Starting phenix.real_space_refine on Fri Aug 9 06:42:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cll_16717/08_2024/8cll_16717.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cll_16717/08_2024/8cll_16717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cll_16717/08_2024/8cll_16717.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cll_16717/08_2024/8cll_16717.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cll_16717/08_2024/8cll_16717.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cll_16717/08_2024/8cll_16717.cif" } resolution = 3.4 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= 0.006 sd= 0.083 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: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 164 5.16 5 C 16150 2.51 5 N 4418 2.21 5 O 4490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 880": "OE1" <-> "OE2" Residue "C PHE 889": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25226 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2514 Classifications: {'peptide': 308} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 291} Chain breaks: 2 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: "F" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2514 Classifications: {'peptide': 308} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 291} Chain breaks: 2 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: "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 7735 SG CYS B 788 46.027 71.017 193.545 1.00136.96 S ATOM 7946 SG CYS B 814 43.778 70.655 195.239 1.00147.83 S ATOM 7970 SG CYS B 817 45.511 73.585 194.267 1.00143.68 S ATOM 7396 SG CYS B 747 51.101 54.207 211.937 1.00220.65 S ATOM 7416 SG CYS B 750 53.312 52.131 214.131 1.00223.84 S ATOM 7530 SG CYS B 764 53.738 56.069 214.244 1.00223.21 S ATOM 20007 SG CYS G 747 72.488 100.730 31.075 1.00213.20 S ATOM 20027 SG CYS G 750 74.590 100.422 28.018 1.00221.15 S ATOM 20141 SG CYS G 764 71.171 101.753 27.648 1.00222.55 S ATOM 20346 SG CYS G 788 54.142 93.316 47.252 1.00137.47 S ATOM 20557 SG CYS G 814 53.321 97.170 46.227 1.00130.31 S ATOM 20581 SG CYS G 817 51.369 94.087 46.694 1.00134.83 S Time building chain proxies: 14.37, per 1000 atoms: 0.57 Number of scatterers: 25226 At special positions: 0 Unit cell: (107.682, 134.808, 230.982, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 164 16.00 O 4490 8.00 N 4418 7.00 C 16150 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: 8.83 Conformation dependent library (CDL) restraints added in 4.2 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 817 " pdb="ZN ZN B 901 " - pdb=" SG CYS B 788 " pdb=" ZN B 902 " pdb="ZN ZN B 902 " - pdb=" NE2 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 764 " pdb="ZN ZN G 901 " - pdb=" SG CYS G 747 " 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 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5916 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 41 sheets defined 28.0% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.31 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 3.722A pdb=" N GLU A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 31 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 187 Processing helix chain 'A' and resid 188 through 191 Processing helix chain 'A' and resid 194 through 200 Processing helix chain 'A' and resid 205 through 219 removed outlier: 4.159A pdb=" N ILE A 215 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 4.485A 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 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 'B' and resid 122 through 136 Processing helix chain 'B' and resid 138 through 148 Processing helix chain 'B' and resid 208 through 218 removed outlier: 3.525A pdb=" N GLU B 214 " --> pdb=" O GLU B 210 " (cutoff:3.500A) 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 468 through 473 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: 3.654A 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: 3.675A pdb=" N TRP B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 698 Processing helix chain 'B' and resid 708 through 716 Processing helix chain 'B' and resid 724 through 738 Processing helix chain 'B' and resid 803 through 811 Processing helix chain 'C' and resid 300 through 322 Proline residue: C 306 - end of helix removed outlier: 3.793A pdb=" N LEU C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 3.939A 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 448 through 452 Processing helix chain 'C' and resid 515 through 523 removed outlier: 3.524A pdb=" N LEU C 519 " --> pdb=" O HIS C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 744 Processing helix chain 'C' and resid 746 through 749 Processing helix chain 'C' and resid 786 through 792 Processing helix chain 'C' and resid 812 through 822 removed outlier: 3.650A pdb=" N GLU C 820 " --> pdb=" O LEU C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 889 Processing helix chain 'F' and resid 2 through 14 removed outlier: 3.640A pdb=" N GLU F 14 " --> pdb=" O