Starting phenix.real_space_refine on Sun Aug 9 01:39:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8clj_16714/08_2026/8clj_16714.cif Found real_map, /net/cci-nas-00/data/ceres_data/8clj_16714/08_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_16714/08_2026/8clj_16714.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8clj_16714/08_2026/8clj_16714.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8clj_16714/08_2026/8clj_16714.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8clj_16714/08_2026/8clj_16714.cif" model { file = "/net/cci-nas-00/data/ceres_data/8clj_16714/08_2026/8clj_16714.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8clj_16714/08_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-2.2rc3-6140/lib/python3.11/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: 6.85, 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: 2.61 Conformation dependent library (CDL) restraints added in 1.4 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: 3.96 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: 8.40 Time building geometry restraints manager: 3.34 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=" C3' DT I 10 " pdb=" C2' DT I 10 " ideal model delta sigma weight residual 1.516 1.558 -0.042 8.00e-03 1.56e+04 2.69e+01 bond pdb=" C3' DT D 10 " pdb=" C2' DT D 10 " ideal model delta sigma weight residual 1.516 1.556 -0.040 8.00e-03 1.56e+04 2.52e+01 bond pdb=" C3' DT D 7 " pdb=" C2' DT D 7 " ideal model delta sigma weight residual 1.516 1.555 -0.039 8.00e-03 1.56e+04 2.34e+01 bond pdb=" C3' DT I 7 " pdb=" C2' DT I 7 " ideal model delta sigma weight residual 1.516 1.553 -0.037 8.00e-03 1.56e+04 2.18e+01 bond pdb=" C3' DC E 63 " pdb=" C2' DC E 63 " ideal model delta sigma weight residual 1.516 1.550 -0.034 8.00e-03 1.56e+04 1.79e+01 ... (remaining 32931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 43640 1.95 - 3.90: 1376 3.90 - 5.84: 174 5.84 - 7.79: 20 7.79 - 9.74: 2 Bond angle restraints: 45212 Sorted by residual: angle pdb=" O5' DG D 5 " pdb=" C5' DG D 5 " pdb=" C4' DG D 5 " ideal model delta sigma weight residual 109.40 116.09 -6.69 8.00e-01 1.56e+00 6.98e+01 angle pdb=" O5' DG I 5 " pdb=" C5' DG I 5 " pdb=" C4' DG I 5 " ideal model delta sigma weight residual 109.40 115.57 -6.17 8.00e-01 1.56e+00 5.95e+01 angle pdb=" O5' DA I 4 " pdb=" C5' DA I 4 " pdb=" C4' DA I 4 " ideal model delta sigma weight residual 109.40 115.32 -5.92 8.00e-01 1.56e+00 5.47e+01 angle pdb=" O5' DA D 4 " pdb=" C5' DA D 4 " pdb=" C4' DA D 4 " ideal model delta sigma weight residual 109.40 115.29 -5.89 8.00e-01 1.56e+00 5.41e+01 angle pdb=" O5' DG E 52 " pdb=" C5' DG E 52 " pdb=" C4' DG E 52 " ideal model delta sigma weight residual 109.40 114.91 -5.51 8.00e-01 1.56e+00 4.74e+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 - 0.080: 4359 0.080 - 0.161: 621 0.161 - 0.241: 33 0.241 - 0.321: 1 0.321 - 0.401: 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 -2.73 -2.33 -0.40 2.00e-01 2.50e+01 4.03e+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 -2.73 -2.34 -0.39 2.00e-01 2.50e+01 3.87e+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 2.43 2.17 0.26 2.00e-01 2.50e+01 1.75e+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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 37.130 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.080 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 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 : 0.005 0.069 32950 Z= 0.320 Angle : 0.790 9.740 45218 Z= 0.528 Chirality : 0.053 0.401 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/Z covalent geometry : bond 0.00483 / 0.32 (32936) covalent geometry : angle 0.78826 / 0.53 (45212) hydrogen bonds : bond 0.17179 / 11.30 ( 1387) hydrogen bonds : angle 7.19516 / 5.05 ( 3807) metal coordination : bond 0.02567 / 1.25 ( 14) metal coordination : angle 3.97684 / 1.53 ( 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 : 1.247 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: 0.7973 (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: 0.2323 time to fit residues: 160.3906 Evaluate side-chains 259 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 1.225 ------------------------------------------------------------------------------- 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: 9.