.904A pdb=" N SER C 378 " --> pdb=" O PHE C 392 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU C 860 " --> pdb=" O GLY C 856 " (cutoff:3.500A) removed outlier: 3.643A 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: 3.784A pdb=" N ASP C 472 " --> pdb=" O ALA C 502 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU C 513 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU C 498 " --> pdb=" O PHE C 511 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE C 511 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA C 500 " --> pdb=" O LEU C 509 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU C 509 " --> pdb=" O ALA C 500 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 557 through 562 removed outlier: 4.156A pdb=" N MET C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN C 607 " --> pdb=" O PHE C 582 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 616 through 621 removed outlier: 3.919A pdb=" N LYS C 637 " --> pdb=" O GLY C 633 " (cutoff:3.500A) removed outlier: 3.656A 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: 4.035A pdb=" N GLU C 660 " --> pdb=" O ALA C 673 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN C 674 " --> pdb=" O GLY C 685 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLY C 685 " --> pdb=" O GLN C 674 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE C 686 " --> pdb=" O THR C 701 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 19 through 20 Processing sheet with id=AC6, first strand: chain 'F' and resid 75 through 76 Processing sheet with id=AC7, first strand: chain 'F' and resid 102 through 103 removed outlier: 4.539A pdb=" N GLY F 112 " --> pdb=" O ILE F 103 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 222 through 230 Processing sheet with id=AC9, first strand: chain 'F' and resid 273 through 275 Processing sheet with id=AD1, first strand: chain 'F' and resid 384 through 385 Processing sheet with id=AD2, first strand: chain 'F' and resid 580 through 583 Processing sheet with id=AD3, first strand: chain 'G' and resid 53 through 59 removed outlier: 7.317A pdb=" N ARG G 54 " --> pdb=" O THR G 514 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N THR G 514 " --> pdb=" O ARG G 54 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N PHE G 512 " --> pdb=" O PRO G 56 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TYR G 488 " --> pdb=" O VAL G 482 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL G 482 " --> pdb=" O TYR G 488 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA G 490 " --> pdb=" O ILE G 480 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE G 480 " --> pdb=" O ALA G 490 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE G 492 " --> pdb=" O HIS G 478 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 70 through 72 removed outlier: 4.161A pdb=" N VAL G 103 " --> pdb=" O ILE G 92 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 164 through 169 removed outlier: 6.907A pdb=" N LEU G 191 " --> pdb=" O ASP G 207 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASP G 207 " --> pdb=" O LEU G 191 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE G 193 " --> pdb=" O LEU G 205 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 248 through 257 removed outlier: 6.602A pdb=" N LEU G 279 " --> pdb=" O VAL G 249 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N MET G 251 " --> pdb=" O ALA G 277 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA G 277 " --> pdb=" O MET G 251 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TRP G 253 " --> pdb=" O LEU G 275 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU G 275 " --> pdb=" O TRP G 253 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY G 255 " --> pdb=" O SER G 273 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER G 273 " --> pdb=" O GLY G 255 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN G 284 " --> pdb=" O PHE G 280 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLN G 291 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE G 300 " --> pdb=" O GLN G 291 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 313 through 323 removed outlier: 6.628A pdb=" N GLY G 334 " --> pdb=" O SER G 314 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU G 316 " --> pdb=" O ILE G 332 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE G 332 " --> pdb=" O LEU G 316 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TRP G 318 " --> pdb=" O GLY G 330 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY G 330 " --> pdb=" O TRP G 318 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU G 320 " --> pdb=" O MET G 328 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N MET G 328 " --> pdb=" O GLU G 320 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU G 322 " --> pdb=" O ARG G 326 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG G 326 " --> pdb=" O GLU G 322 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE G 340 " --> pdb=" O LEU G 362 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 371 through 381 removed outlier: 6.580A pdb=" N SER G 387 " --> pdb=" O ILE G 406 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ILE G 406 " --> pdb=" O SER G 387 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL G 399 " --> pdb=" O VAL G 418 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 428 through 431 removed outlier: 3.646A pdb=" N SER G 428 " --> pdb=" O CYS G 441 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS G 446 " --> pdb=" O SER G 442 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL G 447 " --> pdb=" O ILE G 466 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 761 through 764 removed outlier: 3.870A pdb=" N HIS G 768 " --> pdb=" O CYS G 764 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 786 through 787 Processing sheet with id=AE3, first strand: chain 'H' and resid 337 through 339 removed outlier: 4.948A pdb=" N VAL H 535 " --> pdb=" O ALA H 464 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N PHE H 459 " --> pdb=" O GLY H 443 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLY H 443 " --> pdb=" O PHE H 459 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR H 461 " --> pdb=" O LEU H 441 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU H 439 " --> pdb=" O SER H 419 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N SER H 419 " --> pdb=" O LEU H 439 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N LEU H 441 " --> pdb=" O LEU H 417 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU H 417 " --> pdb=" O LEU H 441 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLY H 443 " --> pdb=" O VAL H 415 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL H 415 " --> pdb=" O GLY H 443 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY H 445 " --> pdb=" O GLN H 413 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N