GLU F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 31 Processing helix chain 'F' and resid 40 through 54 removed outlier: 4.093A pdb=" N PHE F 46 " --> pdb=" O CYS F 42 " (cutoff:3.500A) 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 188 removed outlier: 3.558A pdb=" N ARG F 188 " --> pdb=" O LEU F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 200 Processing helix chain 'F' and resid 205 through 219 removed outlier: 4.121A pdb=" N ILE F 215 " --> pdb=" O TYR F 211 " (cutoff:3.500A) removed outlier: 4.452A 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 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 'G' and resid 122 through 136 Processing helix chain 'G' and resid 138 through 148 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 533 through 535 No H-bonds generated for 'chain 'G' and resid 533 through 535' Processing helix chain 'G' and resid 536 through 551 removed outlier: 3.847A pdb=" N LEU G 542 " --> pdb=" O ASP G 538 " (cutoff:3.500A) Processing helix chain 'G' and resid 554 through 568 Processing helix chain 'G' and resid 570 through 588 removed outlier: 3.635A 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 708 through 719 Processing helix chain 'G' and resid 720 through 723 Processing helix chain 'G' and resid 724 through 738 Processing helix chain 'G' and resid 765 through 767 No H-bonds generated for 'chain 'G' and resid 765 through 767' Processing helix chain 'G' and resid 803 through 810 Processing helix chain 'H' and resid 300 through 322 Proline residue: H 306 - end of helix removed outlier: 3.684A pdb=" N HIS H 312 " --> pdb=" O TRP H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 327 through 331 removed outlier: 3.985A pdb=" N ILE H 331 " --> pdb=" O ALA H 328 " (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 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 867 through 870 Processing helix chain 'H' and resid 871 through 889 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 102 through 103 removed outlier: 4.396A pdb=" N GLY A 112 " --> pdb=" O ILE A 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 192 through 193 Processing sheet with id=AA4, first strand: chain 'A' and resid 384 through 385 Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 59 removed outlier: 4.216A pdb=" N GLY B 479 " --> pdb=" O ILE B 492 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N THR B 494 " --> pdb=" O THR B 477 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N THR B 477 " --> pdb=" O THR B 494 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 70 through 72 removed outlier: 4.133A pdb=" N VAL B 103 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 164 through 169 removed outlier: 6.851A pdb=" N LEU B 185 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR B 167 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA B 183 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU B 191 " --> pdb=" O ASP B 207 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ASP B 207 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE B 193 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 248 through 257 removed outlier: 6.646A pdb=" N LEU B 279 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N MET B 251 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA B 277 " --> pdb=" O MET B 251 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TRP B 253 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU B 275 " --> pdb=" O TRP B 253 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY B 255 " --> pdb=" O SER B 273 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N SER B 273 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASN B 284 " --> pdb=" O PHE B 280 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 302 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLN B 291 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE B 300 " --> pdb=" O GLN B 291 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 313 through 323 removed outlier: 6.722A pdb=" N GLY B 334 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU B 316 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE B 332 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TRP B 318 " --> pdb=" O GLY B 330 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLY B 330 " --> pdb=" O TRP B 318 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU B 320 " --> pdb=" O MET B 328 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N MET B 328 " --> pdb=" O GLU B 320 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU B 322 " --> pdb=" O ARG B 326 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ARG B 326 " --> pdb=" O GLU B 322 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LYS B 327 " --> pdb=" O PHE B 354 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 313 through 323 removed outlier: 6.722A pdb=" N GLY B 334 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU B 316 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE B 332 