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 198 HIS ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 627 ASN B 152 ASN C 687 HIS C 857 GLN C 884 HIS ** F 619 ASN ** 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.132034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.093092 restraints weight = 52948.543| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.06 r_work: 0.2959 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 32950 Z= 0.168 Angle : 0.691 14.718 45218 Z= 0.375 Chirality : 0.047 0.367 5016 Planarity : 0.005 0.094 5280 Dihedral : 18.646 159.324 5466 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.06 % Allowed : 4.72 % Favored : 94.22 % 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: 0.33 (0.14), residues: 3580 helix: 0.75 (0.15), residues: 1062 sheet: 0.25 (0.17), residues: 856 loop : -0.01 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG G 787 TYR 0.040 0.002 TYR A 296 PHE 0.018 0.002 PHE C 317 TRP 0.020 0.002 TRP B 805 HIS 0.009 0.001 HIS G 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (32936) covalent geometry : angle 0.69057 / 0.37 (45212) hydrogen bonds : bond 0.05153 / 3.40 ( 1387) hydrogen bonds : angle 5.23087 / 3.69 ( 3807) metal coordination : bond 0.00728 / 0.40 ( 14) metal coordination : angle 2.04895 / 0.96 ( 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 306 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 272 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ARG cc_start: 0.6617 (ttp80) cc_final: 0.6348 (mmm160) REVERT: A 296 TYR cc_start: 0.7708 (m-80) cc_final: 0.7147 (m-80) REVERT: A 329 MET cc_start: 0.8761 (tpp) cc_final: 0.8163 (tpp) REVERT: A 377 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8097 (mt-10) REVERT: A 623 GLU cc_start: 0.8799 (tt0) cc_final: 0.8487 (tt0) REVERT: A 635 PHE cc_start: 0.8029 (t80) cc_final: 0.7795 (t80) REVERT: B 710 ARG cc_start: 0.8611 (ttm110) cc_final: 0.8280 (ptp-170) REVERT: C 294 MET cc_start: 0.8554 (tpp) cc_final: 0.8253 (mmm) REVERT: C 683 LEU cc_start: 0.8672 (mp) cc_final: 0.8323 (tp) REVERT: F 290 PHE cc_start: 0.8973 (t80) cc_final: 0.8768 (t80) REVERT: F 627 ASN cc_start: 0.8920 (m-40) cc_final: 0.8407 (p0) REVERT: F 630 LEU cc_start: 0.9014 (tt) cc_final: 0.8468 (mp) REVERT: G 328 MET cc_start: 0.7179 (mmt) cc_final: 0.5862 (ptm) REVERT: G 590 LYS cc_start: 0.8093 (ptpp) cc_final: 0.7502 (mtpt) REVERT: G 722 TYR cc_start: 0.6539 (t80) cc_final: 0.6332 (t80) REVERT: H 304 MET cc_start: 0.9105 (mmm) cc_final: 0.8578 (mmm) REVERT: H 785 ARG cc_start: 0.7377 (tpp-160) cc_final: 0.7043 (tpp-160) outliers start: 34 outliers final: 24 residues processed: 294 average time/residue: 0.2218 time to fit residues: 103.4362 Evaluate side-chains 264 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 1.340 ------------------------------------------------------------------------------- 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 696 MET Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain C residue 401 ASP 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 641 ILE 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 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 852 LEU 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: 8.9990 chunk 298 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 274 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 278 optimal weight: 0.5980 chunk 168 optimal weight: 0.9990 chunk 187 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 294 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 ASN G 152 ASN G 304 ASN G 478 HIS 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 = 0.3766 r_free = 0.3766 target = 0.130368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.091148 restraints weight = 53121.263| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.06 r_work: 0.2926 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 32950 Z= 0.212 Angle : 0.663 13.295 45218 Z= 0.356 Chirality : 0.047 0.342 5016 Planarity : 0.005 0.059 5280 Dihedral : 18.757 159.088 5466 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.38 % Allowed : 6.07 % Favored : 92.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.43 (0.14), residues: 3580 helix: 1.08 (0.16), residues: 1070 sheet: 0.08 (0.17), residues: 850 loop : -0.00 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 309 TYR 0.027 0.002 TYR A 296 PHE 0.025 0.002 PHE F 290 TRP 0.019 0.002 TRP B 805 HIS 0.010 0.001 HIS B 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 (32936) covalent geometry : angle 0.66269 / 0.36 (45212) hydrogen bonds : bond 0.04831 / 3.19 ( 1387) hydrogen bonds : angle 4.93956 / 3.50 ( 3807) metal coordination : bond 0.01002 / 0.51 ( 14) metal coordination : angle 2.74288 / 1.37 ( 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 286 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 242 time to evaluate : 1.241 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 296 TYR cc_start: 0.7747 (m-80) cc_final: 0.7547 (m-80) REVERT: A 329 MET cc_start: 0.8913 (tpp) cc_final: 0.8453 (tpp) REVERT: A 623 GLU cc_start: 0.8813 (tt0) cc_final: 0.8549 (tt0) REVERT: A 686 LYS cc_start: 0.8966 (tptp) cc_final: 0.8641 (tptp) REVERT: B 728 ARG cc_start: 0.8640 (ttp-110) cc_final: 0.8010 (mtm-85) REVERT: C 683 LEU cc_start: 0.8708 (mp) cc_final: 0.8207 (tp) REVERT: C 811 ARG cc_start: 0.8577 (mtm180) cc_final: 0.8291 (ttp-110) REVERT: F 294 TYR cc_start: 0.8640 (t80) cc_final: 0.8384 (m-80) REVERT: F 295 GLN cc_start: 0.9093 (pt0) cc_final: 0.8692 (pp30) REVERT: F 623 