TYR H 414 " --> pdb=" O TRP H 402 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N TRP H 402 " --> pdb=" O TYR H 414 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA H 416 " --> pdb=" O LEU H 400 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU H 400 " --> pdb=" O ALA H 416 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE H 418 " --> pdb=" O TRP H 398 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 358 through 362 removed outlier: 6.248A pdb=" N SER H 359 " --> pdb=" O PHE H 798 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ASP H 800 " --> pdb=" O SER H 359 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN H 361 " --> pdb=" O ASP H 800 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ARG H 751 " --> pdb=" O ILE H 733 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE H 733 " --> pdb=" O ARG H 751 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ALA H 731 " --> pdb=" O PRO H 753 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU H 728 " --> pdb=" O ASP H 724 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 378 through 379 removed outlier: 3.879A pdb=" N SER H 378 " --> pdb=" O PHE H 392 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LEU H 860 " --> pdb=" O GLY H 856 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY H 856 " --> pdb=" O LEU H 860 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 470 through 475 removed outlier: 3.843A pdb=" N ASP H 472 " --> pdb=" O ALA H 502 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU H 513 " --> pdb=" O LEU H 496 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU H 498 " --> pdb=" O PHE H 511 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE H 511 " --> pdb=" O LEU H 498 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA H 500 " --> pdb=" O LEU H 509 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU H 509 " --> pdb=" O ALA H 500 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA H 539 " --> pdb=" O LEU H 510 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR H 540 " --> pdb=" O LEU H 603 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 557 through 562 removed outlier: 4.206A pdb=" N MET H 579 " --> pdb=" O TYR H 575 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN H 607 " --> pdb=" O PHE H 582 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 618 through 621 Processing sheet with id=AE9, first strand: chain 'H' and resid 657 through 662 removed outlier: 3.786A pdb=" N LEU H 657 " --> pdb=" O ASP H 675 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA H 673 " --> pdb=" O THR H 659 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU H 661 " --> pdb=" O THR H 671 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR H 671 " --> pdb=" O LEU H 661 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN H 674 " --> pdb=" O GLY H 685 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLY H 685 " --> pdb=" O GLN H 674 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TYR H 688 " --> pdb=" O PHE H 700 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N PHE H 700 " --> pdb=" O TYR H 688 " (cutoff:3.500A) 1210 hydrogen bonds defined for protein. 3453 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 177 hydrogen bonds 354 hydrogen bond angles 0 basepair planarities 70 basepair parallelities 125 stacking parallelities Total time for adding SS restraints: 7.40 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 10059 1.35 - 1.48: 8843 1.48 - 1.61: 13753 1.61 - 1.74: 7 1.74 - 1.88: 274 Bond restraints: 32936 Sorted by residual: bond pdb=" CB CYS G 817 " pdb=" SG CYS G 817 " ideal model delta sigma weight residual 1.808 1.877 -0.069 3.30e-02 9.18e+02 4.42e+00 bond pdb=" CB CYS G 773 " pdb=" SG CYS G 773 " ideal model delta sigma weight residual 1.808 1.752 0.056 3.30e-02 9.18e+02 2.86e+00 bond pdb=" C4' DT D 10 " pdb=" O4' DT D 10 " ideal model delta sigma weight residual 1.450 1.417 0.033 2.00e-02 2.50e+03 2.73e+00 bond pdb=" C3' DT I 10 " pdb=" C2' DT I 10 " ideal model delta sigma weight residual 1.525 1.558 -0.033 2.00e-02 2.50e+03 2.65e+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 2.43e+00 ... (remaining 32931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 43785 1.95 - 3.90: 1307 3.90 - 5.84: 106 5.84 - 7.79: 12 7.79 - 9.74: 2 Bond angle restraints: 45212 Sorted by residual: angle pdb=" C4' DG I 6 " pdb=" C3' DG I 6 " pdb=" O3' DG I 6 " ideal model delta sigma weight residual 110.00 115.87 -5.87 1.50e+00 4.44e-01 1.53e+01 angle pdb=" C CYS G 817 " pdb=" N ASP G 818 " pdb=" CA ASP G 818 " ideal model delta sigma weight residual 121.24 115.63 5.61 1.44e+00 4.82e-01 1.52e+01 angle pdb=" C4' DG D 6 " pdb=" C3' DG D 6 " pdb=" O3' DG D 6 " ideal model delta sigma weight residual 110.00 115.59 -5.59 1.50e+00 4.44e-01 1.39e+01 angle pdb=" C3' DG D 6 " pdb=" O3' DG D 6 " pdb=" P DT D 7 " ideal model delta sigma weight residual 120.20 125.76 -5.56 1.50e+00 4.44e-01 1.37e+01 angle pdb=" C3' DG I 6 " pdb=" O3' DG I 6 " pdb=" P DT I 7 " ideal model delta sigma weight residual 120.20 125.63 -5.43 1.50e+00 4.44e-01 1.31e+01 ... (remaining 45207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.19: 18594 32.19 - 64.37: 835 64.37 - 96.56: 49 96.56 - 128.74: 0 128.74 - 160.93: 4 Dihedral angle restraints: 19482 sinusoidal: 8948 harmonic: 10534 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 -150.90 -29.10 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA LEU G 459 " pdb=" C LEU G 459 " pdb=" N LYS G 460 " pdb=" CA LYS G 460 " ideal model delta harmonic sigma weight residual 180.00 151.20 28.80 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA LYS G 364 " pdb=" C LYS G 364 " pdb=" N GLU G 365 " pdb=" CA GLU G 365 " ideal model delta harmonic sigma weight residual -180.00 -151.30 -28.70 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 19479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 4147 0.066 - 0.132: 798 0.132 - 0.199: 66 0.199 - 0.265: 3 0.265 - 0.331: 2 Chirality restraints: 5016 Sorted by residual: chirality pdb=" C3' DG I 6 " pdb=" C4' DG I 6 " pdb=" O3' DG I 6 " pdb=" C2' DG I 6 " both_signs ideal model delta sigma weight residual False -2.66 -2.33 -0.33 2.00e-01 2.50e+01 2.74e+00 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 2.17 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 5013 not shown) Planarity restraints: 5280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 186 " -0.307 9.50e-02 1.11e+02 1.39e-01 1.53e+01 pdb=" NE ARG A 186 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 186 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG A 186 " 0.014 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=" C1' DC I 26 " -0.034 2.00e-02 2.50e+03 2.54e-02 1.45e+01 pdb=" N1 DC I 26 " 0.060 2.00e-02 2.50e+03 pdb=" C2 DC I 26 " -0.028 2.00e-02 2.50e+03 pdb=" O2 DC I 26 