Starting phenix.real_space_refine on Wed Feb 21 20:45:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8clj_16714/02_2024/8clj_16714.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8clj_16714/02_2024/8clj_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8clj_16714/02_2024/8clj_16714.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8clj_16714/02_2024/8clj_16714.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8clj_16714/02_2024/8clj_16714.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8clj_16714/02_2024/8clj_16714.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: 16.40, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.56 Conformation dependent library (CDL) restraints added in 5.8 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: 11.37 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: 14.88 Time building geometry restraints manager: 14.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 10059 1.35 - 1.48: 8843 1.48 - 1.61: 13753 1.61 - 1.74: 7 1.74 - 1.88: 274 Bond restraints: 32936 Sorted by residual: bond pdb=" CB CYS G 817 " pdb=" SG CYS G 817 " ideal model delta sigma weight residual 1.808 1.877 -0.069 3.30e-02 9.18e+02 4.42e+00 bond pdb=" CB CYS G 773 " pdb=" SG CYS G 773 " ideal model delta sigma weight residual 1.808 1.752 0.056 3.30e-02 9.18e+02 2.86e+00 bond pdb=" C4' DT D 10 " pdb=" O4' DT D 10 " ideal model delta sigma weight residual 1.450 1.417 0.033 2.00e-02 2.50e+03 2.73e+00 bond pdb=" C3' DT I 10 " pdb=" C2' DT I 10 " ideal model delta sigma weight residual 1.525 1.558 -0.033 2.00e-02 2.50e+03 2.65e+00 bond pdb=" C3' DT D 10 " pdb=" C2' DT D 10 " ideal model delta sigma weight residual 1.525 1.556 -0.031 2.00e-02 2.50e+03 2.43e+00 ... (remaining 32931 not shown) Histogram of bond angle deviations from ideal: 98.26 - 105.45: 1352 105.45 - 112.63: 17140 112.63 - 119.82: 11426 119.82 - 127.00: 14490 127.00 - 134.18: 804 Bond angle restraints: 45212 Sorted by residual: angle pdb=" C4' DG I 6 " pdb=" C3' DG I 6 " pdb=" O3' DG I 6 " ideal model delta sigma weight residual 110.00 115.87 -5.87 1.50e+00 4.44e-01 1.53e+01 angle pdb=" C CYS G 817 " pdb=" N ASP G 818 " pdb=" CA ASP G 818 " ideal model delta sigma weight residual 121.24 115.63 5.61 1.44e+00 4.82e-01 1.52e+01 angle pdb=" C4' DG D 6 " pdb=" C3' DG D 6 " pdb=" O3' DG D 6 " ideal model delta sigma weight residual 110.00 115.59 -5.59 1.50e+00 4.44e-01 1.39e+01 angle pdb=" C3' DG D 6 " pdb=" O3' DG D 6 " pdb=" P DT D 7 " ideal model delta sigma weight residual 120.20 125.76 -5.56 1.50e+00 4.44e-01 1.37e+01 angle pdb=" C3' DG I 6 " pdb=" O3' DG I 6 " pdb=" P DT I 7 " ideal model delta sigma weight residual 120.20 125.63 -5.43 1.50e+00 4.44e-01 1.31e+01 ... (remaining 45207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.19: 18594 32.19 - 64.37: 835 64.37 - 96.56: 49 96.56 - 128.74: 0 128.74 - 160.93: 4 Dihedral angle restraints: 19482 sinusoidal: 8948 harmonic: 10534 Sorted by residual: dihedral pdb=" CA GLU B 68 " pdb=" C GLU B 68 " pdb=" N PRO B 69 " pdb=" CA PRO B 69 " ideal model delta harmonic sigma weight residual -180.00 -150.90 -29.10 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA LEU G 459 " pdb=" C LEU G 459 " pdb=" N LYS G 460 " pdb=" CA LYS G 460 " ideal model delta harmonic sigma weight residual 180.00 151.20 28.80 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA LYS G 364 " pdb=" C LYS G 364 " pdb=" N GLU G 365 " pdb=" CA GLU G 365 " ideal model delta harmonic sigma weight residual -180.00 -151.30 -28.70 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 19479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 4147 0.066 - 0.132: 798 0.132 - 0.199: 66 0.199 - 0.265: 3 0.265 - 0.331: 2 Chirality restraints: 5016 Sorted by residual: chirality pdb=" C3' DG I 6 " pdb=" C4' DG I 6 " pdb=" O3' DG I 6 " pdb=" C2' DG I 6 " both_signs ideal model delta sigma weight residual False -2.66 -2.33 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C3' DG D 6 " pdb=" C4' DG D 6 " pdb=" O3' DG D 6 " pdb=" C2' DG D 6 " both_signs ideal model delta sigma weight residual False -2.66 -2.34 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" C1' DA D 18 " pdb=" O4' DA D 18 " pdb=" C2' DA D 18 " pdb=" N9 DA D 18 " both_signs ideal model delta sigma weight residual False 2.42 2.17 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 5013 not shown) Planarity restraints: 5280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 186 " -0.307 9.50e-02 1.11e+02 1.39e-01 1.53e+01 pdb=" NE ARG A 186 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 186 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG A 186 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 186 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 26 " -0.034 2.00e-02 2.50e+03 2.54e-02 1.45e+01 pdb=" N1 DC I 26 " 0.060 2.00e-02 2.50e+03 pdb=" C2 DC I 26 " -0.028 2.00e-02 2.50e+03 pdb=" O2 DC I 26 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DC I 26 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC I 26 " -0.004 2.00e-02 2.50e+03 pdb=" N4 DC I 26 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DC I 26 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DC I 26 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 796 " 0.294 9.50e-02 1.11e+02 1.33e-01 1.42e+01 pdb=" NE ARG B 796 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 796 " 0.029 2.00e-02 