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8602 (mm-30) REVERT: F 627 ASN cc_start: 0.8906 (m-40) cc_final: 0.8439 (p0) REVERT: F 630 LEU cc_start: 0.8973 (tt) cc_final: 0.8468 (mp) REVERT: G 328 MET cc_start: 0.7223 (mmt) cc_final: 0.5857 (ptm) REVERT: G 590 LYS cc_start: 0.8294 (ptpp) cc_final: 0.7746 (mtpt) REVERT: G 724 ASP cc_start: 0.8377 (t0) cc_final: 0.8130 (t0) REVERT: H 785 ARG cc_start: 0.7383 (tpp-160) cc_final: 0.7002 (tpp-160) outliers start: 44 outliers final: 31 residues processed: 269 average time/residue: 0.2116 time to fit residues: 91.0213 Evaluate side-chains 263 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 232 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 F residue 641 ILE 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 117 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 815 MET Chi-restraints excluded: chain H residue 852 LEU 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: 2.9990 chunk 180 optimal weight: 9.9990 chunk 30 optimal weight: 30.0000 chunk 56 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 27 optimal weight: 30.0000 chunk 366 optimal weight: 20.0000 chunk 69 optimal weight: 0.3980 chunk 142 optimal weight: 0.3980 chunk 65 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 272 HIS B 96 HIS B 368 GLN C 794 HIS C 807 HIS G 552 HIS ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 433 HIS 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 = 0.3764 r_free = 0.3764 target = 0.130171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.090714 restraints weight = 52747.111| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.08 r_work: 0.2919 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 32950 Z= 0.205 Angle : 0.640 12.392 45218 Z= 0.342 Chirality : 0.046 0.326 5016 Planarity : 0.005 0.059 5280 Dihedral : 18.818 158.126 5466 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.78 % Allowed : 7.25 % Favored : 90.96 % 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: 0.42 (0.14), residues: 3580 helix: 1.30 (0.16), residues: 1070 sheet: -0.08 (0.17), residues: 860 loop : -0.07 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 759 TYR 0.028 0.002 TYR G 722 PHE 0.021 0.002 PHE A 290 TRP 0.017 0.001 TRP B 805 HIS 0.013 0.001 HIS B 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (32936) covalent geometry : angle 0.63869 / 0.34 (45212) hydrogen bonds : bond 0.04475 / 2.95 ( 1387) hydrogen bonds : angle 4.79022 / 3.39 ( 3807) metal coordination : bond 0.01103 / 0.58 ( 14) metal coordination : angle 2.91924 / 1.45 ( 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: 57 poor density : 255 time to evaluate : 1.014 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 230 ARG cc_start: 0.6653 (ttp80) cc_final: 0.6398 (mmm160) REVERT: A 255 TYR cc_start: 0.8323 (m-10) cc_final: 0.8068 (m-10) REVERT: A 296 TYR cc_start: 0.7726 (m-80) cc_final: 0.7291 (m-80) REVERT: A 329 MET cc_start: 0.8905 (tpp) cc_final: 0.8492 (tpp) REVERT: A 623 GLU cc_start: 0.8808 (tt0) cc_final: 0.8568 (tt0) REVERT: A 690 LEU cc_start: 0.8659 (mt) cc_final: 0.8392 (pp) REVERT: B 75 ASP cc_start: 0.8270 (t70) cc_final: 0.8037 (t0) REVERT: B 172 MET cc_start: 0.8415 (mtp) cc_final: 0.8168 (mtp) REVERT: B 728 ARG cc_start: 0.8604 (ttp-110) cc_final: 0.7966 (mtm-85) REVERT: B 733 HIS cc_start: 0.8715 (m170) cc_final: 0.8409 (m90) REVERT: C 683 LEU cc_start: 0.8685 (mp) cc_final: 0.8191 (tp) REVERT: C 811 ARG cc_start: 0.8620 (mtm180) cc_final: 0.8364 (ttp-110) REVERT: C 813 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7672 (pm20) REVERT: C 866 VAL cc_start: 0.8514 (OUTLIER) cc_final: 0.8178 (t) REVERT: F 72 GLN cc_start: 0.6025 (mt0) cc_final: 0.5822 (mt0) REVERT: F 294 TYR cc_start: 0.8676 (t80) cc_final: 0.8420 (m-80) REVERT: F 295 GLN cc_start: 0.9018 (pt0) cc_final: 0.8813 (pt0) REVERT: F 297 MET cc_start: 0.8492 (mmm) cc_final: 0.7908 (tpp) REVERT: F 329 MET cc_start: 0.8249 (mmm) cc_final: 0.7994 (mmm) REVERT: F 623 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8720 (mm-30) REVERT: F 630 LEU cc_start: 0.8946 (tt) cc_final: 0.8453 (mp) REVERT: G 328 MET cc_start: 0.7234 (mmt) cc_final: 0.5806 (ptm) REVERT: G 590 LYS cc_start: 0.8319 (ptpp) cc_final: 0.7712 (mtpt) REVERT: H 785 ARG cc_start: 0.7425 (tpp-160) cc_final: 0.7051 (tpp-160) REVERT: H 842 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.8139 (m-80) outliers start: 57 outliers final: 35 residues processed: 296 average time/residue: 0.2039 time to fit residues: 96.2514 Evaluate side-chains 267 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 229 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 298 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 636 THR 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 794 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 43 THR 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 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 552 HIS 