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DC I 26 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC I 26 " -0.004 2.00e-02 2.50e+03 pdb=" N4 DC I 26 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DC I 26 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DC I 26 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 796 " 0.294 9.50e-02 1.11e+02 1.33e-01 1.42e+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 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG B 796 " -0.000 2.00e-02 2.50e+03 ... (remaining 5277 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 117 2.54 - 3.13: 24323 3.13 - 3.72: 50034 3.72 - 4.31: 72988 4.31 - 4.90: 119373 Nonbonded interactions: 266835 Sorted by model distance: nonbonded pdb=" OD2 ASP G 792 " pdb="ZN ZN G 902 " model vdw 1.951 2.230 nonbonded pdb=" OD1 ASP B 792 " pdb="ZN ZN B 901 " model vdw 1.983 2.230 nonbonded pdb=" OD1 ASP G 792 " pdb="ZN ZN G 902 " model vdw 1.987 2.230 nonbonded pdb=" OD2 ASP B 792 " pdb="ZN ZN B 901 " model vdw 2.035 2.230 nonbonded pdb=" CG ASP G 792 " pdb="ZN ZN G 902 " model vdw 2.166 2.460 ... (remaining 266830 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' } 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: 8.730 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.740 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 35.910 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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 0.069 32950 Z= 0.190 Angle : 0.755 9.740 45218 Z= 0.436 Chirality : 0.051 0.331 5016 Planarity : 0.010 0.139 5280 Dihedral : 16.677 160.927 12658 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.13), residues: 3580 helix: -0.86 (0.13), residues: 1058 sheet: 0.23 (0.17), residues: 874 loop : -0.53 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.003 ARG G 796 TYR 0.025 0.005 TYR B 439 PHE 0.020 0.002 PHE C 700 TRP 0.034 0.003 TRP H 471 HIS 0.007 0.001 HIS F 210 Details of bonding type rmsd covalent geometry : bond 0.00446 (32936) covalent geometry : angle 0.75400 (45212) hydrogen bonds : bond 0.17179 ( 1387) hydrogen bonds : angle 7.19516 ( 3807) metal coordination : bond 0.02567 ( 14) metal coordination : angle 3.97684 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 447 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ARG cc_start: 0.6484 (ttp80) cc_final: 0.6082 (mmm160) REVERT: A 255 TYR cc_start: 0.8276 (m-10) cc_final: 0.7972 (m-10) REVERT: B 75 ASP cc_start: 0.7835 (t0) cc_final: 0.7615 (t0) REVERT: B 222 ARG cc_start: 0.8078 (mtm180) cc_final: 0.7856 (mtm-85) REVERT: B 681 MET cc_start: 0.8726 (tpt) cc_final: 0.8426 (tpt) REVERT: B 710 ARG cc_start: 0.8200 (ttm110) cc_final: 0.7996 (ptp-170) REVERT: B 733 HIS cc_start: 0.8968 (m170) cc_final: 0.8679 (m90) REVERT: C 294 MET cc_start: 0.8427 (tpp) cc_final: 0.7750 (mmm) REVERT: C 683 LEU cc_start: 0.8641 (mp) cc_final: 0.8134 (tp) REVERT: F 293 LEU cc_start: 0.9302 (mt) cc_final: 0.9018 (mm) REVERT: F 294 TYR cc_start: 0.8946 (t80) cc_final: 0.8540 (t80) REVERT: F 295 GLN cc_start: 0.9024 (pt0) cc_final: 0.8560 (pp30) REVERT: F 627 ASN cc_start: 0.9097 (m110) cc_final: 0.8483 (p0) REVERT: F 693 HIS cc_start: 0.7740 (t-90) cc_final: 0.7268 (t-90) REVERT: F 711 ARG cc_start: 0.9519 (ttt180) cc_final: 0.9234 (ttm110) REVERT: G 328 MET cc_start: 0.6787 (mmt) cc_final: 0.5532 (ptm) REVERT: H 304 MET cc_start: 0.9228 (mmm) cc_final: 0.8800 (mmm) outliers start: 0 outliers final: 0 residues processed: 447 average time/residue: 0.2234 time to fit residues: 153.5629 Evaluate side-chains 258 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 627 ASN B 152 ASN B 240 GLN C 467 ASN C 687 HIS C 857 GLN C 884 HIS ** F 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 627 ASN G 114 ASN G 284 ASN G 531 GLN G 552 HIS ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 448 GLN H 467 ASN H 620 GLN H 625 ASN H 687 HIS H 857 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.132257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.093310 restraints weight = 52912.558| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.10 r_work: 0.2962 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32950 Z= 0.164 Angle : 0.658 15.089 45218 Z= 0.353 Chirality : 0.044 0.163 5016 Planarity : 0.005 0.052 5280 Dihedral : 18.565 156.397 5466 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.06 % Allowed : 4.60 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.14), residues: 3580 helix: 0.90 (0.15), residues: 1072 sheet: 0.30 (0.17), residues: 866 loop : 0.02 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 713 TYR 0.054 0.002 TYR A 296 PHE 0.016 0.002 PHE C 391 TRP 0.018 0.002 TRP B 805 HIS 0.009 0.001 HIS G 552 Details of bonding type rmsd covalent geometry : bond 0.00370 (32936) covalent geometry : angle 0.65755 (45212) hydrogen bonds : bond 0.04622 ( 1387) hydrogen bonds : angle 5.04593 ( 3807) metal coordination : bond 0.01051 ( 14) metal coordination : angle 2.30706 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 278 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ARG cc_start: 0.6565 (ttp80) cc_final: 0.6211 (mmm160) REVERT: A 296 TYR cc_start: 0.7874 (m-80) cc_final: 0.7283 (m-80) REVERT: A 329 MET cc_start: 0.8756 (tpp) cc_final: 0.8481 (tpp) REVERT: A 623 GLU cc_start: 0.8801 (tt0) cc_final: 0.8487 (tt0) REVERT: A 635 PHE cc_start: 0.7987 (t80) cc_final: 0.7728 (t80) REVERT: A 686 LYS cc_start: 0.8993 (tptp) cc_final: 0.8472 (tptp) REVERT: A 690 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8507 (pp) REVERT: B 728 ARG cc_start: 0.8589 (ttp-110) cc_final: 0.7993 (mtm-85) REVERT: B 733 HIS cc_start: 0.8791 (m170) cc_final: 0.8552 (m90) REVERT: C 683 LEU cc_start: 0.8691 (mp) cc_final: 0.8204 (tp) REVERT: C 811 ARG cc_start: 0.8574 (mtm180) cc_final: 0.8306 (ttp-110) REVERT: F 64 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7692 (ttp80) REVERT: F 302 LEU cc_start: 0.7743 (mm) cc_final: 0.7260 (pp) REVERT: F 627 ASN cc_start: 0.8900 (m-40) cc_final: 0.8425 (p0) REVERT: F 630 LEU cc_start: 0.9006 (tt) cc_final: 0.8530 (mp) REVERT: G 328 MET cc_start: 0.7097 (mmt) cc_final: 0.5798 (ptm) REVERT: G 590 LYS cc_start: 0.8105 (ptpp) cc_final: 0.7684 (mtpt) REVERT: H 304 MET cc_start: 0.9102 (mmm) cc_final: 0.8587 (mmm) REVERT: H 785 ARG cc_start: 0.7366 (tpp-160) cc_final: 0.7031 (tpp-160) outliers start: 34 outliers final: 21 residues processed: 298 average time/residue: 0.2156 time to fit residues: 100.9878 Evaluate side-chains 258 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 235 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 677 GLU 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 F residue 64 ARG Chi-restraints excluded: chain F residue 642 MET Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 702 LEU Chi-restraints excluded: chain G residue 465 LEU Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 