2.50e+03 pdb=" NH1 ARG B 796 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG B 796 " -0.000 2.00e-02 2.50e+03 ... (remaining 5277 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 117 2.54 - 3.13: 24323 3.13 - 3.72: 50034 3.72 - 4.31: 72988 4.31 - 4.90: 119373 Nonbonded interactions: 266835 Sorted by model distance: nonbonded pdb=" OD2 ASP G 792 " pdb="ZN ZN G 902 " model vdw 1.951 2.230 nonbonded pdb=" OD1 ASP B 792 " pdb="ZN ZN B 901 " model vdw 1.983 2.230 nonbonded pdb=" OD1 ASP G 792 " pdb="ZN ZN G 902 " model vdw 1.987 2.230 nonbonded pdb=" OD2 ASP B 792 " pdb="ZN ZN B 901 " model vdw 2.035 2.230 nonbonded pdb=" CG ASP G 792 " pdb="ZN ZN G 902 " model vdw 2.166 2.460 ... (remaining 266830 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 23.990 Check model and map are aligned: 0.530 Set scattering table: 0.290 Process input model: 98.810 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 32936 Z= 0.287 Angle : 0.754 9.740 45212 Z= 0.436 Chirality : 0.051 0.331 5016 Planarity : 0.010 0.139 5280 Dihedral : 16.677 160.927 12658 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.13), 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 TRP 0.034 0.003 TRP H 471 HIS 0.007 0.001 HIS F 210 PHE 0.020 0.002 PHE C 700 TYR 0.025 0.005 TYR B 439 ARG 0.033 0.003 ARG G 796 *********************** 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 fitting. rotamer outliers: 0 poor density : 447 time to evaluate : 3.666 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: 0.6483 (ttp80) cc_final: 0.6082 (mmm160) REVERT: A 255 TYR cc_start: 0.8276 (m-10) cc_final: 0.7972 (m-10) REVERT: A 708 GLU cc_start: 0.9470 (mm-30) cc_final: 0.9248 (mm-30) 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 294 TYR cc_start: 0.8946 (t80) cc_final: 0.8547 (t80) REVERT: F 295 GLN cc_start: 0.9024 (pt0) cc_final: 0.8561 (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: 0.9233 (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: 0.4930 time to fit residues: 334.9711 Evaluate side-chains 259 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 3.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 312 optimal weight: 2.9990 chunk 280 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 290 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 176 optimal weight: 0.7980 chunk 215 optimal weight: 8.9990 chunk 336 optimal weight: 0.0770 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 627 ASN B 152 ASN B 240 GLN C 687 HIS C 857 GLN C 884 HIS ** F 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 627 ASN G 114 ASN G 152 ASN G 189 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: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32936 Z= 0.219 Angle : 0.640 14.785 45212 Z= 0.344 Chirality : 0.044 0.160 5016 Planarity : 0.005 0.049 5280 Dihedral : 18.566 157.266 5466 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.00 % Allowed : 4.69 % Favored : 94.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.14), residues: 3580 helix: 0.88 (0.16), residues: 1070 sheet: 0.36 (0.17), residues: 854 loop : 0.05 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 805 HIS 0.009 0.001 HIS G 552 PHE 0.015 0.002 PHE F 290 TYR 0.047 0.001 TYR A 296 ARG 0.005 0.001 ARG G 190 *********************** 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 fitting. rotamer outliers: 32 poor density : 274 time to evaluate : 4.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 TYR cc_start: 0.7863 (m-80) cc_final: 0.7329 (m-80) REVERT: A 329 MET cc_start: 0.9123 (tpp) cc_final: 0.8886 (tpp) REVERT: A 377 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8077 (mt-10) REVERT: A 444 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8319 (mt0) REVERT: A 623 GLU cc_start: 0.8771 (tt0) cc_final: 0.8448 (tt0) REVERT: A 635 PHE cc_start: 0.7762 (t80) cc_final: 0.7550 (t80) REVERT: A 642 MET cc_start: 0.8548 (mtp) cc_final: 0.8346 (mtp) REVERT: A 708 GLU cc_start: 0.9455 (mm-30) cc_final: 0.9210 (mm-30) REVERT: B 75 ASP cc_start: 0.7869 (t0) cc_final: 0.7522 (t0) REVERT: B 733 HIS cc_start: 0.8925 (m170) cc_final: 0.8671 (m90) REVERT: C 683 LEU cc_start: 0.8641 (mp) cc_final: 0.8198 (tp) REVERT: F 302 LEU cc_start: 0.7474 (mm) cc_final: 0.7084 (pp) REVERT: F 630 LEU cc_start: 0.8981 (tt) cc_final: 0.8460 (mp) REVERT: G 206 VAL cc_start: 0.8991 (p) cc_final: 0.8763 (m) REVERT: G 328 MET cc_start: 0.6905 (mmt) cc_final: 0.5613 (ptm) REVERT: H 304 MET cc_start: 0.9162 (mmm) cc_final: 0.8741 (mmm) REVERT: H 785 ARG cc_start: 0.6774 (tpp-160) cc_final: 0.6451 (tpp-160) outliers start: 32 outliers final: 21 residues processed: 291 average time/residue: 0.4642 time to fit residues: 214.3423 Evaluate side-chains 253 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 232 time to evaluate : 3.781 ------------------------------------------------------------------------------- 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 427 VAL Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain F residue 642 MET Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 696 MET 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 710 ARG Chi-restraints excluded: chain G residue 784 ILE Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 434 SER Chi-restraints excluded: chain H residue 472 ASP Chi-restraints excluded: chain H residue 725 ILE Chi-restraints excluded: chain H residue 863 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 186 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 279 optimal weight: 0.0670 chunk 228 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 336 optimal weight: 0.0370 chunk 363 optimal weight: 4.9990 chunk 299 optimal weight: 9.9990 chunk 333 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 270 optimal weight: 2.