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TRP B 318 " --> pdb=" O GLY B 330 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLY B 330 " --> pdb=" O TRP B 318 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU B 320 " --> pdb=" O MET B 328 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N MET B 328 " --> pdb=" O GLU B 320 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU B 322 " --> pdb=" O ARG B 326 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ARG B 326 " --> pdb=" O GLU B 322 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE B 340 " --> pdb=" O LEU B 362 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 371 through 381 removed outlier: 3.755A pdb=" N SER B 373 " --> pdb=" O ALA B 394 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N SER B 387 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE B 406 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 399 " --> pdb=" O VAL B 418 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 428 through 431 removed outlier: 3.684A pdb=" N SER B 428 " --> pdb=" O CYS B 441 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL B 447 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 761 through 763 Processing sheet with id=AB5, first strand: chain 'B' and resid 786 through 787 Processing sheet with id=AB6, first strand: chain 'C' and resid 337 through 340 removed outlier: 4.648A pdb=" N ILE C 532 " --> pdb=" O LEU C 340 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL C 535 " --> pdb=" O ALA C 464 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N PHE C 459 " --> pdb=" O GLY C 443 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLY C 443 " --> pdb=" O PHE C 459 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR C 461 " --> pdb=" O LEU C 441 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LEU C 438 " --> pdb=" O SER C 419 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER C 419 " --> pdb=" O LEU C 438 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 358 through 362 removed outlier: 5.988A pdb=" N ARG C 751 " --> pdb=" O ILE C 733 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE C 733 " --> pdb=" O ARG C 751 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA C 731 " --> pdb=" O PRO C 753 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR C 755 " --> pdb=" O LEU C 729 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLU C 728 " --> pdb=" O ASP C 724 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR C 719 " --> pdb=" O SER C 714 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER C 710 " --> pdb=" O GLY C 723 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 389 through 392 Processing sheet with id=AB9, first strand: chain 'C' and resid 470 through 475 removed outlier: 6.570A pdb=" N ALA C 502 " --> pdb=" O TRP C 471 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU C 473 " --> pdb=" O ALA C 500 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA C 500 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE C 475 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU C 498 " --> pdb=" O PHE C 475 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU C 513 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU C 498 " --> pdb=" O PHE C 511 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE C 511 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA C 500 " --> pdb=" O LEU C 509 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU C 509 " --> pdb=" O ALA C 500 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 557 through 562 removed outlier: 3.715A pdb=" N SER C 559 " --> pdb=" O GLY C 574 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N MET C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN C 607 " --> pdb=" O PHE C 582 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 616 through 621 removed outlier: 3.827A pdb=" N GLY C 633 " --> pdb=" O LYS C 637 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LYS C 637 " --> pdb=" O GLY C 633 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN C 651 " --> pdb=" O PHE C 640 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 658 through 662 removed outlier: 3.797A pdb=" N GLU C 660 " --> pdb=" O ALA C 673 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN C 674 " --> pdb=" O GLY C 685 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N GLY C 685 " --> pdb=" O GLN C 674 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N TYR C 688 " --> pdb=" O PHE C 700 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N PHE C 700 " --> pdb=" O TYR C 688 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 121 through 122 Processing sheet with id=AC5, first strand: chain 'F' and resid 102 through 103 removed outlier: 4.346A pdb=" N GLY F 112 " --> pdb=" O ILE F 103 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 222 through 230 Processing sheet with id=AC7, first strand: chain 'F' and resid 384 through 385 Processing sheet with id=AC8, first strand: chain 'G' and resid 53 through 59 removed outlier: 5.017A