784 ILE Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 368 ASP Chi-restraints excluded: chain H residue 434 SER Chi-restraints excluded: chain H residue 472 ASP Chi-restraints excluded: chain H residue 725 ILE Chi-restraints excluded: chain H residue 863 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 150 optimal weight: 2.9990 chunk 192 optimal weight: 6.9990 chunk 298 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 274 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 278 optimal weight: 0.4980 chunk 168 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 294 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN A 627 ASN C 467 ASN G 152 ASN G 304 ASN G 478 HIS G 536 GLN ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 448 GLN H 838 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.131109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.090870 restraints weight = 52979.899| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.43 r_work: 0.2941 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 32950 Z= 0.184 Angle : 0.621 13.425 45218 Z= 0.332 Chirality : 0.044 0.161 5016 Planarity : 0.005 0.057 5280 Dihedral : 18.515 155.977 5466 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.25 % Allowed : 6.16 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.14), residues: 3580 helix: 1.29 (0.16), residues: 1072 sheet: 0.14 (0.17), residues: 856 loop : 0.04 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 759 TYR 0.031 0.002 TYR G 722 PHE 0.024 0.002 PHE F 635 TRP 0.022 0.001 TRP B 805 HIS 0.006 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00434 (32936) covalent geometry : angle 0.62074 (45212) hydrogen bonds : bond 0.04410 ( 1387) hydrogen bonds : angle 4.79953 ( 3807) metal coordination : bond 0.01073 ( 14) metal coordination : angle 2.64037 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 251 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ARG cc_start: 0.6597 (ttp80) cc_final: 0.6358 (mmm160) REVERT: A 296 TYR cc_start: 0.7825 (m-80) cc_final: 0.7472 (m-80) REVERT: A 329 MET cc_start: 0.8933 (tpp) cc_final: 0.8417 (tpp) REVERT: A 417 MET cc_start: 0.8278 (mmm) cc_final: 0.8032 (mmm) REVERT: A 623 GLU cc_start: 0.8806 (tt0) cc_final: 0.8531 (tt0) REVERT: A 686 LYS cc_start: 0.9067 (tptp) cc_final: 0.8617 (tptp) REVERT: B 172 MET cc_start: 0.8425 (mtp) cc_final: 0.8176 (mtp) REVERT: B 733 HIS cc_start: 0.8811 (m170) cc_final: 0.8556 (m90) REVERT: C 683 LEU cc_start: 0.8722 (mp) cc_final: 0.8191 (tp) REVERT: C 811 ARG cc_start: 0.8617 (mtm180) cc_final: 0.8318 (ttp-110) REVERT: C 813 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7701 (pm20) REVERT: F 294 TYR cc_start: 0.8960 (t80) cc_final: 0.8685 (m-80) REVERT: F 623 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8555 (mm-30) REVERT: F 627 ASN cc_start: 0.8935 (m-40) cc_final: 0.8457 (p0) REVERT: F 630 LEU cc_start: 0.8986 (tt) cc_final: 0.8488 (mp) REVERT: G 50 MET cc_start: 0.4265 (ptt) cc_final: 0.3937 (ptt) REVERT: G 328 MET cc_start: 0.7179 (mmt) cc_final: 0.5782 (ptm) REVERT: G 590 LYS cc_start: 0.8282 (ptpp) cc_final: 0.7738 (mtpt) REVERT: H 785 ARG cc_start: 0.7323 (tpp-160) cc_final: 0.6937 (tpp-160) outliers start: 40 outliers final: 28 residues processed: 277 average time/residue: 0.2190 time to fit residues: 94.5612 Evaluate side-chains 257 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 228 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 113 SER Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 50 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 B residue 794 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 813 GLU Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 702 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 465 LEU Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 784 ILE Chi-restraints excluded: chain G residue 794 ILE Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 368 ASP Chi-restraints excluded: chain H residue 434 SER Chi-restraints excluded: chain H residue 472 ASP Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 725 ILE Chi-restraints excluded: chain H residue 808 ASP Chi-restraints excluded: chain H residue 863 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 146 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 366 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 142 optimal weight: 0.0270 chunk 65 optimal weight: 0.2980 overall best weight: 1.2442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 HIS B 368 GLN C 794 HIS C 807 HIS F 295 GLN G 552 HIS ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 433 HIS H 448 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.130831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.091450 restraints weight = 52747.622| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.11 r_work: 0.2931 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 32950 Z= 0.182 Angle : 0.608 13.051 45218 Z= 0.323 Chirality : 0.043 0.159 5016 Planarity : 0.005 0.072 5280 Dihedral : 18.492 154.614 5466 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.91 % Allowed : 7.22 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.14), residues: 3580 helix: 1.46 (0.16), residues: 1072 sheet: -0.01 (0.17), residues: 850 loop : -0.04 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 64 TYR 0.022 0.001 TYR A 296 PHE 0.042 0.002 PHE A 290 TRP 0.015 0.001 TRP B 805 HIS 0.010 0.001 HIS G 552 Details of bonding type rmsd covalent geometry : bond 0.00429 (32936) covalent geometry : angle 0.60765 (45212) hydrogen bonds : bond 0.04061 ( 1387) hydrogen bonds : angle 4.61388 ( 3807) metal coordination : bond 0.01220 ( 14) metal coordination : angle 2.73302 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 251 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 TYR cc_start: 0.8336 (m-10) cc_final: 0.8051 (m-10) REVERT: A 296 TYR cc_start: 0.7830 (m-80) cc_final: 0.7370 (m-80) REVERT: A 623 GLU cc_start: 0.8789 (tt0) cc_final: 0.8545 (tt0) REVERT: A 686 LYS cc_start: 0.9021 (tptp) cc_final: 0.8553 (tptp) REVERT: B 172 MET cc_start: 0.8401 (mtp) cc_final: 0.8161 (mtp) REVERT: B 728 ARG cc_start: 0.8840 (ttm170) cc_final: 0.8357 (mtm-85) REVERT: C 683 LEU cc_start: 0.8660 (mp) cc_final: 0.8179 (tp) REVERT: C 811 ARG cc_start: 0.8602 (mtm180) cc_final: 0.8342 (ttp-110) REVERT: C 813 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7684 (pm20) REVERT: F 64 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7695 (ttp80) REVERT: F 294 TYR cc_start: 0.8828 (t80) cc_final: 0.8606 (m-80) REVERT: F 623 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8602 (mm-30) REVERT: G 50 MET cc_start: 0.4373 (ptt) cc_final: 0.4124 (ptt) REVERT: G 328 MET cc_start: 0.7187 (mmt) cc_final: 0.5763 (ptm) REVERT: H 785 ARG cc_start: 0.7388 (tpp-160) cc_final: 0.7029 (tpp-160) REVERT: H 842 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.8172 (m-80) outliers start: 61 outliers final: 35 residues processed: 295 average time/residue: 0.2143 time to fit residues: 100.2230 Evaluate side-chains 260 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 113 SER Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 813 GLU Chi-restraints excluded: chain C residue 866 VAL Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 702 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain G residue 465 LEU Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 697 LEU Chi-restraints excluded: chain G residue 716 LEU Chi-restraints excluded: chain G residue 784 ILE Chi-restraints excluded: chain G residue 794 ILE Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 368 ASP Chi-restraints excluded: chain H residue 434 SER Chi-restraints excluded: chain H residue 472 ASP Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 808 ASP Chi-restraints excluded: chain H residue 842 PHE Chi-restraints excluded: chain H residue 852 LEU Chi-restraints excluded: chain H residue 863 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 273 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 115 optimal weight: 9.9990 chunk 235 optimal weight: 20.0000 chunk 298 optimal weight: 6.9990 chunk 318 optimal weight: 2.9990 chunk 272 optimal weight: 0.5980 chunk 285 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 HIS C 467 ASN C 807 HIS F 295 GLN G 324 ASN G 552 HIS ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 448 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.130532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.091049 restraints weight = 52834.167| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.09 r_work: 0.2924 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 32950 Z= 0.186 Angle : 0.603 12.025 45218 Z= 0.320 Chirality : 0.043 0.159 5016 Planarity : 0.005 0.058 5280 Dihedral : 18.465 154.032 5466 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.78 % Allowed : 8.69 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.14), residues: 3580 helix: 1.55 (0.16), residues: 1080 sheet: -0.04 (0.17), residues: 860 loop : -0.10 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 811 TYR 0.017 0.001 TYR A 296 PHE 0.035 0.002 PHE A 635 TRP 0.015 0.001 TRP B 805 HIS 0.012 0.001 HIS B 733 Details of bonding type rmsd covalent geometry : bond 0.00439 (32936) covalent geometry : angle 0.60217 (45212) hydrogen bonds : bond 0.03980 ( 1387) hydrogen bonds : angle 4.56282 ( 3807) metal coordination : bond 0.01279 ( 14) metal coordination : angle 2.79027 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 245 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 SER cc_start: 0.8067 (m) cc_final: 0.7535 (p) REVERT: A 255 TYR cc_start: 0.8359 (m-10) cc_final: 0.8080 (m-10) REVERT: A 296 TYR cc_start: 0.7726 (m-80) cc_final: 0.7378 (m-80) REVERT: A 329 MET cc_start: 0.8524 (tpp) cc_final: 0.8080 (tpp) REVERT: A 623 GLU cc_start: 0.8765 (tt0) cc_final: 0.8554 (tt0) REVERT: B 172 MET cc_start: 0.8398 (mtp) cc_final: 0.8172 (mtp) REVERT: B 728 ARG cc_start: 0.8878 (ttm170) cc_final: 0.8352 (mtm-85) REVERT: B 733 HIS cc_start: 0.8741 (m170) cc_final: 0.8483 (m170) REVERT: C 449 GLN cc_start: 0.8489 (tm-30) cc_final: 0.7977 (tt0) REVERT: C 683 LEU cc_start: 0.8683 (mp) cc_final: 0.8180 (tp) REVERT: C 811 ARG cc_start: 0.8627 (mtm180) cc_final: 0.8329 (ttp-110) REVERT: C 813 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7673 (pm20) REVERT: F 329 MET cc_start: 0.8435 (mmm) cc_final: 0.7748 (tpp) REVERT: G 50 MET cc_start: 0.4418 (ptt) cc_final: 0.4179 (ptt) REVERT: G 328 MET cc_start: 0.7253 (mmt) cc_final: 0.5790 (ptm) REVERT: G 590 LYS cc_start: 0.8430 (ptpt) cc_final: 0.8137 (mttt) REVERT: H 785 ARG cc_start: 0.7329 (tpp-160) cc_final: 0.6997 (tpp-160) REVERT: H 842 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8205 (m-80) outliers start: 57 outliers final: 38 residues processed: 285 average time/residue: 0.2072 time to fit residues: 94.6079 Evaluate side-chains 264 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 224 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 113 SER Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 696 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 794 ILE Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 813 GLU Chi-restraints excluded: chain C residue 866 VAL Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 702 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 465 LEU Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 552 HIS Chi-restraints excluded: chain G residue 716 LEU Chi-restraints excluded: chain G residue 717 MET Chi-restraints excluded: chain G residue 753 ILE Chi-restraints excluded: chain G residue 784 ILE Chi-restraints excluded: chain G residue 794 ILE Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 368 ASP Chi-restraints excluded: chain H residue 434 SER Chi-restraints excluded: chain H residue 472 ASP Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 653 ILE Chi-restraints excluded: chain H residue 710 SER Chi-restraints excluded: chain H residue 842 PHE Chi-restraints excluded: chain H residue 852 LEU Chi-restraints excluded: chain H residue 863 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 2 optimal weight: 2.9990 chunk 234 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 277 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 358 optimal weight: 7.9990 chunk 272 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 360 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 807 HIS G 552 HIS ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 448 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.130719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.091179 restraints weight = 52640.834| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.10 r_work: 0.2925 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 32950 Z= 0.165 Angle : 0.586 11.588 45218 Z= 0.310 Chirality : 0.043 0.158 5016 Planarity : 0.004 0.057 5280 Dihedral : 18.433 153.727 5466 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.69 % Allowed : 9.54 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.14), residues: 3580 helix: 1.61 (0.16), residues: 1080 sheet: -0.04 (0.17), residues: 834 loop : -0.11 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 728 TYR 0.017 0.001 TYR H 755 PHE 0.036 0.002 PHE A 635 TRP 0.015 0.001 TRP B 805 HIS 0.030 0.001 HIS G 552 Details of bonding type rmsd covalent geometry : bond 0.00387 (32936) covalent geometry : angle 0.58558 (45212) hydrogen bonds : bond 0.03822 ( 1387) hydrogen bonds : angle 4.48142 ( 3807) metal coordination : bond 0.01287 ( 14) metal coordination : angle 2.70530 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 246 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 