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32936 Z= 0.243 Angle : 0.602 13.441 45212 Z= 0.320 Chirality : 0.043 0.157 5016 Planarity : 0.004 0.054 5280 Dihedral : 18.498 156.485 5466 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.72 % Allowed : 5.78 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.14), residues: 3580 helix: 1.33 (0.16), residues: 1072 sheet: 0.24 (0.17), residues: 844 loop : 0.04 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 805 HIS 0.009 0.001 HIS G 552 PHE 0.024 0.002 PHE F 635 TYR 0.030 0.001 TYR A 296 ARG 0.006 0.000 ARG F 711 *********************** 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 302 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 247 time to evaluate : 3.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 TYR cc_start: 0.8361 (m-10) cc_final: 0.8012 (m-10) REVERT: A 296 TYR cc_start: 0.7868 (m-80) cc_final: 0.7386 (m-80) REVERT: A 329 MET cc_start: 0.9159 (tpp) cc_final: 0.8681 (tpp) REVERT: A 377 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8096 (mt-10) REVERT: A 444 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8283 (mt0) REVERT: A 623 GLU cc_start: 0.8750 (tt0) cc_final: 0.8506 (tt0) REVERT: A 686 LYS cc_start: 0.8954 (tptp) cc_final: 0.8643 (tptp) REVERT: A 690 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8464 (pp) REVERT: B 172 MET cc_start: 0.8391 (mtp) cc_final: 0.8079 (mtp) REVERT: B 328 MET cc_start: 0.6809 (mmt) cc_final: 0.6528 (mmp) REVERT: B 681 MET cc_start: 0.8485 (tpt) cc_final: 0.8285 (tpt) REVERT: B 728 ARG cc_start: 0.8903 (ttm170) cc_final: 0.7754 (ttm170) REVERT: B 793 SER cc_start: 0.8667 (p) cc_final: 0.8402 (p) REVERT: C 683 LEU cc_start: 0.8609 (mp) cc_final: 0.8003 (tp) REVERT: C 813 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7683 (pm20) REVERT: F 64 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7305 (ttp80) REVERT: F 290 PHE cc_start: 0.8974 (t80) cc_final: 0.7718 (t80) REVERT: F 293 LEU cc_start: 0.9652 (mp) cc_final: 0.9438 (tp) REVERT: F 294 TYR cc_start: 0.8963 (t80) cc_final: 0.8700 (m-80) REVERT: F 623 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8581 (mm-30) REVERT: F 630 LEU cc_start: 0.8940 (tt) cc_final: 0.8419 (mp) REVERT: F 689 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7309 (p0) REVERT: G 50 MET cc_start: 0.4000 (ptt) cc_final: 0.3701 (ptt) REVERT: G 328 MET cc_start: 0.6991 (mmt) cc_final: 0.5599 (ptm) REVERT: G 724 ASP cc_start: 0.8490 (t0) cc_final: 0.8287 (t0) REVERT: G 778 GLN cc_start: 0.8371 (tt0) cc_final: 0.8139 (tt0) REVERT: H 785 ARG cc_start: 0.6721 (tpp-160) cc_final: 0.6369 (tpp-160) REVERT: H 882 ARG cc_start: 0.8503 (tpp80) cc_final: 0.8287 (mtp-110) outliers start: 55 outliers final: 29 residues processed: 282 average time/residue: 0.4519 time to fit residues: 202.8400 Evaluate side-chains 264 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 231 time to evaluate : 3.325 ------------------------------------------------------------------------------- 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 672 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 691 VAL 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 C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 813 GLU Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 642 MET Chi-restraints excluded: chain F residue 689 ASP 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 710 ARG 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 758 ASP Chi-restraints excluded: chain H residue 863 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 332 optimal weight: 0.9990 chunk 253 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 226 optimal weight: 0.9980 chunk 337 optimal weight: 0.9980 chunk 357 optimal weight: 0.0170 chunk 176 optimal weight: 0.7980 chunk 320 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 GLN B 733 HIS C 584 ASN C 807 HIS ** F 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 295 GLN F 647 GLN G 304 ASN G 552 HIS ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 448 GLN H 523 GLN H 838 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32936 Z= 0.201 Angle : 0.562 12.910 45212 Z= 0.299 Chirality : 0.042 0.153 5016 Planarity : 0.004 0.056 5280 Dihedral : 18.421 155.189 5466 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.69 % Allowed : 7.29 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.14), residues: 3580 helix: 1.59 (0.16), residues: 1072 sheet: 0.22 (0.17), residues: 860 loop : 0.04 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 805 HIS 0.010 0.001 HIS G 552 PHE 0.029 0.001 PHE A 290 TYR 0.022 0.001 TYR A 296 ARG 0.006 0.000 ARG F 711 *********************** 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 302 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 248 time to evaluate : 3.