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 725 ILE 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: 2.9990 chunk 73 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 235 optimal weight: 20.0000 chunk 298 optimal weight: 4.9990 chunk 318 optimal weight: 1.9990 chunk 272 optimal weight: 0.9990 chunk 285 optimal weight: 0.2980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 807 HIS ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.130746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.090081 restraints weight = 52819.249| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.43 r_work: 0.2929 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 32950 Z= 0.167 Angle : 0.609 12.232 45218 Z= 0.327 Chirality : 0.045 0.327 5016 Planarity : 0.004 0.059 5280 Dihedral : 18.787 157.886 5466 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.69 % Allowed : 8.29 % Favored : 90.03 % 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: 0.45 (0.14), residues: 3580 helix: 1.43 (0.16), residues: 1072 sheet: -0.11 (0.17), residues: 866 loop : -0.12 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 711 TYR 0.032 0.001 TYR G 722 PHE 0.039 0.002 PHE A 635 TRP 0.015 0.001 TRP C 402 HIS 0.030 0.001 HIS G 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (32936) covalent geometry : angle 0.60798 / 0.33 (45212) hydrogen bonds : bond 0.04236 / 2.79 ( 1387) hydrogen bonds : angle 4.66596 / 3.32 ( 3807) metal coordination : bond 0.01160 / 0.63 ( 14) metal coordination : angle 2.69924 / 1.33 ( 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 297 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 243 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 TYR cc_start: 0.8318 (m-10) cc_final: 0.8076 (m-10) REVERT: A 296 TYR cc_start: 0.7735 (m-80) cc_final: 0.7325 (m-80) REVERT: A 329 MET cc_start: 0.9009 (tpp) cc_final: 0.8612 (tpp) REVERT: A 623 GLU cc_start: 0.8798 (tt0) cc_final: 0.8580 (tt0) REVERT: B 75 ASP cc_start: 0.8178 (t70) cc_final: 0.7978 (t0) REVERT: B 172 MET cc_start: 0.8408 (mtp) cc_final: 0.8170 (mtp) REVERT: B 710 ARG cc_start: 0.8929 (ttm170) cc_final: 0.8700 (mtm180) REVERT: B 728 ARG cc_start: 0.8659 (ttp-110) cc_final: 0.8001 (mtm-85) REVERT: B 733 HIS cc_start: 0.8797 (m170) cc_final: 0.8543 (m90) REVERT: C 449 GLN cc_start: 0.8522 (tm-30) cc_final: 0.7997 (tt0) REVERT: C 683 LEU cc_start: 0.8675 (mp) cc_final: 0.8173 (tp) REVERT: C 811 ARG cc_start: 0.8649 (mtm180) cc_final: 0.8363 (ttp-110) REVERT: C 813 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7692 (pm20) REVERT: C 866 VAL cc_start: 0.8501 (OUTLIER) cc_final: 0.8170 (t) REVERT: F 294 TYR cc_start: 0.8785 (t80) cc_final: 0.8455 (m-80) REVERT: F 295 GLN cc_start: 0.9049 (pt0) cc_final: 0.8721 (pt0) REVERT: F 297 MET cc_start: 0.8508 (mmm) cc_final: 0.7874 (tpp) REVERT: F 329 MET cc_start: 0.8388 (mmm) cc_final: 0.7778 (tpp) REVERT: F 623 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8671 (mm-30) REVERT: F 630 LEU cc_start: 0.8943 (tt) cc_final: 0.8451 (mp) REVERT: F 711 ARG cc_start: 0.9182 (ptp-110) cc_final: 0.8949 (ttm110) REVERT: G 50 MET cc_start: 0.4351 (ptt) cc_final: 0.4006 (ptt) REVERT: G 328 MET cc_start: 0.7253 (mmt) cc_final: 0.5812 (ptm) REVERT: G 590 LYS cc_start: 0.8318 (ptpp) cc_final: 0.7674 (mtpt) REVERT: H 785 ARG cc_start: 0.7373 (tpp-160) cc_final: 0.6991 (tpp-160) REVERT: H 842 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8165 (m-80) outliers start: 54 outliers final: 35 residues processed: 281 average time/residue: 0.1913 time to fit residues: 87.5817 Evaluate side-chains 266 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 228 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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 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 43 THR 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 117 LEU Chi-restraints excluded: chain G residue 465 LEU Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 753 ILE Chi-restraints excluded: chain G residue 763 VAL 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 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: 0.6980 chunk 234 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 0.0980 chunk 277 optimal weight: 1.9990 chunk 30 optimal weight: 20.0000 chunk 358 optimal weight: 8.9990 chunk 272 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 360 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3769 r_free = 0.3769 target = 0.130580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.091071 restraints weight = 52772.175| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.07 r_work: 0.2921 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.2618 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= 0.172 Angle : 0.610 15.050 45218 Z= 0.325 Chirality : 0.045 0.323 5016 Planarity : 0.004 0.059 5280 Dihedral : 18.770 157.372 5466 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.75 % Allowed : 9.35 % Favored : 88.90 % 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: 0.51 (0.14), residues: 3580 helix: 1.57 (0.16), residues: 1072 sheet: -0.10 (0.17), residues: 850 loop : -0.14 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 230 TYR 0.019 0.001 TYR G 722 PHE 0.036 0.002 PHE F 635 TRP 0.014 0.001 TRP B 805 HIS 0.007 0.001 HIS G 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (32936) covalent geometry : angle 0.60923 / 0.32 (45212) hydrogen bonds : bond 0.04105 / 2.70 ( 1387) hydrogen bonds : angle 4.57337 / 3.26 ( 3807) metal coordination : bond 0.01195 / 0.66 ( 14) metal coordination : angle 2.64365 / 1.28 ( 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 295 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 239 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 TYR cc_start: 0.8280 (m-10) cc_final: 0.8064 (m-10) REVERT: A 292 ARG cc_start: 0.8216 (mmm160) cc_final: 0.7750 (mmm160) REVERT: A 296 TYR cc_start: 0.7757 (m-10) cc_final: 0.7268 (m-80) REVERT: A 623 GLU cc_start: 0.8778 (tt0) cc_final: 0.8563 (tt0) REVERT: B 75 ASP cc_start: 0.8194 (t70) cc_final: 0.7994 (t0) REVERT: B 172 MET cc_start: 0.8410 (mtp) cc_final: 0.8176 (mtp) REVERT: B 441 CYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8377 (t) REVERT: B 728 ARG cc_start: 0.8603 (ttp-110) cc_final: 0.7948 (mtm-85) REVERT: C 449 GLN cc_start: 0.8511 (tm-30) cc_final: 0.8077 (tt0) REVERT: C 683 LEU cc_start: 0.8667 (mp) cc_final: 0.8179 (tp) REVERT: C 811 ARG cc_start: 0.8633 (mtm180) cc_final: 0.8360 (ttp-110) REVERT: C 813 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7650 (pm20) REVERT: F 297 MET cc_start: 0.8443 (mmm) cc_final: 0.7830 (tpp) REVERT: F 329 MET cc_start: 0.8179 (mmm) cc_final: 0.7528 (tpp) REVERT: F 623 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8666 (mm-30) REVERT: F 711 ARG cc_start: 0.9089 (ptp-110) cc_final: 0.8847 (ttm110) REVERT: G 50 MET cc_start: 0.4359 (ptt) cc_final: 0.4131 (ptt) REVERT: G 328 MET cc_start: 0.7254 (mmt) cc_final: 0.5838 (ptm) REVERT: H 785 ARG cc_start: 0.7358 (tpp-160) cc_final: 0.6991 (tpp-160) REVERT: H 842 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.8170 (m-80) outliers start: 56 outliers final: 37 residues processed: 283 average time/residue: 0.1986 time to fit residues: 91.6497 Evaluate side-chains 267 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 227 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 50 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 43 THR 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 717 MET Chi-restraints excluded: chain G residue 763 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 221 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 64 optimal weight: 0.0770 chunk 116 optimal weight: 0.9980 chunk 329 optimal weight: 0.9990 chunk 324 optimal weight: 0.6980 chunk 279 optimal weight: 1.9990 chunk 362 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 733 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 = 0.3783 r_free = 0.3783 target = 0.131646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.092319 restraints weight = 52901.700| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.13 r_work: 0.2946 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2787 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= 0.133 Angle : 0.579 11.617 45218 Z= 0.310 Chirality : 0.044 0.325 5016 Planarity : 0.004 0.059 5280 Dihedral : 18.710 157.179 5466 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.59 % Allowed : 9.85 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.64 (0.14), residues: 3580 helix: 1.69 (0.16), residues: 1072 sheet: -0.03 (0.17), residues: 858 loop : -0.06 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 811 TYR 0.018 0.001 TYR A 294 PHE 0.047 0.001 PHE A 290 TRP 0.015 0.001 TRP H 641 HIS 0.014 0.001 HIS B 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (32936) covalent geometry : angle 0.57869 / 0.31 (45212) hydrogen bonds : bond 0.03856 / 2.54 ( 1387) hydrogen bonds : angle 4.45307 / 3.18 ( 3807) metal coordination : bond 0.01249 / 0.71 ( 14) metal coordination : angle 2.41321 / 1.13 ( 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 299 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 248 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 SER cc_start: 0.7895 (m) cc_final: 0.7429 (p) REVERT: A 296 TYR cc_start: 0.7671 (m-10) cc_final: 0.7315 (m-80) REVERT: A 329 MET cc_start: 0.8399 (tpp) cc_final: 0.7913 (tpp) REVERT: A 629 ARG cc_start: 0.8588 (mmm-85) cc_final: 0.7980 (mmm-85) REVERT: A 686 LYS cc_start: 0.9041 (tptp) cc_final: 0.8600 (tptp) REVERT: B 172 MET cc_start: 0.8390 (mtp) cc_final: 0.8159 (mtp) REVERT: B 441 CYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8439 (t) REVERT: B 710 ARG cc_start: 0.8787 (ttm170) cc_final: 0.8292 (ptp-170) REVERT: B 728 ARG cc_start: 0.8637 (ttp-110) cc_final: 0.7961 (mtm-85) REVERT: C 449 