Starting phenix.real_space_refine on Sun Aug 11 08:46:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8clj_16714/08_2024/8clj_16714.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8clj_16714/08_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_16714/08_2024/8clj_16714.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8clj_16714/08_2024/8clj_16714.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8clj_16714/08_2024/8clj_16714.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8clj_16714/08_2024/8clj_16714.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 18.30, per 1000 atoms: 0.57 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: 13.82 Conformation dependent library (CDL) restraints added in 5.5 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: 12.73 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: 15.27 Time building geometry restraints manager: 15.07 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 Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.960 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: 0.040 Extract box with map and model: 1.390 Check model and map are aligned: 0.250 Set scattering table: 0.330 Process input model: 104.690 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.690 ------------------------------------------------------------------------------- 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 : 3.504 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: 0.5039 time to fit residues: 343.5213 Evaluate side-chains 259 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 3.726 ------------------------------------------------------------------------------- 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: 0.6980 chunk 149 optimal weight: 0.1980 chunk 290 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 215 optimal weight: 10.0000 chunk 336 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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: 0.8349 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32936 Z= 0.209 Angle : 0.645 15.206 45212 Z= 0.348 Chirality : 0.044 0.161 5016 Planarity : 0.005 0.051 5280 Dihedral : 18.539 156.547 5466 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.00 % Allowed : 4.57 % Favored : 94.43 % 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: 0.45 (0.14), residues: 3580 helix: 0.87 (0.15), residues: 1072 sheet: 0.33 (0.17), residues: 866 loop : 0.04 (0.15), residues: 1642 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 0.016 0.002 PHE F 290 TYR 0.047 0.002 TYR A 296 ARG 0.008 0.001 ARG A 713 *********************** 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 314 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 282 time to evaluate : 3.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 TYR cc_start: 0.7848 (m-80) cc_final: 0.7282 (m-80) REVERT: A 329 MET cc_start: 0.9075 (tpp) cc_final: 0.8831 (tpp) REVERT: A 444 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8317 (mt0) REVERT: A 623 GLU cc_start: 0.8774 (tt0) cc_final: 0.8457 (tt0) REVERT: A 635 PHE cc_start: 0.7723 (t80) cc_final: 0.7462 (t80) REVERT: A 642 MET cc_start: 0.8567 (mtp) cc_final: 0.8363 (mtp) REVERT: A 686 LYS cc_start: 0.9009 (tptp) cc_final: 0.8554 (tptp) REVERT: A 708 GLU cc_start: 0.9457 (mm-30) cc_final: 0.9216 (mm-30) REVERT: B 75 ASP cc_start: 0.7945 (t0) cc_final: 0.7667 (t0) REVERT: B 733 HIS cc_start: 0.8938 (m170) cc_final: 0.8688 (m90) REVERT: C 683 LEU cc_start: 0.8650 (mp) cc_final: 0.8011 (tp) REVERT: C 811 ARG cc_start: 0.8397 (mtm180) cc_final: 0.8071 (ttp-110) REVERT: F 64 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7484 (ttp80) REVERT: F 302 LEU cc_start: 0.7532 (mm) cc_final: 0.7134 (pp) REVERT: F 630 LEU cc_start: 0.9002 (tt) cc_final: 0.8497 (mp) REVERT: G 328 MET cc_start: 0.6901 (mmt) cc_final: 0.5654 (ptm) REVERT: G 778 GLN cc_start: 0.8327 (tt0) cc_final: 0.8112 (tt0) REVERT: H 304 MET cc_start: 0.9150 (mmm) cc_final: 0.8693 (mmm) REVERT: H 785 ARG cc_start: 0.6843 (tpp-160) cc_final: 0.6511 (tpp-160) outliers start: 32 outliers final: 20 residues