pdb=" N PHE G 512 " --> pdb=" O ARG G 54 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL G 510 " --> pdb=" O PRO G 56 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TYR G 488 " --> pdb=" O VAL G 482 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL G 482 " --> pdb=" O TYR G 488 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA G 490 " --> pdb=" O ILE G 480 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE G 480 " --> pdb=" O ALA G 490 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE G 492 " --> pdb=" O HIS G 478 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 70 through 72 removed outlier: 4.298A pdb=" N VAL G 103 " --> pdb=" O ILE G 92 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 164 through 169 removed outlier: 7.184A pdb=" N LEU G 191 " --> pdb=" O ASP G 207 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASP G 207 " --> pdb=" O LEU G 191 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE G 193 " --> pdb=" O LEU G 205 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 248 through 257 removed outlier: 5.848A pdb=" N MET G 251 " --> pdb=" O LEU G 279 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU G 279 " --> pdb=" O MET G 251 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N TRP G 253 " --> pdb=" O ALA G 277 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA G 277 " --> pdb=" O TRP G 253 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLY G 255 " --> pdb=" O LEU G 275 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU G 275 " --> pdb=" O GLY G 255 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASN G 284 " --> pdb=" O PHE G 280 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLN G 291 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ILE G 300 " --> pdb=" O GLN G 291 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 313 through 323 removed outlier: 6.077A pdb=" N ILE G 340 " --> pdb=" O LEU G 362 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL G 360 " --> pdb=" O ILE G 342 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 371 through 381 removed outlier: 3.787A pdb=" N SER G 373 " --> pdb=" O ALA G 394 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS G 386 " --> pdb=" O HIS G 381 " (cutoff:3.500A) removed outlier: 6.674A 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: 3.510A pdb=" N VAL G 399 " --> pdb=" O VAL G 418 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 428 through 431 removed outlier: 3.648A pdb=" N SER G 428 " --> pdb=" O CYS G 441 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL G 447 " --> pdb=" O ILE G 466 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 761 through 763 Processing sheet with id=AD7, first strand: chain 'G' and resid 786 through 787 Processing sheet with id=AD8, first strand: chain 'H' and resid 337 through 339 removed outlier: 4.759A pdb=" N VAL H 535 " --> pdb=" O ALA H 464 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N PHE H 459 " --> pdb=" O GLY H 443 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY H 443 " --> pdb=" O PHE H 459 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR H 461 " --> pdb=" O LEU H 441 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU H 438 " --> pdb=" O SER H 419 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER H 419 " --> pdb=" O LEU H 438 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N TYR H 414 " --> pdb=" O TRP H 402 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N TRP H 402 " --> pdb=" O TYR H 414 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA H 416 " --> pdb=" O LEU H 400 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU H 400 " --> pdb=" O ALA H 416 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE H 418 " --> pdb=" O TRP H 398 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 358 through 362 removed outlier: 6.460A pdb=" N SER H 359 " --> pdb=" O PHE H 798 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ASP H 800 " --> pdb=" O SER H 359 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLN H 361 " --> pdb=" O ASP H 800 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ARG H 751 " --> pdb=" O ILE H 733 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE H 733 " --> pdb=" O ARG H 751 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ALA H 731 " --> pdb=" O PRO H 753 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU H 728 " --> pdb=" O ASP H 724 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR H 719 " --> pdb=" O GLY H 713 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLY H 713 " --> pdb=" O THR H 719 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA H 721 " --> pdb=" O LEU H 711 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU H 711 " --> pdb=" O ALA H 721 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLY H 723 " --> pdb=" O TRP H 709 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 378 through 379 removed outlier: 4.051A pdb=" N SER H 378 " --> pdb=" O PHE H 392 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU H 860 " --> pdb=" O GLY H 856 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY H 856 " --> pdb=" O LEU H 860 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 470 through 475 removed outlier: 6.647A pdb=" N ALA H 502 " --> pdb=" O TRP H 471 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU H 473 " --> pdb=" O ALA H 500 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA H 500 " --> pdb=" O LEU H 473 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE H 475 " --> pdb=" O LEU H 498 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU H 498 " --> pdb=" O PHE H 475 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU H 513 " --> pdb=" O LEU H 496 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU H 498 " --> pdb=" O PHE H 511 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N PHE H 511 " --> pdb=" O LEU H 498 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA H 500 " --> pdb=" O LEU H 509 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU H 509 " --> pdb=" O ALA H 500 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 557 through 562 removed outlier: 6.298A pdb=" N GLY H 574 " --> pdb=" O LEU H 558 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU H 560 " --> pdb=" O ALA H 572 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA H 572 " --> pdb=" O LEU H 560 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N TRP H 562 " --> pdb=" O HIS H 570 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N HIS H 570 " --> pdb=" O TRP H 562 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N MET H 579 " --> pdb=" O TYR H 575 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN H 607 " --> pdb=" O PHE H 582 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 618 through 621 removed outlier: 3.634A pdb=" N ALA H 632 " --> pdb=" O THR H 618 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN H 651 " --> pdb=" O PHE H 640 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 658 through 662 removed outlier: 3.763A pdb=" N GLU H 660 " --> pdb=" O ALA H 673 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLN H 674 " --> pdb=" O GLY H 685 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLY H 685 " --> pdb=" O GLN H 674 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TYR H 688 " --> pdb=" O PHE H 700 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N PHE H 700 " --> pdb=" O TYR H 688 " (cutoff:3.500A) 972 hydrogen bonds defined for protein. 2754 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.44 Time building geometry restraints manager: 9.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8210 1.35 - 1.47: 6388 1.47 - 1.60: 11042 1.60 - 1.72: 0 1.72 - 1.85: 238 Bond restraints: 25878 Sorted by residual: bond pdb=" CB CYS G 817 " pdb=" SG CYS G 817 " ideal model delta sigma weight residual 1.808 1.846 -0.038 3.30e-02 9.18e+02 1.33e+00 bond pdb=" CG1 ILE H 720 " pdb=" CD1 ILE H 720 " ideal model delta sigma weight residual 1.513 1.475 0.038 3.90e-02 6.57e+02 9.42e-01 bond pdb=" CA GLU G 68 " pdb=" C GLU G 68 " ideal model delta sigma weight residual 1.524 1.535 -0.012 1.26e-02 6.30e+03 8.41e-01 bond pdb=" CB ILE A 163 " pdb=" CG2 ILE A 163 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.42e-01 bond pdb=" CB VAL H 581 " pdb=" CG1 VAL H 581 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.15e-01 ... (remaining 25873 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.71: 1010 106.71 - 113.57: 14001 113.57 - 120.44: 9550 120.44 - 127.31: 10127 127.31 - 134.17: 418 Bond angle restraints: 35106 Sorted by residual: angle pdb=" N GLY B 338 " pdb=" CA GLY B 338 " pdb=" C GLY B 338 " ideal model delta sigma weight residual 112.34 120.95 -8.61 2.04e+00 2.40e-01 1.78e+01 angle pdb=" N ASP G 75 " pdb=" CA ASP G 75 " pdb=" C ASP G 75 " ideal model delta sigma weight residual 112.54 108.01 4.53 1.51e+00 4.39e-01 9.01e+00 angle pdb=" C CYS G 817 " pdb=" N ASP G 818 " pdb=" CA ASP G 818 " ideal model delta sigma weight residual 122.31 117.04 5.27 1.81e+00 3.05e-01 8.47e+00 angle pdb=" N ALA H 346 " pdb=" CA ALA H 346 " pdb=" C ALA H 346 " ideal model delta sigma weight residual 109.81 116.13 -6.32 2.21e+00 2.05e-01 8.19e+00 angle pdb=" CA GLN G 358 " pdb=" CB GLN G 358 " pdb=" CG GLN G 358 " ideal model delta sigma weight residual 114.10 119.76 -5.66 2.00e+00 2.50e-01 8.01e+00 ... (remaining 35101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 14430 17.98 - 35.95: 892 35.95 - 53.93: 124 53.93 - 71.90: 44 71.90 - 89.88: 26 Dihedral angle restraints: 15516 sinusoidal: 6368 harmonic: 9148 Sorted by residual: dihedral pdb=" CA LEU G 775 " pdb=" C LEU G 775 " pdb=" N THR G 776 " pdb=" CA THR G 776 " ideal model delta harmonic sigma weight residual 180.00 150.20 29.80 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA LYS G 760 " pdb=" C LYS G 760 " pdb=" N GLN G 761 " pdb=" CA GLN G 761 " ideal model delta harmonic sigma weight residual -180.00 -150.93 -29.07 0 5.00e+00 4.00e-02 3.38e+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 180.00 151.11 