SER cc_start: 0.7973 (m) cc_final: 0.7498 (p) REVERT: A 255 TYR cc_start: 0.8337 (m-10) cc_final: 0.8119 (m-10) REVERT: A 296 TYR cc_start: 0.7629 (m-80) cc_final: 0.7374 (m-80) REVERT: B 172 MET cc_start: 0.8402 (mtp) cc_final: 0.8179 (mtp) REVERT: B 441 CYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8441 (t) REVERT: B 710 ARG cc_start: 0.8675 (mtm180) cc_final: 0.8425 (ptp-170) REVERT: B 728 ARG cc_start: 0.8886 (ttm170) cc_final: 0.8505 (mtt90) REVERT: B 733 HIS cc_start: 0.8743 (m170) cc_final: 0.8529 (m170) REVERT: C 449 GLN cc_start: 0.8492 (tm-30) cc_final: 0.8020 (tt0) REVERT: C 683 LEU cc_start: 0.8669 (mp) cc_final: 0.8182 (tp) REVERT: C 811 ARG cc_start: 0.8647 (mtm180) cc_final: 0.8335 (ttp-110) REVERT: C 813 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7664 (pm20) REVERT: F 64 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7729 (ttp80) REVERT: F 329 MET cc_start: 0.8227 (mmm) cc_final: 0.7585 (tpp) REVERT: F 711 ARG cc_start: 0.9087 (ptp-110) cc_final: 0.8855 (ttm110) REVERT: G 50 MET cc_start: 0.4456 (ptt) cc_final: 0.4183 (ptt) REVERT: G 328 MET cc_start: 0.7242 (mmt) cc_final: 0.5869 (ptm) REVERT: G 590 LYS cc_start: 0.8418 (ptpt) cc_final: 0.8094 (mttt) REVERT: H 785 ARG cc_start: 0.7391 (tpp-160) cc_final: 0.7060 (tpp-160) REVERT: H 842 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.8228 (m-80) outliers start: 54 outliers final: 36 residues processed: 286 average time/residue: 0.1972 time to fit residues: 91.3250 Evaluate side-chains 266 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 226 time to evaluate : 1.197 ------------------------------------------------------------------------------- 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 113 SER Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 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 677 GLU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 813 GLU Chi-restraints excluded: chain C residue 866 VAL Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain F residue 294 TYR Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 702 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 360 VAL Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain G residue 465 LEU Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 716 LEU Chi-restraints excluded: chain G residue 717 MET Chi-restraints excluded: chain G residue 784 ILE Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 368 ASP Chi-restraints excluded: chain H residue 472 ASP Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 710 SER Chi-restraints excluded: chain H residue 842 PHE Chi-restraints excluded: chain H residue 852 LEU Chi-restraints excluded: chain H residue 863 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 221 optimal weight: 0.8980 chunk 157 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 109 optimal weight: 0.6980 chunk 64 optimal weight: 0.4980 chunk 116 optimal weight: 0.8980 chunk 329 optimal weight: 0.2980 chunk 324 optimal weight: 0.5980 chunk 279 optimal weight: 1.9990 chunk 362 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 797 HIS C 807 HIS F 295 GLN G 189 ASN G 552 HIS ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 448 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.132159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.092849 restraints weight = 52866.248| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.11 r_work: 0.2957 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32950 Z= 0.127 Angle : 0.557 11.265 45218 Z= 0.296 Chirality : 0.041 0.157 5016 Planarity : 0.004 0.057 5280 Dihedral : 18.359 153.636 5466 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.59 % Allowed : 9.88 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.14), residues: 3580 helix: 1.77 (0.16), residues: 1078 sheet: -0.03 (0.17), residues: 868 loop : -0.04 (0.16), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 811 TYR 0.017 0.001 TYR A 294 PHE 0.044 0.001 PHE A 635 TRP 0.016 0.001 TRP H 641 HIS 0.011 0.001 HIS G 552 Details of bonding type rmsd covalent geometry : bond 0.00287 (32936) covalent geometry : angle 0.55681 (45212) hydrogen bonds : bond 0.03518 ( 1387) hydrogen bonds : angle 4.33991 ( 3807) metal coordination : bond 0.01356 ( 14) metal coordination : angle 2.27763 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 263 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.7816 (ttp) cc_final: 0.7612 (ttp) REVERT: A 239 SER cc_start: 0.7972 (m) cc_final: 0.7508 (p) REVERT: A 255 TYR cc_start: 0.8300 (m-10) cc_final: 0.8085 (m-10) REVERT: A 329 MET cc_start: 0.8301 (tpp) cc_final: 0.7808 (tpp) REVERT: A 686 LYS cc_start: 0.9153 (tppt) cc_final: 0.8873 (mptt) REVERT: B 172 MET cc_start: 0.8375 (mtp) cc_final: 0.8167 (mtp) REVERT: B 710 ARG cc_start: 0.8641 (mtm180) cc_final: 0.8422 (ptp-170) REVERT: C 449 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8061 (tt0) REVERT: C 811 ARG cc_start: 0.8607 (mtm180) cc_final: 0.8315 (ttp-110) REVERT: C 813 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7674 (pm20) REVERT: F 64 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7624 (ttp80) REVERT: F 72 GLN cc_start: 0.5436 (mt0) cc_final: 0.4784 (mt0) REVERT: F 329 MET cc_start: 0.8383 (mmm) cc_final: 0.7699 (tpp) REVERT: F 676 ARG cc_start: 0.9244 (tpp-160) cc_final: 0.8768 (tpp-160) REVERT: F 711 ARG cc_start: 0.9061 (ptp-110) cc_final: 0.8703 (ttm110) REVERT: G 50 MET cc_start: 0.4423 (ptt) cc_final: 0.4149 (ptt) REVERT: G 328 MET cc_start: 0.7200 (mmt) cc_final: 0.5844 (ptm) REVERT: G 590 LYS cc_start: 0.8424 (ptpt) cc_final: 0.8170 (mttt) REVERT: H 785 ARG cc_start: 0.7397 (tpp-160) cc_final: 0.7093 (tpp-160) REVERT: H 842 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8207 (m-80) outliers start: 51 outliers final: 36 residues processed: 298 average time/residue: 0.1961 time to fit residues: 94.4324 Evaluate side-chains 275 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 236 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 113 SER Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 187 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 677 GLU 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 813 GLU Chi-restraints excluded: chain C residue 866 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain G residue 325 ASN Chi-restraints excluded: chain G residue 360 VAL Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain G residue 465 LEU Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 552 HIS Chi-restraints excluded: chain G residue 716 LEU Chi-restraints excluded: chain G residue 717 MET Chi-restraints excluded: chain G residue 784 ILE Chi-restraints excluded: chain H residue 368 ASP Chi-restraints excluded: chain H residue 434 SER Chi-restraints excluded: chain H residue 472 ASP Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 