processed: 300 average time/residue: 0.4616 time to fit residues: 217.4003 Evaluate side-chains 255 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 234 time to evaluate : 3.603 ------------------------------------------------------------------------------- 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 616 VAL Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 642 MET Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 702 LEU Chi-restraints excluded: chain G residue 465 LEU Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 784 ILE Chi-restraints excluded: chain H residue 368 ASP Chi-restraints excluded: chain H residue 434 SER Chi-restraints excluded: chain H residue 472 ASP Chi-restraints excluded: chain H residue 725 ILE Chi-restraints excluded: chain H residue 863 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 186 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 279 optimal weight: 2.9990 chunk 228 optimal weight: 0.0170 chunk 92 optimal weight: 5.9990 chunk 336 optimal weight: 0.6980 chunk 363 optimal weight: 5.9990 chunk 299 optimal weight: 0.7980 chunk 333 optimal weight: 0.0770 chunk 114 optimal weight: 10.0000 chunk 270 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 ASN B 797 HIS C 467 ASN G 304 ASN G 552 HIS ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 448 GLN H 838 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2241 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= 0.183 Angle : 0.579 14.168 45212 Z= 0.311 Chirality : 0.042 0.156 5016 Planarity : 0.004 0.055 5280 Dihedral : 18.438 156.457 5466 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.50 % Allowed : 5.66 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.14), residues: 3580 helix: 1.38 (0.16), residues: 1072 sheet: 0.31 (0.17), residues: 844 loop : 0.10 (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 0.035 0.002 PHE A 290 TYR 0.034 0.001 TYR G 722 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 315 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 267 time to evaluate : 3.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 TYR cc_start: 0.8299 (m-10) cc_final: 0.7957 (m-10) REVERT: A 296 TYR cc_start: 0.7876 (m-80) cc_final: 0.7400 (m-80) REVERT: A 329 MET cc_start: 0.9135 (tpp) cc_final: 0.8664 (tpp) REVERT: A 444 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8279 (mt0) REVERT: A 623 GLU cc_start: 0.8782 (tt0) cc_final: 0.8491 (tt0) REVERT: A 686 LYS cc_start: 0.9087 (tptp) cc_final: 0.8822 (tptp) REVERT: A 708 GLU cc_start: 0.9461 (mm-30) cc_final: 0.9213 (mm-30) REVERT: B 75 ASP cc_start: 0.8031 (t0) cc_final: 0.7700 (t0) REVERT: B 172 MET cc_start: 0.8346 (mtp) cc_final: 0.8040 (mtp) REVERT: B 728 ARG cc_start: 0.8916 (ttm170) cc_final: 0.7716 (ttm170) REVERT: C 683 LEU cc_start: 0.8604 (mp) cc_final: 0.8014 (tp) REVERT: C 811 ARG cc_start: 0.8406 (mtm180) cc_final: 0.8091 (ttp-110) REVERT: C 813 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7649 (pm20) REVERT: F 294 TYR cc_start: 0.8966 (t80) cc_final: 0.8695 (m-80) REVERT: F 623 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8517 (mm-30) REVERT: G 50 MET cc_start: 0.3842 (ptt) cc_final: 0.3550 (ptt) REVERT: G 328 MET cc_start: 0.6890 (mmt) cc_final: 0.5654 (ptm) REVERT: G 724 ASP cc_start: 0.8586 (t0) cc_final: 0.8266 (t0) REVERT: G 728 ARG cc_start: 0.7884 (mtt90) cc_final: 0.7530 (tpt-90) REVERT: G 778 GLN cc_start: 0.8318 (tt0) cc_final: 0.8116 (tt0) REVERT: H 785 ARG cc_start: 0.6801 (tpp-160) cc_final: 0.6446 (tpp-160) outliers start: 48 outliers final: 30 residues processed: 298 average time/residue: 0.4622 time to fit residues: 218.6711 Evaluate side-chains 264 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 233 time to evaluate : 3.