28.89 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 15513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2319 0.036 - 0.071: 1012 0.071 - 0.107: 348 0.107 - 0.142: 141 0.142 - 0.178: 14 Chirality restraints: 3834 Sorted by residual: chirality pdb=" CB VAL H 866 " pdb=" CA VAL H 866 " pdb=" CG1 VAL H 866 " pdb=" CG2 VAL H 866 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.90e-01 chirality pdb=" CA TYR B 777 " pdb=" N TYR B 777 " pdb=" C TYR B 777 " pdb=" CB TYR B 777 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CA ARG H 636 " pdb=" N ARG H 636 " pdb=" C ARG H 636 " pdb=" CB ARG H 636 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.26e-01 ... (remaining 3831 not shown) Planarity restraints: 4494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 796 " 0.304 9.50e-02 1.11e+02 1.37e-01 1.47e+01 pdb=" NE ARG G 796 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG G 796 " 0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG G 796 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG G 796 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 796 " -0.254 9.50e-02 1.11e+02 1.15e-01 1.03e+01 pdb=" NE ARG B 796 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG B 796 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG B 796 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG B 796 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 186 " -0.249 9.50e-02 1.11e+02 1.12e-01 9.76e+00 pdb=" NE ARG F 186 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG F 186 " -0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG F 186 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG F 186 " -0.001 2.00e-02 2.50e+03 ... (remaining 4491 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 127 2.57 - 3.15: 20539 3.15 - 3.73: 38499 3.73 - 4.32: 56095 4.32 - 4.90: 93429 Nonbonded interactions: 208689 Sorted by model distance: nonbonded pdb=" OD1 ASP B 792 " pdb="ZN ZN B 901 " model vdw 1.984 2.230 nonbonded pdb=" OD1 ASP G 792 " pdb="ZN ZN G 902 " model vdw 1.998 2.230 nonbonded pdb=" OD2 ASP B 792 " pdb="ZN ZN B 901 " model vdw 2.000 2.230 nonbonded pdb=" OD2 ASP G 792 " pdb="ZN ZN G 902 " model vdw 2.004 2.230 nonbonded pdb=" OG SER B 793 " pdb="ZN ZN B 901 " model vdw 2.084 2.230 ... (remaining 208684 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' } 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: 7.160 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: 0.950 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 74.350 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.130 Set refine NCS operators: 0.010 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 : 0.003 0.039 25878 Z= 0.204 Angle : 0.663 8.615 35106 Z= 0.370 Chirality : 0.047 0.178 3834 Planarity : 0.009 0.137 4494 Dihedral : 12.967 89.880 9600 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 3120 helix: -0.76 (0.15), residues: 790 sheet: 0.05 (0.18), residues: 784 loop : -0.52 (0.15), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP H 481 HIS 0.008 0.001 HIS B 768 PHE 0.014 0.002 PHE H 391 TYR 0.028 0.004 TYR A 98 ARG 0.031 0.004 ARG G 796 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 3.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.8589 (tmm) cc_final: 0.8271 (ptm) REVERT: B 174 CYS cc_start: 0.8612 (m) cc_final: 0.8074 (m) REVERT: B 406 ILE cc_start: 0.7977 (mt) cc_final: 0.7553 (mt) REVERT: B 681 MET cc_start: 0.9304 (tpt) cc_final: 0.8874 (tpp) REVERT: B 685 ARG cc_start: 0.8848 (mmm-85) cc_final: 0.8631 (mtp180) REVERT: B 715 PHE cc_start: 0.8522 (t80) cc_final: 0.8158 (t80) REVERT: B 783 LEU cc_start: 0.8660 (mt) cc_final: 0.8364 (mt) REVERT: C 387 TRP cc_start: 0.7898 (m-10) cc_final: 0.7315 (m-10) REVERT: C 563 MET cc_start: 0.8727 (ttt) cc_final: 0.8510 (ttm) REVERT: C 683 LEU cc_start: 0.7368 (mt) cc_final: 0.7050 (mm) REVERT: C 737 MET cc_start: 0.8956 (mmt) cc_final: 0.8597 (mmt) REVERT: C 888 MET cc_start: 0.8351 (ttm) cc_final: 0.7956 (ttm) REVERT: F 116 TYR cc_start: 0.8492 (m-80) cc_final: 0.7931 (m-10) REVERT: F 178 TYR cc_start: 0.7728 (t80) cc_final: 0.7493 (t80) REVERT: F 211 TYR cc_start: 0.8833 (t80) cc_final: 0.8506 (t80) REVERT: G 200 LEU cc_start: 0.8388 (mp) cc_final: 0.8146 (tp) REVERT: G 696 TYR cc_start: 0.9296 (t80) cc_final: 0.8720 (t80) REVERT: G 743 PHE cc_start: 0.8407 (m-80) cc_final: 0.8012 (m-80) REVERT: G 771 LEU cc_start: 0.8678 (mt) cc_final: 0.8402 (mm) REVERT: H 489 LYS cc_start: 0.7513 (mmmt) cc_final: 0.6945 (pttt) REVERT: H 563 MET cc_start: 0.8920 (ttt) cc_final: 0.8666 (ttt) REVERT: H 720 ILE cc_start: 0.9060 (mt) cc_final: 0.8774 (pt) REVERT: H 815 MET cc_start: 0.8683 (tpt) cc_final: 0.8450 (tpp) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 0.3915 time to fit residues: 237.4191 Evaluate side-chains 191 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 3.