808 ASP Chi-restraints excluded: chain H residue 842 PHE Chi-restraints excluded: chain H residue 852 LEU Chi-restraints excluded: chain H residue 863 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 88 optimal weight: 0.6980 chunk 226 optimal weight: 1.9990 chunk 292 optimal weight: 0.0970 chunk 89 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 283 optimal weight: 3.9990 chunk 270 optimal weight: 0.6980 chunk 159 optimal weight: 0.7980 chunk 288 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 195 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 807 HIS G 552 HIS ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 778 GLN H 448 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.132278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.093017 restraints weight = 52581.438| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.08 r_work: 0.2960 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32950 Z= 0.130 Angle : 0.565 10.939 45218 Z= 0.300 Chirality : 0.041 0.176 5016 Planarity : 0.004 0.056 5280 Dihedral : 18.342 153.237 5466 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.44 % Allowed : 10.07 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.14), residues: 3580 helix: 1.82 (0.16), residues: 1080 sheet: 0.06 (0.17), residues: 878 loop : -0.05 (0.16), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 725 TYR 0.056 0.001 TYR A 296 PHE 0.061 0.001 PHE F 290 TRP 0.017 0.001 TRP B 805 HIS 0.032 0.001 HIS G 552 Details of bonding type rmsd covalent geometry : bond 0.00295 (32936) covalent geometry : angle 0.56490 (45212) hydrogen bonds : bond 0.03501 ( 1387) hydrogen bonds : angle 4.31994 ( 3807) metal coordination : bond 0.01337 ( 14) metal coordination : angle 2.26552 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 251 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 SER cc_start: 0.7961 (m) cc_final: 0.7492 (p) REVERT: A 296 TYR cc_start: 0.7386 (m-80) cc_final: 0.6956 (m-80) REVERT: A 329 MET cc_start: 0.8350 (tpp) cc_final: 0.7872 (tpp) REVERT: A 669 GLU cc_start: 0.8619 (tp30) cc_final: 0.7778 (mt-10) REVERT: A 686 LYS cc_start: 0.9125 (tppt) cc_final: 0.8775 (mptt) REVERT: B 172 MET cc_start: 0.8355 (mtp) cc_final: 0.8150 (mtp) REVERT: C 449 GLN cc_start: 0.8482 (tm-30) cc_final: 0.8090 (tt0) REVERT: C 811 ARG cc_start: 0.8603 (mtm180) cc_final: 0.8302 (ttp-110) REVERT: C 813 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7663 (pm20) REVERT: F 64 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7623 (ttp80) REVERT: F 329 MET cc_start: 0.8373 (mmm) cc_final: 0.7695 (tpp) REVERT: G 50 MET cc_start: 0.4355 (ptt) cc_final: 0.4082 (ptt) REVERT: G 328 MET cc_start: 0.7178 (mmt) cc_final: 0.5841 (ptm) REVERT: G 590 LYS cc_start: 0.8399 (ptpt) cc_final: 0.8158 (mttt) REVERT: H 785 ARG cc_start: 0.7405 (tpp-160) cc_final: 0.7133 (tpp-160) REVERT: H 842 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8197 (m-80) outliers start: 46 outliers final: 35 residues processed: 281 average time/residue: 0.2029 time to fit residues: 91.4457 Evaluate side-chains 278 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 240 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 113 SER Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 187 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 677 GLU Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 813 GLU Chi-restraints excluded: chain C residue 866 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 360 VAL Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain G residue 465 LEU Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 716 LEU Chi-restraints excluded: chain G residue 717 MET Chi-restraints excluded: chain G residue 784 ILE Chi-restraints excluded: chain G residue 821 VAL Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 434 SER Chi-restraints excluded: chain H residue 472 ASP Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 842 PHE Chi-restraints excluded: chain H residue 863 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 50 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 268 optimal weight: 0.6980 chunk 253 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 22 optimal weight: 0.0770 overall best weight: 0.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 807 HIS G 552 HIS ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 448 GLN H 793 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.131575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.092095 restraints weight = 52392.977| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.11 r_work: 0.2943 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32950 Z= 0.154 Angle : 0.579 10.405 45218 Z= 0.306 Chirality : 0.042 0.164 5016 Planarity : 0.004 0.056 5280 Dihedral : 18.359 152.590 5466 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.53 % Allowed : 10.38 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.14), residues: 3580 helix: 1.83 (0.16), residues: 1080 sheet: 0.02 (0.17), residues: 880 loop : -0.06 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 673 TYR 0.042 0.001 TYR A 296 PHE 0.068 0.002 PHE F 290 TRP 0.013 0.001 TRP B 805 HIS 0.012 0.001 HIS G 552 Details of bonding type rmsd covalent geometry : bond 0.00359 (32936) covalent geometry : angle 0.57823 (45212) hydrogen bonds : bond 0.03605 ( 1387) hydrogen bonds : angle 4.34987 ( 3807) metal coordination : bond 0.01360 ( 14) metal coordination : angle 2.46660 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 244 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 SER cc_start: 0.8003 (m) cc_final: 0.7487 (p) REVERT: A 329 MET cc_start: 0.8352 (tpp) cc_final: 0.7890 (tpp) REVERT: A 669 GLU cc_start: 0.8641 (tp30) cc_final: 0.7688 (mt-10) REVERT: A 686 LYS cc_start: 0.9084 (tppt) cc_final: 0.8747 (mptt) REVERT: B 172 MET cc_start: 0.8382 (mtp) cc_final: 0.8172 (mtp) REVERT: B 497 MET cc_start: 0.9091 (mmm) cc_final: 0.8865 (mtp) REVERT: B 733 HIS cc_start: 0.8792 (m170) cc_final: 0.8590 (m170) REVERT: C 449 GLN cc_start: 0.8448 (tm-30) cc_final: 0.8090 (tt0) REVERT: C 811 ARG cc_start: 0.8572 (mtm180) cc_final: 0.8268 (ttp-110) REVERT: C 813 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7806 (pm20) REVERT: F 64 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7614 (ttp80) REVERT: F 708 GLU cc_start: 0.9315 (mm-30) cc_final: 0.9078 (mt-10) REVERT: F 711 ARG cc_start: 0.9322 (ptm160) cc_final: 0.8957 (ttm110) REVERT: G 50 MET cc_start: 0.4336 (ptt) cc_final: 0.4095 (ptt) REVERT: G 328 MET cc_start: 0.7210 (mmt) cc_final: 0.5855 (ptm) REVERT: G 590 LYS cc_start: 0.8404 (ptpt) cc_final: 0.8163 (mttt) REVERT: H 785 ARG cc_start: 0.7355 (tpp-160) cc_final: 0.7084 (tpp-160) REVERT: H 842 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8211 (m-80) outliers start: 49 outliers final: 37 residues processed: 276 