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 696 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 B residue 695 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 813 GLU Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 702 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 465 LEU Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 784 ILE Chi-restraints excluded: chain 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 725 ILE Chi-restraints excluded: chain H residue 758 ASP Chi-restraints excluded: chain H residue 808 ASP Chi-restraints excluded: chain H residue 815 MET Chi-restraints excluded: chain H residue 852 LEU Chi-restraints excluded: chain H residue 863 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 332 optimal weight: 0.8980 chunk 253 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 226 optimal weight: 1.9990 chunk 337 optimal weight: 0.3980 chunk 357 optimal weight: 4.9990 chunk 176 optimal weight: 0.9980 chunk 320 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN A 272 HIS C 807 HIS F 133 GLN F 295 GLN 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32936 Z= 0.212 Angle : 0.583 13.049 45212 Z= 0.309 Chirality : 0.042 0.156 5016 Planarity : 0.004 0.056 5280 Dihedral : 18.405 154.857 5466 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.69 % Allowed : 7.07 % Favored : 91.24 % 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: 1.58 (0.16), residues: 1072 sheet: 0.15 (0.17), residues: 846 loop : 0.07 (0.15), residues: 1662 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 0.002 PHE A 290 TYR 0.021 0.001 TYR A 296 ARG 0.008 0.000 ARG H 811 *********************** 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 303 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 249 time to evaluate : 3.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 TYR cc_start: 0.8256 (m-10) cc_final: 0.7921 (m-10) REVERT: A 296 TYR cc_start: 0.7849 (m-80) cc_final: 0.7394 (m-80) REVERT: A 444 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8259 (mt0) REVERT: A 623 GLU cc_start: 0.8753 (tt0) cc_final: 0.8518 (tt0) REVERT: B 75 ASP cc_start: 0.8128 (t0) cc_final: 0.7654 (t0) REVERT: B 172 MET cc_start: 0.8367 (mtp) cc_final: 0.8061 (mtp) REVERT: C 449 GLN cc_start: 0.8390 (tm-30) cc_final: 0.7900 (tt0) REVERT: C 683 LEU cc_start: 0.8599 (mp) cc_final: 0.7975 (tp) REVERT: C 724 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7423 (t70) REVERT: C 811 ARG cc_start: 0.8387 (mtm180) cc_final: 0.8072 (ttp-110) REVERT: C 813 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7685 (pm20) REVERT: F 294 TYR cc_start: 0.8898 (t80) cc_final: 0.8677 (m-80) REVERT: F 623 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8498 (mm-30) REVERT: G 50 MET cc_start: 0.3655 (ptt) cc_final: 0.3404 (ptt) REVERT: G 328 MET cc_start: 0.6942 (mmt) cc_final: 0.5651 (ptm) REVERT: G 753 ILE cc_start: 0.8213 (pt) cc_final: 0.7997 (tt) REVERT: G 778 GLN cc_start: 0.8312 (tt0) cc_final: 0.8099 (tt0) REVERT: H 785 ARG cc_start: 0.6809 (tpp-160) cc_final: 0.6494 (tpp-160) REVERT: H 842 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8114 (m-80) outliers start: 54 outliers final: 32 residues processed: 282 average time/residue: 0.4605 time to fit residues: 206.6995 Evaluate side-chains 264 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 229 time to evaluate : 3.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 724 ASP Chi-restraints excluded: chain C residue 813 GLU Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 702 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 465 LEU Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 716 LEU 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 594 ILE Chi-restraints excluded: chain H residue 725 ILE Chi-restraints excluded: chain H residue 808 ASP Chi-restraints excluded: chain H residue 842 PHE Chi-restraints excluded: chain H residue 863 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 297 optimal weight: 0.1980 chunk 203 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 266 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 305 optimal weight: 0.7980 chunk 247 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 182 optimal weight: 10.0000 chunk 321 optimal weight: 0.4980 chunk 90 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 GLN B 435 ASN C 807 HIS F 70 GLN F 295 GLN G 552 HIS ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 433 HIS H 448 