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8051 (tt0) REVERT: C 811 ARG cc_start: 0.8639 (mtm180) cc_final: 0.8344 (ttp-110) REVERT: C 813 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7860 (pm20) REVERT: F 290 PHE cc_start: 0.8741 (t80) cc_final: 0.7753 (t80) REVERT: F 297 MET cc_start: 0.8316 (mmm) cc_final: 0.7768 (tpp) REVERT: F 329 MET cc_start: 0.8369 (mmm) cc_final: 0.7700 (tpp) REVERT: F 623 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8642 (mm-30) REVERT: F 711 ARG cc_start: 0.9126 (ptp-110) cc_final: 0.8910 (ttm110) REVERT: G 50 MET cc_start: 0.4303 (ptt) cc_final: 0.4023 (ptt) REVERT: G 328 MET cc_start: 0.7221 (mmt) cc_final: 0.5834 (ptm) REVERT: G 590 LYS cc_start: 0.8445 (ptpt) cc_final: 0.8124 (mttt) REVERT: H 785 ARG cc_start: 0.7412 (tpp-160) cc_final: 0.7056 (tpp-160) REVERT: H 842 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8235 (m-80) outliers start: 51 outliers final: 34 residues processed: 285 average time/residue: 0.2006 time to fit residues: 92.2840 Evaluate side-chains 269 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 232 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 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 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 G residue 117 LEU Chi-restraints excluded: chain G residue 325 ASN 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 717 MET Chi-restraints excluded: chain G residue 763 VAL 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 417 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 88 optimal weight: 0.6980 chunk 226 optimal weight: 0.9980 chunk 292 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 283 optimal weight: 3.9990 chunk 270 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 288 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 807 HIS F 295 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 = 0.3776 r_free = 0.3776 target = 0.131116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.090878 restraints weight = 52741.819| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.17 r_work: 0.2917 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2863 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= 0.161 Angle : 0.596 11.208 45218 Z= 0.316 Chirality : 0.044 0.324 5016 Planarity : 0.004 0.058 5280 Dihedral : 18.706 156.877 5466 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.38 % Allowed : 10.29 % Favored : 88.34 % 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: 0.64 (0.14), residues: 3580 helix: 1.68 (0.16), residues: 1076 sheet: -0.03 (0.17), residues: 856 loop : -0.07 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 713 TYR 0.019 0.001 TYR F 294 PHE 0.044 0.002 PHE F 635 TRP 0.014 0.001 TRP B 805 HIS 0.007 0.001 HIS G 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (32936) covalent geometry : angle 0.59514 / 0.32 (45212) hydrogen bonds : bond 0.03904 / 2.56 ( 1387) hydrogen bonds : angle 4.43589 / 3.16 ( 3807) metal coordination : bond 0.01232 / 0.69 ( 14) metal coordination : angle 2.42902 / 1.13 ( 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 285 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 241 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 SER cc_start: 0.7870 (m) cc_final: 0.7393 (p) REVERT: A 329 MET cc_start: 0.8385 (tpp) cc_final: 0.7907 (tpp) REVERT: A 629 ARG cc_start: 0.8604 (mmm-85) cc_final: 0.8126 (mmm-85) REVERT: A 686 LYS cc_start: 0.9045 (tptp) cc_final: 0.8611 (tptp) REVERT: B 172 MET cc_start: 0.8205 (mtp) cc_final: 0.7976 (mtp) REVERT: B 441 CYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8245 (t) REVERT: B 728 ARG cc_start: 0.8680 (ttp-110) cc_final: 0.8037 (mtm-85) REVERT: C 449 GLN cc_start: 0.8355 (tm-30) cc_final: 0.8076 (tt0) REVERT: C 811 ARG cc_start: 0.8457 (mtm180) cc_final: 0.8196 (ttp-110) REVERT: C 813 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7731 (pm20) REVERT: F 64 ARG cc_start: 0.7842 (ttp-110) cc_final: 0.7495 (tmm160) REVERT: F 297 MET cc_start: 0.8217 (mmm) cc_final: 0.7807 (tpp) REVERT: F 329 MET cc_start: 0.8321 (mmm) cc_final: 0.7626 (tpp) REVERT: F 623 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8545 (mm-30) REVERT: G 50 MET cc_start: 0.4407 (ptt) cc_final: 0.4159 (ptt) REVERT: G 328 MET cc_start: 0.7112 (mmt) cc_final: 0.5764 (ptm) REVERT: G 590 LYS cc_start: 0.8449 (ptpt) cc_final: 0.8158 (mttt) REVERT: H 785 ARG cc_start: 0.7221 (tpp-160) cc_final: 0.6929 (tpp-160) REVERT: H 842 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.8195 (m-80) outliers start: 44 outliers final: 37 residues processed: 275 average time/residue: 0.1998 time to fit residues: 89.5377 Evaluate side-chains 267 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 227 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 441 CYS 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 238 HIS Chi-restraints excluded: chain F residue 641 ILE 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 