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 TYR cc_start: 0.8279 (m-10) cc_final: 0.7860 (m-10) REVERT: A 292 ARG cc_start: 0.8391 (mmm160) cc_final: 0.7937 (mmm160) REVERT: A 296 TYR cc_start: 0.7839 (m-80) cc_final: 0.7205 (m-80) REVERT: A 377 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8079 (mt-10) REVERT: A 444 GLN cc_start: 0.8581 (mm-40) cc_final: 0.8275 (mt0) REVERT: A 623 GLU cc_start: 0.8720 (tt0) cc_final: 0.8504 (tt0) REVERT: A 669 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6790 (mt-10) REVERT: A 686 LYS cc_start: 0.8920 (tptp) cc_final: 0.8550 (tptp) REVERT: B 172 MET cc_start: 0.8369 (mtp) cc_final: 0.8049 (mtp) REVERT: B 793 SER cc_start: 0.8811 (p) cc_final: 0.8553 (p) REVERT: C 683 LEU cc_start: 0.8614 (mp) cc_final: 0.8002 (tp) REVERT: C 813 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7719 (pm20) REVERT: F 64 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7275 (ttp80) REVERT: F 294 TYR cc_start: 0.8932 (t80) cc_final: 0.8696 (m-80) REVERT: F 297 MET cc_start: 0.8398 (ptp) cc_final: 0.8021 (mtm) REVERT: F 329 MET cc_start: 0.8460 (mmm) cc_final: 0.7809 (tpp) REVERT: F 623 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8509 (mm-30) REVERT: F 676 ARG cc_start: 0.9159 (tpp-160) cc_final: 0.8891 (tpp-160) REVERT: G 50 MET cc_start: 0.4003 (ptt) cc_final: 0.3728 (ptt) REVERT: G 328 MET cc_start: 0.6951 (mmt) cc_final: 0.5593 (ptm) REVERT: G 778 GLN cc_start: 0.8392 (tt0) cc_final: 0.8163 (tt0) REVERT: H 725 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8741 (tt) REVERT: H 785 ARG cc_start: 0.6779 (tpp-160) cc_final: 0.6428 (tpp-160) REVERT: H 842 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.8057 (m-80) outliers start: 54 outliers final: 29 residues processed: 284 average time/residue: 0.4861 time to fit residues: 221.6478 Evaluate side-chains 257 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 224 time to evaluate : 3.681 ------------------------------------------------------------------------------- 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 672 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 733 HIS 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 F residue 64 ARG Chi-restraints excluded: chain F residue 642 MET Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 702 LEU Chi-restraints excluded: chain G residue 117 LEU 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 784 ILE Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 368 ASP Chi-restraints excluded: chain H residue 472 ASP Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 653 ILE Chi-restraints excluded: chain H residue 725 ILE Chi-restraints excluded: chain H residue 842 PHE 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 297 optimal weight: 0.9990 chunk 203 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 266 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 305 optimal weight: 0.8980 chunk 247 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 182 optimal weight: 10.0000 chunk 321 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 733 HIS C 467 ASN C 807 HIS ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 295 GLN ** G 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 552 HIS ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 433 HIS H 448 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32936 Z= 0.220 Angle : 0.566 12.225 45212 Z= 0.300 Chirality : 0.042 0.175 5016 Planarity : 0.004 0.056 5280 Dihedral : 18.393 154.588 5466 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.75 % Allowed : 8.10 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.14), residues: 3580 helix: 1.72 (0.16), residues: 1072 sheet: 0.19 (0.17), residues: 860 loop : 0.01 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 805 HIS 0.010 0.001 HIS G 552 PHE 0.028 0.001 PHE A 290 TYR 0.016 0.001 TYR A 296 ARG 0.005 0.000 ARG F 711 *********************** 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 298 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 242 time to evaluate : 3.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 SER cc_start: 0.7675 (m) cc_final: 0.7294 (p) REVERT: A 255 TYR cc_start: 0.8356 (m-10) cc_final: 0.8063 (m-10) REVERT: A 296 TYR cc_start: 0.7826 (m-80) cc_final: 0.7399 (m-80) REVERT: A 329 MET cc_start: 0.8894 (tpp) cc_final: 0.8497 (tpp) REVERT: A 377 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8080 (mt-10) REVERT: A 444 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8287 (mt0) REVERT: B 172 MET cc_start: 0.8366 (mtp) cc_final: 0.8084 (mtp) REVERT: B 728 ARG cc_start: 0.8656 (ttm110) cc_final: 0.7917 (mtm-85) REVERT: B 793 SER cc_start: 0.8861 (p) cc_final: 0.8590 (p) REVERT: C 683 LEU cc_start: 0.8600 (mp) cc_final: 0.7980 (tp) REVERT: C 811 ARG cc_start: 0.8309 (mtm180) cc_final: 0.7911 (ttp-110) REVERT: C 813 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7692 (pm20) REVERT: F 64 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7286 (ttp80) REVERT: F 329 MET cc_start: 0.8566 (mmm) cc_final: 0.7881 (tpp) REVERT: F 623 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8708 (mm-30) REVERT: F 676 ARG cc_start: 0.9155 (tpp-160) cc_final: 0.8851 (tpp-160) REVERT: G 50 MET cc_start: 0.4023 (ptt) cc_final: 0.3733 (ptt) REVERT: G 328 MET cc_start: 0.6984 (mmt) cc_final: 0.5703 (ptm) REVERT: G 753 ILE cc_start: 0.8204 (pt) cc_final: 0.7999 (tt) REVERT: H 785 ARG cc_start: 0.6808 (tpp-160) cc_final: 0.6473 (tpp-160) REVERT: H 842 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8072 (m-80) outliers start: 