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32936 Z= 0.187 Angle : 0.558 12.103 45212 Z= 0.296 Chirality : 0.042 0.155 5016 Planarity : 0.004 0.056 5280 Dihedral : 18.356 154.362 5466 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.69 % Allowed : 7.88 % Favored : 90.43 % 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: 1.75 (0.16), residues: 1072 sheet: 0.12 (0.17), residues: 848 loop : 0.06 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 805 HIS 0.012 0.001 HIS B 733 PHE 0.032 0.001 PHE A 635 TYR 0.017 0.001 TYR A 296 ARG 0.008 0.000 ARG H 811 *********************** 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 312 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 258 time to evaluate : 3.890 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 255 TYR cc_start: 0.8304 (m-10) cc_final: 0.8074 (m-10) REVERT: A 292 ARG cc_start: 0.8354 (mmm160) cc_final: 0.8036 (mmm160) REVERT: A 296 TYR cc_start: 0.7800 (m-80) cc_final: 0.7431 (m-80) REVERT: A 329 MET cc_start: 0.8800 (tpp) cc_final: 0.8397 (tpp) REVERT: A 444 GLN cc_start: 0.8533 (mm-40) cc_final: 0.8281 (mt0) REVERT: A 623 GLU cc_start: 0.8740 (tt0) cc_final: 0.8523 (tt0) REVERT: A 669 GLU cc_start: 0.8540 (tp30) cc_final: 0.7215 (mt-10) REVERT: A 671 LEU cc_start: 0.8042 (mp) cc_final: 0.7841 (mt) REVERT: B 75 ASP cc_start: 0.8129 (t0) cc_final: 0.7627 (t0) REVERT: B 172 MET cc_start: 0.8325 (mtp) cc_final: 0.8069 (mtp) REVERT: C 449 GLN cc_start: 0.8358 (tm-30) cc_final: 0.7919 (tt0) REVERT: C 683 LEU cc_start: 0.8603 (mp) cc_final: 0.7975 (tp) REVERT: C 811 ARG cc_start: 0.8425 (mtm180) cc_final: 0.8074 (ttp-110) REVERT: C 813 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7637 (pm20) REVERT: F 64 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7459 (ttp80) REVERT: F 70 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: F 623 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8495 (mm-30) REVERT: G 50 MET cc_start: 0.3763 (ptt) cc_final: 0.3516 (ptt) REVERT: G 328 MET cc_start: 0.6959 (mmt) cc_final: 0.5680 (ptm) REVERT: G 753 ILE cc_start: 0.8275 (pt) cc_final: 0.8035 (tt) REVERT: G 778 GLN cc_start: 0.8300 (tt0) cc_final: 0.8074 (tt0) REVERT: H 785 ARG cc_start: 0.6842 (tpp-160) cc_final: 0.6554 (tpp-160) REVERT: H 842 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.8089 (m-80) outliers start: 54 outliers final: 31 residues processed: 294 average time/residue: 0.4473 time to fit residues: 210.1213 Evaluate side-chains 268 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 233 time to evaluate : 3.554 ------------------------------------------------------------------------------- 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 691 VAL Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 813 GLU Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 70 GLN 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 717 MET 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 594 ILE Chi-restraints excluded: chain H residue 653 ILE Chi-restraints excluded: chain H residue 808 ASP Chi-restraints excluded: chain H residue 842 PHE Chi-restraints excluded: chain H residue 863 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 120 optimal weight: 0.6980 chunk 322 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 357 optimal weight: 1.9990 chunk 297 optimal weight: 3.9990 chunk 165 optimal weight: 0.5980 chunk 29 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 187 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 ASN B 733 HIS C 467 ASN C 807 HIS F 72 GLN F 295 GLN F 681 GLN G 324 ASN G 552 HIS ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 448 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 32936 Z= 0.275 Angle : 0.585 11.320 45212 Z= 0.309 Chirality : 0.043 0.160 5016 Planarity : 0.004 0.056 5280 Dihedral : 18.390 153.562 5466 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.38 % Allowed : 9.01 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.14), residues: 3580 helix: 1.74 (0.16), residues: 1076 sheet: 0.01 (0.17), residues: 868 loop : 0.01 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 805 HIS 0.019 0.001 HIS G 552 PHE 0.039 0.002 PHE A 635 TYR 0.016 0.001 TYR H 755 ARG 0.017 0.000 ARG B 685 *********************** 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 290 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 246 time to evaluate : 3.