716 LEU Chi-restraints excluded: chain G residue 717 MET Chi-restraints excluded: chain G residue 753 ILE Chi-restraints excluded: chain G residue 763 VAL 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 594 ILE Chi-restraints excluded: chain H residue 653 ILE Chi-restraints excluded: chain H residue 710 SER Chi-restraints excluded: chain H residue 808 ASP 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: 9.9990 chunk 98 optimal weight: 0.6980 chunk 244 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 239 optimal weight: 0.9990 chunk 268 optimal weight: 3.9990 chunk 253 optimal weight: 0.6980 chunk 187 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 733 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 807 HIS F 295 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 = 0.3774 r_free = 0.3774 target = 0.130979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.090851 restraints weight = 52455.846| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.16 r_work: 0.2921 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 32950 Z= 0.162 Angle : 0.599 11.073 45218 Z= 0.319 Chirality : 0.044 0.326 5016 Planarity : 0.004 0.058 5280 Dihedral : 18.699 156.675 5466 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.34 % Allowed : 10.82 % Favored : 87.84 % 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: 0.64 (0.14), residues: 3580 helix: 1.69 (0.16), residues: 1074 sheet: -0.01 (0.17), residues: 866 loop : -0.08 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 811 TYR 0.050 0.002 TYR A 296 PHE 0.072 0.002 PHE F 290 TRP 0.014 0.001 TRP B 805 HIS 0.018 0.001 HIS B 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (32936) covalent geometry : angle 0.59844 / 0.32 (45212) hydrogen bonds : bond 0.03888 / 2.55 ( 1387) hydrogen bonds : angle 4.44873 / 3.17 ( 3807) metal coordination : bond 0.01264 / 0.71 ( 14) metal coordination : angle 2.51970 / 1.17 ( 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 284 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 241 time to evaluate : 1.085 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: 0.7891 (m) cc_final: 0.7381 (p) REVERT: A 292 ARG cc_start: 0.8295 (mmm160) cc_final: 0.7933 (mmm160) REVERT: A 329 MET cc_start: 0.8369 (tpp) cc_final: 0.7892 (tpp) REVERT: A 629 ARG cc_start: 0.8558 (mmm-85) cc_final: 0.7923 (mmm-85) REVERT: B 172 MET cc_start: 0.8201 (mtp) cc_final: 0.7966 (mtp) REVERT: B 710 ARG cc_start: 0.8705 (ttm170) cc_final: 0.8247 (ptp-170) REVERT: C 449 GLN cc_start: 0.8351 (tm-30) cc_final: 0.8078 (tt0) REVERT: C 811 ARG cc_start: 0.8428 (mtm180) cc_final: 0.8169 (ttp-110) REVERT: C 813 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7726 (pm20) REVERT: F 64 ARG cc_start: 0.7851 (ttp-110) cc_final: 0.7328 (ttp80) REVERT: F 297 MET cc_start: 0.8111 (mmm) cc_final: 0.7822 (tpp) REVERT: F 329 MET cc_start: 0.8319 (mmm) cc_final: 0.7625 (tpp) REVERT: F 623 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8613 (mm-30) REVERT: F 673 ARG cc_start: 0.8047 (mmm-85) cc_final: 0.7585 (mmm-85) REVERT: G 50 MET cc_start: 0.4388 (ptt) cc_final: 0.4146 (ptt) REVERT: G 328 MET cc_start: 0.7107 (mmt) cc_final: 0.5728 (ptm) REVERT: G 590 LYS cc_start: 0.8462 (ptpt) cc_final: 0.8171 (mttt) REVERT: H 785 ARG cc_start: 0.7201 (tpp-160) cc_final: 0.6910 (tpp-160) REVERT: H 842 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8198 (m-80) outliers start: 43 outliers final: 36 residues processed: 273 average time/residue: 0.2029 time to fit residues: 89.9729 Evaluate side-chains 270 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 232 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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 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 672 VAL Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 813 GLU Chi-restraints excluded: chain C residue 866 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain F residue 641 ILE 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 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 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 710 SER 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: 1.9990 chunk 203 optimal weight: 0.7980 chunk 296 optimal weight: 0.9980 chunk 223 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 chunk 312 optimal weight: 1.9990 chunk 348 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 733 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 807 HIS ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3784 r_free = 0.3784 target = 0.131771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.091665 restraints weight = 52796.782| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.13 r_work: 0.2936 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32950 Z= 0.138 Angle : 0.586 11.092 45218 Z= 0.312 Chirality : 0.043 0.328 5016 Planarity : 0.004 0.058 5280 Dihedral : 18.667 156.525 5466 