56 outliers final: 35 residues processed: 280 average time/residue: 0.4493 time to fit residues: 201.5757 Evaluate side-chains 268 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 230 time to evaluate : 3.518 ------------------------------------------------------------------------------- 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 672 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL 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 F residue 64 ARG Chi-restraints excluded: chain F residue 205 ASP 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 716 LEU Chi-restraints excluded: chain G residue 784 ILE Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 368 ASP Chi-restraints excluded: chain H residue 472 ASP Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 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 120 optimal weight: 3.9990 chunk 322 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 209 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 357 optimal weight: 0.7980 chunk 297 optimal weight: 0.6980 chunk 165 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 187 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 HIS C 807 HIS F 295 GLN F 647 GLN ** G 324 ASN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32936 Z= 0.201 Angle : 0.553 11.771 45212 Z= 0.293 Chirality : 0.041 0.155 5016 Planarity : 0.004 0.056 5280 Dihedral : 18.359 154.157 5466 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.63 % Allowed : 8.79 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.14), residues: 3580 helix: 1.78 (0.16), residues: 1076 sheet: 0.17 (0.17), residues: 860 loop : 0.02 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 805 HIS 0.022 0.001 HIS G 552 PHE 0.034 0.001 PHE A 635 TYR 0.015 0.001 TYR A 296 ARG 0.004 0.000 ARG G 84 *********************** 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 297 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 245 time to evaluate : 3.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 SER cc_start: 0.7616 (m) cc_final: 0.7227 (p) REVERT: A 255 TYR cc_start: 0.8358 (m-10) cc_final: 0.8078 (m-10) REVERT: A 296 TYR cc_start: 0.7784 (m-80) cc_final: 0.7444 (m-80) REVERT: A 377 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8078 (mt-10) REVERT: A 444 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8281 (mt0) REVERT: B 172 MET cc_start: 0.8351 (mtp) cc_final: 0.8083 (mtp) REVERT: B 728 ARG cc_start: 0.8613 (ttm110) cc_final: 0.7930 (mtm-85) REVERT: B 793 SER cc_start: 0.8897 (p) cc_final: 0.8629 (p) REVERT: C 449 GLN cc_start: 0.8385 (tm-30) cc_final: 0.7916 (tt0) REVERT: C 683 LEU cc_start: 0.8603 (mp) cc_final: 0.7979 (tp) REVERT: C 811 ARG cc_start: 0.8344 (mtm180) cc_final: 0.7931 (ttp-110) REVERT: C 813 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7689 (pm20) REVERT: F 64 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7293 (ttp80) REVERT: F 329 MET cc_start: 0.8528 (mmm) cc_final: 0.7865 (tpp) REVERT: F 623 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8689 (mm-30) REVERT: G 50 MET cc_start: 0.3961 (ptt) cc_final: 0.3687 (ptt) REVERT: G 328 MET cc_start: 0.6980 (mmt) cc_final: 0.5709 (ptm) REVERT: G 778 GLN cc_start: 0.8351 (tt0) cc_final: 0.8122 (tt0) REVERT: H 785 ARG cc_start: 0.6752 (tpp-160) cc_final: 0.6442 (tpp-160) REVERT: H 842 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8061 (m-80) outliers start: 52 outliers final: 35 residues processed: 283 average time/residue: 0.4290 time to fit residues: 195.9324 Evaluate side-chains 272 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 234 time to evaluate : 3.406 ------------------------------------------------------------------------------- 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 672 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 813 GLU Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 294 TYR Chi-restraints excluded: chain F residue 642 MET Chi-restraints excluded: chain F residue 660 VAL 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 538 ASP Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 710 ARG Chi-restraints excluded: chain G residue 716 LEU 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 653 ILE Chi-restraints excluded: chain H residue 707 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 345 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 203 optimal weight: 0.9990 chunk 261 optimal weight: 2.9990 chunk 202 optimal weight: 0.9990 chunk 301 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 chunk 356 optimal weight: 5.9990 chunk 223 optimal weight: 0.7980 chunk 217 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 807 HIS F 295 GLN F 647 GLN ** G 324 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 32936 Z= 0.229 Angle : 0.565 11.230 45212 Z= 0.299 Chirality : 0.042 0.165 5016 Planarity : 0.004 0.056 5280 Dihedral : 18.355 153.536 5466 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.66 % Allowed : 9.47 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.14), residues: 3580 helix: 1.81 (0.16), residues: 1076 sheet: 0.16 (0.17), residues: 852 loop : 0.00 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 805 HIS 0.010 0.001 HIS G 552 PHE 0.037 0.002 PHE A 290 TYR 0.018 0.001 TYR A 294 ARG 0.007 0.000 ARG F 711 *********************** 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 310 