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 SER cc_start: 0.7664 (m) cc_final: 0.7252 (p) REVERT: A 255 TYR cc_start: 0.8327 (m-10) cc_final: 0.8097 (m-10) REVERT: A 629 ARG cc_start: 0.8684 (mmm-85) cc_final: 0.8462 (mmm-85) REVERT: B 75 ASP cc_start: 0.8274 (t0) cc_final: 0.7721 (t0) REVERT: B 172 MET cc_start: 0.8360 (mtp) cc_final: 0.8086 (mtp) REVERT: B 710 ARG cc_start: 0.8364 (mtm180) cc_final: 0.8061 (ptp-170) REVERT: C 449 GLN cc_start: 0.8375 (tm-30) cc_final: 0.7947 (tt0) REVERT: C 683 LEU cc_start: 0.8584 (mp) cc_final: 0.7946 (tp) REVERT: C 811 ARG cc_start: 0.8438 (mtm180) cc_final: 0.8066 (ttp-110) REVERT: C 813 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7654 (pm20) REVERT: F 64 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7460 (ttp80) REVERT: F 288 ARG cc_start: 0.8846 (mtp-110) cc_final: 0.8614 (mtp85) REVERT: F 623 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8504 (mm-30) REVERT: G 50 MET cc_start: 0.3740 (ptt) cc_final: 0.3457 (ptt) REVERT: G 328 MET cc_start: 0.6969 (mmt) cc_final: 0.5593 (ptm) REVERT: G 753 ILE cc_start: 0.8280 (pt) cc_final: 0.8045 (tt) REVERT: H 785 ARG cc_start: 0.6816 (tpp-160) cc_final: 0.6533 (tpp-160) REVERT: H 842 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8078 (m-80) outliers start: 44 outliers final: 32 residues processed: 274 average time/residue: 0.4702 time to fit residues: 205.3753 Evaluate side-chains 263 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 228 time to evaluate : 3.189 ------------------------------------------------------------------------------- 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 691 VAL Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 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 127 ILE Chi-restraints excluded: chain F residue 294 TYR 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 716 LEU Chi-restraints excluded: chain G residue 717 MET Chi-restraints excluded: chain G residue 784 ILE Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 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 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: 0.7980 chunk 40 optimal weight: 3.9990 chunk 203 optimal weight: 0.5980 chunk 261 optimal weight: 0.0980 chunk 202 optimal weight: 0.4980 chunk 301 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 356 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 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: 0.8372 moved from start: 0.2948 Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 311, in __init__ self.caller(self.show_stats) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 346, in show_stats self.structure_monitor.show(prefix="",log=self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/__init__.py", line 150, in show self.update_statistics(prefix = prefix, log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/__init__.py", line 157, in update_statistics gs.show(prefix=prefix, log=log, uppercase=False) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/model/statistics.py", line 327, in show res = self.result() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/model/statistics.py", line 261, in result clash = self.clash(), File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/model/statistics.py", line 189, in clash nuclear = self.model.is_neutron()) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/validation/clashscore.py", line 176, in __init__ log=out) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/validation/clashscore.py", line 746, in check_and_add_hydrogen output_fname="reduce_fail.pdb") File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/validation/clashscore.py", line 647, in check_and_report_reduce_failure f.write(input_lines) IOError: [Errno 28] No space left on device