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.47 % Allowed : 10.76 % Favored : 87.77 % 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: 0.70 (0.14), residues: 3580 helix: 1.75 (0.16), residues: 1078 sheet: 0.02 (0.17), residues: 866 loop : -0.06 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 711 TYR 0.043 0.001 TYR A 296 PHE 0.063 0.002 PHE F 290 TRP 0.015 0.001 TRP B 805 HIS 0.019 0.001 HIS B 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (32936) covalent geometry : angle 0.58518 / 0.31 (45212) hydrogen bonds : bond 0.03763 / 2.47 ( 1387) hydrogen bonds : angle 4.40728 / 3.15 ( 3807) metal coordination : bond 0.01326 / 0.76 ( 14) metal coordination : angle 2.39116 / 1.08 ( 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 290 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 243 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 SER cc_start: 0.7942 (m) cc_final: 0.7439 (p) REVERT: A 292 ARG cc_start: 0.8263 (mmm160) cc_final: 0.7857 (mmm160) REVERT: A 329 MET cc_start: 0.8494 (tpp) cc_final: 0.8045 (tpp) REVERT: A 629 ARG cc_start: 0.8613 (mmm-85) cc_final: 0.7928 (mmm-85) REVERT: B 172 MET cc_start: 0.8429 (mtp) cc_final: 0.8201 (mtp) REVERT: B 733 HIS cc_start: 0.8652 (m170) cc_final: 0.8410 (m90) REVERT: C 449 GLN cc_start: 0.8491 (tm-30) cc_final: 0.8137 (tt0) REVERT: C 469 CYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7894 (m) REVERT: C 811 ARG cc_start: 0.8628 (mtm180) cc_final: 0.8319 (ttp-110) REVERT: C 813 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7913 (pm20) REVERT: F 64 ARG cc_start: 0.7983 (ttp-110) cc_final: 0.7736 (ttp80) REVERT: F 288 ARG cc_start: 0.8746 (mtp-110) cc_final: 0.8490 (mtp85) REVERT: F 290 PHE cc_start: 0.8730 (t80) cc_final: 0.8257 (t80) REVERT: F 297 MET cc_start: 0.8122 (mmm) cc_final: 0.7820 (tpp) REVERT: F 329 MET cc_start: 0.8472 (mmm) cc_final: 0.7744 (tpp) REVERT: F 623 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8708 (mm-30) REVERT: G 50 MET cc_start: 0.4335 (ptt) cc_final: 0.4079 (ptt) REVERT: G 328 MET cc_start: 0.7238 (mmt) cc_final: 0.5862 (ptm) REVERT: G 590 LYS cc_start: 0.8434 (ptpt) cc_final: 0.8158 (mttt) REVERT: H 785 ARG cc_start: 0.7418 (tpp-160) cc_final: 0.7093 (tpp-160) REVERT: H 842 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8220 (m-80) outliers start: 47 outliers final: 41 residues processed: 277 average time/residue: 0.2024 time to fit residues: 91.3325 Evaluate side-chains 276 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 232 time to evaluate : 1.152 ------------------------------------------------------------------------------- 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 677 GLU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 469 CYS Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 813 GLU Chi-restraints excluded: chain C residue 866 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 89 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 475 VAL Chi-restraints excluded: chain G residue 540 ILE 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 291 CYS 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 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: 0.7980 chunk 33 optimal weight: 1.9990 chunk 288 optimal weight: 0.7980 chunk 135 optimal weight: 0.1980 chunk 265 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 151 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 257 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 733 HIS B 797 HIS C 807 HIS ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 552 HIS ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 448 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- 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 = 33)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.092157 restraints weight = 52652.299| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.14 r_work: 0.2942 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32950 Z= 0.131 Angle : 0.587 11.041 45218 Z= 0.313 Chirality : 0.043 0.332 5016 Planarity : 0.004 0.058 5280 Dihedral : 18.634 156.158 5466 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.41 % Allowed : 11.01 % Favored : 87.59 % 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: 0.72 (0.14), residues: 3580 helix: 1.79 (0.16), residues: 1078 sheet: 0.03 (0.17), residues: 866 loop : -0.06 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 673 TYR 0.056 0.001 TYR A 296 PHE 0.042 0.001 PHE A 635 TRP 0.022 0.001 TRP G 805 HIS 0.019 0.001 HIS B 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (32936) covalent geometry : angle 0.58673 / 0.31 (45212) hydrogen bonds : bond 0.03699 / 2.42 ( 1387) hydrogen bonds : angle 4.37188 / 3.12 ( 3807) metal coordination : bond 0.01379 / 0.80 ( 14) metal coordination : angle 2.33024 / 1.03 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8770.06 seconds wall clock time: 150 minutes 49.08 seconds (9049.08 seconds total)