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 257 time to evaluate : 3.309 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: 0.7637 (m) cc_final: 0.7246 (p) REVERT: A 255 TYR cc_start: 0.8350 (m-10) cc_final: 0.8072 (m-10) REVERT: A 296 TYR cc_start: 0.7690 (m-80) cc_final: 0.7386 (m-80) REVERT: A 329 MET cc_start: 0.8743 (tpp) cc_final: 0.8299 (tpp) REVERT: A 377 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8092 (mt-10) REVERT: A 444 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8284 (mt0) REVERT: A 629 ARG cc_start: 0.8634 (mmm-85) cc_final: 0.7875 (mmm-85) REVERT: A 686 LYS cc_start: 0.9091 (tppt) cc_final: 0.8645 (tptp) REVERT: B 172 MET cc_start: 0.8352 (mtp) cc_final: 0.8076 (mtp) REVERT: B 441 CYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8218 (t) REVERT: B 793 SER cc_start: 0.8945 (p) cc_final: 0.8671 (p) REVERT: C 449 GLN cc_start: 0.8409 (tm-30) cc_final: 0.7950 (tt0) REVERT: C 683 LEU cc_start: 0.8595 (mp) cc_final: 0.7974 (tp) REVERT: C 811 ARG cc_start: 0.8329 (mtm180) cc_final: 0.7916 (ttp-110) REVERT: C 813 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7695 (pm20) REVERT: F 64 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7243 (ttp80) REVERT: F 329 MET cc_start: 0.8553 (mmm) cc_final: 0.7863 (tpp) REVERT: F 623 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8676 (mm-30) REVERT: F 673 ARG cc_start: 0.7812 (mmt90) cc_final: 0.7575 (mmm-85) REVERT: F 676 ARG cc_start: 0.9147 (tpp-160) cc_final: 0.8878 (tpp-160) REVERT: G 50 MET cc_start: 0.4035 (ptt) cc_final: 0.3748 (ptt) REVERT: G 328 MET cc_start: 0.6977 (mmt) cc_final: 0.5709 (ptm) REVERT: G 778 GLN cc_start: 0.8400 (tt0) cc_final: 0.8158 (tt0) REVERT: H 785 ARG cc_start: 0.6783 (tpp-160) cc_final: 0.6457 (tpp-160) REVERT: H 842 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8084 (m-80) outliers start: 53 outliers final: 40 residues processed: 292 average time/residue: 0.4569 time to fit residues: 213.8985 Evaluate side-chains 280 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 236 time to evaluate : 3.454 ------------------------------------------------------------------------------- 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 628 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain B residue 80 VAL 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 736 LYS 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 F residue 64 ARG Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain F residue 294 TYR Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain 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 538 ASP Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 710 ARG Chi-restraints excluded: chain G residue 716 LEU 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 707 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 220 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 212 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 226 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 280 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 HIS C 807 HIS F 295 GLN F 647 GLN ** G 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 511 GLN G 552 HIS ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 448 GLN H 793 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 32936 Z= 0.269 Angle : 0.580 10.882 45212 Z= 0.306 Chirality : 0.042 0.158 5016 Planarity : 0.004 0.056 5280 Dihedral : 18.371 152.952 5466 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.75 % Allowed : 9.54 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.14), residues: 3580 helix: 1.86 (0.16), residues: 1076 sheet: 0.12 (0.17), residues: 842 loop : -0.05 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 402 HIS 0.011 0.001 HIS G 552 PHE 0.040 0.002 PHE A 635 TYR 0.016 0.001 TYR H 755 ARG 0.011 0.000 ARG B 685 *********************** 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 295 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 239 time to evaluate : 3.336 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: 0.7694 (m) cc_final: 0.7258 (p) REVERT: A 255 TYR cc_start: 0.8361 (m-10) cc_final: 0.8068 (m-10) REVERT: A 296 TYR cc_start: 0.7642 (m-80) cc_final: 0.7397 (m-80) REVERT: A 329 MET cc_start: 0.8798 (tpp) cc_final: 0.8363 (tpp) REVERT: A 377 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8090 (mt-10) REVERT: A 444 GLN cc_start: 0.8514 (mm-40) cc_final: 0.8291 (mt0) REVERT: A 686 LYS cc_start: 0.9011 (tppt) cc_final: 0.8606 (tptp) REVERT: B 172 MET cc_start: 0.8365 (mtp) cc_final: 0.8067 (mtp) REVERT: B 441 CYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8211 (t) REVERT: B 681 MET cc_start: 0.8507 (tpt) cc_final: 0.8292 (tpt) REVERT: B 793 SER cc_start: 0.8976 (p) cc_final: 0.8711 (p) REVERT: C 449 GLN cc_start: 0.8427 (tm-30) cc_final: 0.7989 (tt0) REVERT: C 683 LEU cc_start: 0.8577 (mp) cc_final: 0.7949 (tp) REVERT: C 811 ARG cc_start: 0.8311 (mtm180) cc_final: 0.7893 (ttp-110) REVERT: C 813 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8004 (pm20) REVERT: F 64 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7243 (ttp80) REVERT: F 329 MET cc_start: 0.8546 (mmm) cc_final: 0.7855 (tpp) REVERT: F 623 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8492 (mm-30) REVERT: F 673 ARG cc_start: 0.7858 (mmt90) cc_final: 0.7640 (mmm-85) REVERT: F 676 ARG cc_start: 0.9145 (tpp-160) cc_final: 