average time/residue: 0.2042 time to fit residues: 90.3634 Evaluate side-chains 274 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 234 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 113 SER Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 187 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 677 GLU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 813 GLU Chi-restraints excluded: chain C residue 866 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 360 VAL Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain G residue 465 LEU Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 716 LEU Chi-restraints excluded: chain G residue 717 MET Chi-restraints excluded: chain G residue 753 ILE Chi-restraints excluded: chain G residue 784 ILE Chi-restraints excluded: chain G residue 821 VAL Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 434 SER Chi-restraints excluded: chain H residue 472 ASP Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 707 THR Chi-restraints excluded: chain H residue 842 PHE Chi-restraints excluded: chain H residue 863 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 186 optimal weight: 2.9990 chunk 203 optimal weight: 0.9980 chunk 296 optimal weight: 0.8980 chunk 223 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 84 optimal weight: 0.0270 chunk 88 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 312 optimal weight: 2.9990 chunk 348 optimal weight: 0.5980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 807 HIS G 552 HIS ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 448 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.132209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.091567 restraints weight = 52762.558| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.18 r_work: 0.2950 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32950 Z= 0.135 Angle : 0.575 10.411 45218 Z= 0.303 Chirality : 0.042 0.158 5016 Planarity : 0.004 0.056 5280 Dihedral : 18.335 152.237 5466 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.34 % Allowed : 10.54 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.14), residues: 3580 helix: 1.88 (0.16), residues: 1078 sheet: 0.03 (0.17), residues: 858 loop : -0.06 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 280 TYR 0.048 0.001 TYR A 296 PHE 0.064 0.002 PHE F 290 TRP 0.013 0.001 TRP H 641 HIS 0.012 0.001 HIS G 552 Details of bonding type rmsd covalent geometry : bond 0.00310 (32936) covalent geometry : angle 0.57456 (45212) hydrogen bonds : bond 0.03493 ( 1387) hydrogen bonds : angle 4.31940 ( 3807) metal coordination : bond 0.01398 ( 14) metal coordination : angle 2.36019 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 248 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 SER cc_start: 0.7997 (m) cc_final: 0.7474 (p) REVERT: A 329 MET cc_start: 0.8411 (tpp) cc_final: 0.7961 (tpp) REVERT: A 668 GLU cc_start: 0.6418 (mm-30) cc_final: 0.6194 (mm-30) REVERT: A 669 GLU cc_start: 0.8636 (tp30) cc_final: 0.7598 (mt-10) REVERT: A 686 LYS cc_start: 0.9083 (tppt) cc_final: 0.8650 (tptp) REVERT: B 172 MET cc_start: 0.8382 (mtp) cc_final: 0.8178 (mtp) REVERT: B 728 ARG cc_start: 0.8953 (ttm170) cc_final: 0.8503 (mtm-85) REVERT: B 733 HIS cc_start: 0.8813 (m170) cc_final: 0.8599 (m170) REVERT: C 449 GLN cc_start: 0.8435 (tm-30) cc_final: 0.8120 (tt0) REVERT: C 811 ARG cc_start: 0.8576 (mtm180) cc_final: 0.8274 (ttp-110) REVERT: C 813 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7853 (pm20) REVERT: F 64 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7612 (ttp80) REVERT: F 288 ARG cc_start: 0.8758 (mtp-110) cc_final: 0.8556 (mtp180) REVERT: F 708 GLU cc_start: 0.9324 (mm-30) cc_final: 0.9075 (mt-10) REVERT: F 711 ARG cc_start: 0.9363 (ptm160) cc_final: 0.8990 (ttm110) REVERT: G 50 MET cc_start: 0.4374 (ptt) cc_final: 0.4132 (ptt) REVERT: G 328 MET cc_start: 0.7240 (mmt) cc_final: 0.5856 (ptm) REVERT: H 785 ARG cc_start: 0.7376 (tpp-160) cc_final: 0.7109 (tpp-160) REVERT: H 842 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.8222 (m-80) outliers start: 43 outliers final: 38 residues processed: 276 average time/residue: 0.1907 time to fit residues: 85.1775 Evaluate side-chains 279 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 238 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 187 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 677 GLU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 813 GLU Chi-restraints excluded: chain C residue 866 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 360 VAL Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain G residue 465 LEU Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 552 HIS Chi-restraints excluded: chain G residue 716 LEU Chi-restraints excluded: chain G residue 717 MET Chi-restraints excluded: chain G residue 753 ILE Chi-restraints excluded: chain G residue 784 ILE Chi-restraints excluded: chain G residue 821 VAL Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 434 SER Chi-restraints excluded: chain H residue 472 ASP Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 707 THR Chi-restraints excluded: chain H residue 818 MET Chi-restraints excluded: chain H residue 842 PHE Chi-restraints excluded: chain H residue 863 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 195 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 288 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 265 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 257 optimal weight: 0.0020 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 807 HIS F 111 GLN G 552 HIS ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 448 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.131547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.091572 restraints weight = 52564.200| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.13 r_work: 0.2935 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 32950 Z= 0.157 Angle : 0.599 18.776 45218 Z= 0.313 Chirality : 0.042 0.185 5016 Planarity : 0.004 0.056 5280 Dihedral : 18.342 151.792 5466 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.50 % Allowed : 10.51 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.14), residues: 3580 helix: 1.92 (0.16), residues: 1078 sheet: -0.02 (0.17), residues: 886 loop : -0.10 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 280 TYR 0.048 0.001 TYR A 296 PHE 0.064 0.002 PHE F 290 TRP 0.014 0.001 TRP G 805 HIS 0.026 0.001 HIS G 552 Details of bonding type rmsd covalent geometry : bond 0.00369 (32936) covalent geometry : angle 0.59799 (45212) hydrogen bonds : bond 0.03609 ( 1387) hydrogen bonds : angle 4.34965 ( 3807) metal coordination : bond 0.01376 ( 14) metal coordination : angle 2.44503 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9080.35 seconds wall clock time: 155 minutes 36.90 seconds (9336.90 seconds total)