0.8864 (tpp-160) REVERT: G 50 MET cc_start: 0.4195 (ptt) cc_final: 0.3925 (ptt) REVERT: G 328 MET cc_start: 0.6956 (mmt) cc_final: 0.5620 (ptm) REVERT: G 778 GLN cc_start: 0.8404 (tt0) cc_final: 0.8002 (mt0) REVERT: H 785 ARG cc_start: 0.6764 (tpp-160) cc_final: 0.6449 (tpp-160) REVERT: H 842 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8119 (m-80) outliers start: 56 outliers final: 40 residues processed: 281 average time/residue: 0.4688 time to fit residues: 208.6000 Evaluate side-chains 274 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 230 time to evaluate : 3.392 ------------------------------------------------------------------------------- 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 628 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 813 GLU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 294 TYR Chi-restraints excluded: chain F residue 660 VAL 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 538 ASP Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 552 HIS Chi-restraints excluded: chain G residue 710 ARG Chi-restraints excluded: chain G residue 716 LEU 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 707 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 324 optimal weight: 1.9990 chunk 341 optimal weight: 0.9990 chunk 311 optimal weight: 0.8980 chunk 332 optimal weight: 0.7980 chunk 200 optimal weight: 3.9990 chunk 144 optimal weight: 0.6980 chunk 260 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 300 optimal weight: 5.9990 chunk 314 optimal weight: 0.9980 chunk 331 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 584 ASN C 807 HIS F 295 GLN F 647 GLN F 681 GLN ** G 324 ASN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32936 Z= 0.221 Angle : 0.576 17.285 45212 Z= 0.303 Chirality : 0.042 0.180 5016 Planarity : 0.004 0.062 5280 Dihedral : 18.338 152.682 5466 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.50 % Allowed : 9.76 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.14), residues: 3580 helix: 1.91 (0.16), residues: 1076 sheet: 0.14 (0.17), residues: 852 loop : -0.04 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 402 HIS 0.029 0.001 HIS G 552 PHE 0.043 0.001 PHE A 635 TYR 0.017 0.001 TYR F 294 ARG 0.004 0.000 ARG F 288 *********************** 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 292 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 244 time to evaluate : 3.634 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: 0.7685 (m) cc_final: 0.7249 (p) REVERT: A 329 MET cc_start: 0.8776 (tpp) cc_final: 0.8338 (tpp) REVERT: A 377 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8107 (mt-10) REVERT: A 444 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8291 (mt0) REVERT: A 686 LYS cc_start: 0.8950 (tppt) cc_final: 0.8542 (tptp) REVERT: B 172 MET cc_start: 0.8342 (mtp) cc_final: 0.8076 (mtp) REVERT: B 441 CYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8215 (t) REVERT: B 681 MET cc_start: 0.8607 (tpt) cc_final: 0.8316 (tpt) REVERT: B 793 SER cc_start: 0.9005 (p) cc_final: 0.8736 (p) REVERT: C 449 GLN cc_start: 0.8417 (tm-30) cc_final: 0.8016 (tt0) REVERT: C 683 LEU cc_start: 0.8569 (mp) cc_final: 0.7945 (tp) REVERT: C 811 ARG cc_start: 0.8302 (mtm180) cc_final: 0.7913 (ttp-110) REVERT: C 813 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8009 (pm20) REVERT: F 64 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7230 (ttp80) REVERT: F 623 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8733 (mm-30) REVERT: F 672 LEU cc_start: 0.9149 (pp) cc_final: 0.8892 (pp) REVERT: F 673 ARG cc_start: 0.7910 (mmt90) cc_final: 0.7685 (mmm-85) REVERT: F 676 ARG cc_start: 0.9133 (tpp-160) cc_final: 0.8842 (tpp-160) REVERT: G 50 MET cc_start: 0.4227 (ptt) cc_final: 0.3970 (ptt) REVERT: G 222 ARG cc_start: 0.7819 (mmt180) cc_final: 0.7573 (mmm-85) REVERT: G 328 MET cc_start: 0.6969 (mmt) cc_final: 0.5620 (ptm) REVERT: G 586 GLN cc_start: 0.8841 (mm-40) cc_final: 0.7665 (mm-40) REVERT: G 778 GLN cc_start: 0.8417 (tt0) cc_final: 0.8002 (mt0) REVERT: H 785 ARG cc_start: 0.6760 (tpp-160) cc_final: 0.6485 (tpp-160) REVERT: H 842 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.8090 (m-80) outliers start: 48 outliers final: 39 residues processed: 274 average time/residue: 0.4642 time to fit residues: 204.1287 Evaluate side-chains 279 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 236 time to evaluate : 3.842 ------------------------------------------------------------------------------- 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 672 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 813 GLU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 294 TYR Chi-restraints excluded: chain F residue 660 VAL 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 538 ASP Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 552 HIS Chi-restraints excluded: chain G residue 710 ARG Chi-restraints excluded: chain G residue 716 LEU Chi-restraints excluded: chain G residue 753 ILE Chi-restraints excluded: chain G residue 784 ILE Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 368 ASP Chi-restraints excluded: chain H residue 434 SER Chi-restraints excluded: chain H residue 472 ASP Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 707 THR 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 218 optimal weight: 0.8980 chunk 351 optimal weight: 0.0970 chunk 214 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 chunk 244 optimal weight: 0.2980 chunk 368 optimal weight: 4.9990 chunk 339 optimal weight: 0.5980 chunk 293 optimal weight: 0.9990 chunk 30 optimal weight: 20.0000 chunk 226 optimal weight: 0.9980 chunk 179 optimal weight: 10.0000 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 807 HIS ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 647 GLN F 681 GLN ** G 324 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32936 Z= 0.176 Angle : 0.563 11.485 45212 Z= 0.296 Chirality : 0.041 0.156 5016 Planarity : 0.004 0.057 5280 Dihedral : 18.296 152.450 5466 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.44 % Allowed : 9.82 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.14), residues: 3580 helix: 1.97 (0.16), residues: 1076 sheet: 0.14 (0.17), residues: 866 loop : -0.00 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 641 HIS 0.025 0.001 HIS G 552 PHE 0.043 0.001 PHE A 635 TYR 0.013 0.001 TYR H 755 ARG 0.009 0.000 ARG F 711 ********************** 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 289 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 243 time to evaluate : 3.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 SER cc_start: 0.7652 (m) cc_final: 0.7232 (p) REVERT: A 329 MET cc_start: 0.8781 (tpp) cc_final: 0.8359 (tpp) REVERT: A 377 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8104 (mt-10) REVERT: A 444 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8292 (mt0) REVERT: A 686 LYS cc_start: 0.8990 (tppt) cc_final: 0.8580 (tptp) REVERT: B 172 MET cc_start: 0.8326 (mtp) cc_final: 0.8071 (mtp) REVERT: B 441 CYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8201 (t) REVERT: B 710 ARG cc_start: 0.8420 (ttm170) cc_final: 0.8006 (ptp-170) REVERT: B 793 SER cc_start: 0.9027 (p) cc_final: 0.8765 (p) REVERT: C 449 GLN cc_start: 0.8389 (tm-30) cc_final: 0.8003 (tt0) REVERT: C 683 LEU cc_start: 0.8553 (mp) cc_final: 0.8128 (tp) REVERT: C 811 ARG cc_start: 0.8293 (mtm180) cc_final: 0.7915 (ttp-110) REVERT: C 813 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8003 (pm20) REVERT: F 64 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7211 (ttp80) REVERT: F 623 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8731 (mm-30) REVERT: F 672 LEU cc_start: 0.9154 (pp) cc_final: 0.8891 (pp) REVERT: F 673 ARG cc_start: 0.7988 (mmt90) cc_final: 0.7786 (mmm-85) REVERT: F 676 ARG cc_start: 0.9129 (tpp-160) cc_final: 0.8833 (tpp-160) REVERT: F 711 ARG cc_start: 0.9369 (ttm110) cc_final: 0.8966 (tpp80) REVERT: G 50 MET cc_start: 0.4236 (ptt) cc_final: 0.3969 (ptt) REVERT: G 222 ARG cc_start: 0.7796 (mmt180) cc_final: 0.7561 (mmm-85) REVERT: G 328 MET cc_start: 0.7033 (mmt) cc_final: 0.5746 (ptm) REVERT: G 586 GLN cc_start: 0.8844 (mm-40) cc_final: 0.7678 (mm-40) REVERT: G 778 GLN cc_start: 0.8412 (tt0) cc_final: 0.8000 (mt0) REVERT: H 785 ARG cc_start: 0.6758 (tpp-160) cc_final: 0.6486 (tpp-160) REVERT: H 842 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.8068 (m-80) outliers start: 46 outliers final: 38 residues processed: 274 average time/residue: 0.4551 time to fit residues: 200.7577 Evaluate side-chains 278 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 236 time to evaluate : 3.401 ------------------------------------------------------------------------------- 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 628 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 813 GLU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain G residue 465 LEU Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 710 ARG Chi-restraints excluded: chain G residue 716 LEU Chi-restraints excluded: chain G residue 753 ILE Chi-restraints excluded: chain G residue 784 ILE Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 368 ASP Chi-restraints excluded: chain H residue 434 SER Chi-restraints excluded: chain H residue 472 ASP Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 653 ILE Chi-restraints excluded: chain H residue 707 THR 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 233 optimal weight: 2.9990 chunk 312 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 270 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 81 optimal weight: 0.0470 chunk 293 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 301 optimal weight: 0.1980 chunk 37 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 807 HIS F 295 GLN ** G 324 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.131503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.092504 restraints weight = 52774.801| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.04 r_work: 0.2950 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32936 Z= 0.239 Angle : 0.584 14.452 45212 Z= 0.306 Chirality : 0.042 0.161 5016 Planarity : 0.004 0.055 5280 Dihedral : 18.310 151.794 5466 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.66 % Allowed : 9.69 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.14), residues: 3580 helix: 1.98 (0.16), residues: 1076 sheet: 0.12 (0.17), residues: 880 loop : -0.03 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 805 HIS 0.013 0.001 HIS G 552 PHE 0.040 0.002 PHE A 635 TYR 0.041 0.001 TYR A 296 ARG 0.007 0.000 ARG F 711 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6766.19 seconds wall clock time: 124 minutes 7.28 seconds (7447.28 seconds total)