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 0.6980 chunk 234 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 158 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 242 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 180 optimal weight: 0.6980 chunk 281 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN B 152 ASN B 240 GLN B 291 GLN B 435 ASN B 766 ASN C 449 GLN C 794 HIS F 210 HIS G 152 ASN G 282 ASN G 531 GLN G 698 HIS ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 448 GLN H 467 ASN H 523 GLN H 620 GLN H 668 ASN H 819 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25878 Z= 0.231 Angle : 0.643 10.642 35106 Z= 0.333 Chirality : 0.045 0.192 3834 Planarity : 0.005 0.060 4494 Dihedral : 6.071 60.607 3426 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.16 % Allowed : 5.07 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.26 (0.15), residues: 3120 helix: 0.85 (0.18), residues: 812 sheet: 0.16 (0.18), residues: 774 loop : -0.07 (0.16), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 25 HIS 0.011 0.001 HIS F 212 PHE 0.024 0.002 PHE G 756 TYR 0.026 0.002 TYR A 116 ARG 0.009 0.001 ARG G 728 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 227 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.8697 (m-80) cc_final: 0.8310 (m-80) REVERT: A 138 MET cc_start: 0.8606 (tmm) cc_final: 0.8284 (ptm) REVERT: B 174 CYS cc_start: 0.8666 (m) cc_final: 0.8126 (m) REVERT: B 526 LEU cc_start: 0.9330 (tp) cc_final: 0.9107 (mm) REVERT: B 549 LYS cc_start: 0.8872 (mmmm) cc_final: 0.8582 (mmmm) REVERT: B 555 GLN cc_start: 0.8669 (tp40) cc_final: 0.8287 (tp-100) REVERT: B 681 MET cc_start: 0.9333 (tpt) cc_final: 0.8992 (tpp) REVERT: B 685 ARG cc_start: 0.8922 (mmm-85) cc_final: 0.8327 (tpp80) REVERT: B 688 MET cc_start: 0.8901 (mtt) cc_final: 0.8689 (mtp) REVERT: B 770 TRP cc_start: 0.7491 (m100) cc_final: 0.7100 (m100) REVERT: C 563 MET cc_start: 0.8805 (ttt) cc_final: 0.8598 (ttm) REVERT: C 737 MET cc_start: 0.9025 (mmt) cc_final: 0.8677 (mmt) REVERT: F 116 TYR cc_start: 0.8181 (m-80) cc_final: 0.7695 (m-10) REVERT: F 138 MET cc_start: 0.7747 (ptm) cc_final: 0.6963 (ptm) REVERT: F 198 HIS cc_start: 0.8907 (p-80) cc_final: 0.8596 (p-80) REVERT: F 211 TYR cc_start: 0.8909 (t80) cc_final: 0.8661 (t80) REVERT: G 103 VAL cc_start: 0.8750 (OUTLIER) cc_final: 0.8347 (p) REVERT: G 200 LEU cc_start: 0.8432 (mp) cc_final: 0.8172 (tp) REVERT: G 665 MET cc_start: 0.8570 (ttt) cc_final: 0.8139 (ttp) REVERT: G 681 MET cc_start: 0.9433 (tpp) cc_final: 0.9141 (tpp) REVERT: G 696 TYR cc_start: 0.9345 (t80) cc_final: 0.9112 (t80) REVERT: G 743 PHE cc_start: 0.8427 (m-80) cc_final: 0.8050 (m-80) REVERT: G 805 TRP cc_start: 0.8554 (p-90) cc_final: 0.8237 (p-90) REVERT: H 489 LYS cc_start: 0.7533 (mmmt) cc_final: 0.6979 (pttt) REVERT: H 546 MET cc_start: 0.8443 (mmm) cc_final: 0.8131 (mmm) REVERT: H 563 MET cc_start: 0.8878 (ttt) cc_final: 0.8595 (ttt) outliers start: 32 outliers final: 16 residues processed: 249 average time/residue: 0.3920 time to fit residues: 153.0792 Evaluate side-chains 196 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 179 time to evaluate : 2.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 814 CYS Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 725 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 234 optimal weight: 0.8980 chunk 191 optimal weight: 0.0000 chunk 77 optimal weight: 0.6980 chunk 282 optimal weight: 0.6980 chunk 304 optimal weight: 1.9990 chunk 251 optimal weight: 0.8980 chunk 279 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 226 optimal weight: 0.5980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 857 GLN F 210 HIS ** F 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 433 HIS H 523 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25878 Z= 0.179 Angle : 0.579 9.517 35106 Z= 0.295 Chirality : 0.044 0.158 3834 Planarity : 0.004 0.055 4494 Dihedral : 5.520 60.316 3426 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.27 % Allowed : 6.37 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.49 (0.15), residues: 3120 helix: 1.30 (0.18), residues: 808 sheet: 0.11 (0.18), residues: 792 loop : 0.03 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 481 HIS 0.006 0.001 HIS G 733 PHE 0.032 0.002 PHE G 756 TYR 0.015 0.001 TYR A 116 ARG 0.006 0.000 ARG F 195 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 197 time to evaluate : 2.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 CYS cc_start: 0.8661 (OUTLIER) cc_final: 0.7536 (m) REVERT: A 138 MET cc_start: 0.8637 (tmm) cc_final: 0.8318 (ptm) REVERT: B 366 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8165 (tpp) REVERT: B 555 GLN cc_start: 0.8809 (tp40) cc_final: 0.8454 (tp-100) REVERT: B 681 MET cc_start: 0.9443 (tpt) cc_final: 0.9020 (tpp) REVERT: B 685 ARG cc_start: 0.8943 (mmm-85) cc_final: 0.8566 (tpp80) REVERT: B 770 TRP cc_start: 0.7497 (m100) cc_final: 0.7164 (m100) REVERT: C 312 HIS cc_start: 0.8130 (m-70) cc_final: 0.7851 (m-70) REVERT: C 387 TRP cc_start: 0.7802 (m-10) cc_final: 0.7490 (m-10) REVERT: C 455 ASN cc_start: 0.7899 (t0) cc_final: 0.7694 (m-40) REVERT: C 563 MET cc_start: 0.8790 (ttt) cc_final: 0.8553 (ttm) REVERT: C 737 MET cc_start: 0.8979 (mmt) cc_final: 0.8694 (mmt) REVERT: F 138 MET cc_start: 0.7842 (ptm) cc_final: 0.7074 (ptm) REVERT: F 198 HIS cc_start: 0.8943 (p-80) cc_final: 0.8605 (p-80) REVERT: G 103 VAL cc_start: 0.8750 (m) cc_final: 0.8380 (p) REVERT: G 200 LEU cc_start: 0.8447 (mp) cc_final: 0.8173 (tp) REVERT: G 665 MET cc_start: 0.8661 (ttt) cc_final: 0.8115 (tmm) REVERT: G 681 MET cc_start: 0.9444 (tpp) cc_final: 0.9157 (tpp) REVERT: G 696 TYR cc_start: 0.9372 (t80) cc_final: 0.9090 (t80) REVERT: G 743 PHE cc_start: 0.8449 (m-80) cc_final: 0.8075 (m-80) REVERT: G 805 TRP cc_start: 0.8613 (p-90) cc_final: 0.8293 (p-90) REVERT: H 294 MET cc_start: 0.9232 (mmm) cc_final: 0.9025 (mmm) REVERT: H 489 LYS cc_start: 0.7471 (mmmt) cc_final: 0.6951 (pttt) REVERT: H 546 MET cc_start: 0.8398 (mmm) cc_final: 0.8123 (mmm) REVERT: H 563 MET cc_start: 0.8867 (ttt) cc_final: 0.8646 (ttt) outliers start: 35 outliers final: 19 residues processed: 220 average time/residue: 0.3855 time to fit residues: 137.5528 Evaluate side-chains 191 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 170 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 358 GLN Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 847 ASP Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 669 LEU Chi-restraints excluded: chain G residue 771 LEU Chi-restraints excluded: chain G residue 814 CYS Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 725 ILE Chi-restraints excluded: chain H residue 847 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 189 optimal weight: 0.9980 chunk 283 optimal weight: 4.9990 chunk 299 optimal weight: 0.9980 chunk 147 optimal weight: 6.9990 chunk 268 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN B 478 HIS C 433 HIS C 592 GLN C 620 GLN F 194 GLN F 210 HIS ** G 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 704 ASN ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 668 ASN H 857 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 25878 Z= 0.350 Angle : 0.621 9.794 35106 Z= 0.314 Chirality : 0.046 0.163 3834 Planarity : 0.005 0.054 4494 Dihedral : 5.436 61.215 3426 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.67 % Allowed : 7.78 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.32 (0.15), residues: 3120 helix: 1.44 (0.19), residues: 818 sheet: -0.15 (0.18), residues: 802 loop : -0.17 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 481 HIS 0.010 0.001 HIS F 101 PHE 0.025 0.002 PHE B 239 TYR 0.031 0.002 TYR A 116 ARG 0.004 0.000 ARG B 250 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 193 time to evaluate : 2.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 CYS cc_start: 0.8718 (OUTLIER) cc_final: 0.7608 (m) REVERT: A 138 MET cc_start: 0.8717 (tmm) cc_final: 0.8381 (ptm) REVERT: B 354 PHE cc_start: 0.7718 (m-80) cc_final: 0.7316 (m-80) REVERT: B 366 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8220 (tpp) REVERT: B 555 GLN cc_start: 0.8796 (tp40) cc_final: 0.8478 (tp-100) REVERT: B 681 MET cc_start: 0.9477 (tpt) cc_final: 0.9014 (tpp) REVERT: B 685 ARG cc_start: 0.8930 (mmm-85) cc_final: 0.8244 (tpp80) REVERT: C 312 HIS cc_start: 0.8101 (m-70) cc_final: 0.7771 (m-70) REVERT: C 387 TRP cc_start: 0.7881 (m-10) cc_final: 0.7465 (m-10) REVERT: C 563 MET cc_start: 0.8843 (ttt) cc_final: 0.8619 (ttm) REVERT: C 737 MET cc_start: 0.8996 (mmt) cc_final: 0.8677 (mmt) REVERT: F 1 MET cc_start: 0.8218 (tpp) cc_final: 0.8012 (tpp) REVERT: F 116 TYR cc_start: 0.8092 (m-80) cc_final: 0.7829 (m-10) REVERT: F 138 MET cc_start: 0.7707 (ptm) cc_final: 0.6982 (ptm) REVERT: F 198 HIS cc_start: 0.8993 (p-80) cc_final: 0.8620 (p-80) REVERT: G 200 LEU cc_start: 0.8479 (mp) cc_final: 0.8197 (tp) REVERT: G 665 MET cc_start: 0.8650 (ttt) cc_final: 0.8212 (tmm) REVERT: G 681 MET cc_start: 0.9451 (tpp) cc_final: 0.9172 (tpp) REVERT: G 696 TYR cc_start: 0.9398 (t80) cc_final: 0.9110 (t80) REVERT: G 743 PHE cc_start: 0.8455 (m-80) cc_final: 0.7812 (m-80) REVERT: G 805 TRP cc_start: 0.8661 (p-90) cc_final: 0.8330 (p-90) REVERT: H 489 LYS cc_start: 0.7551 (mmmt) cc_final: 0.7054 (pttt) REVERT: H 523 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7753 (tp-100) REVERT: H 888 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8452 (ttm) outliers start: 46 outliers final: 25 residues processed: 226 average time/residue: 0.3530 time to fit residues: 128.7585 Evaluate side-chains 201 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 172 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 358 GLN Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain C residue 653 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 725 ILE Chi-restraints excluded: chain C residue 824 HIS Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 847 ASP Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 669 LEU Chi-restraints excluded: chain G residue 771 LEU Chi-restraints excluded: chain H residue 523 GLN 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 847 ASP Chi-restraints excluded: chain H residue 866 VAL Chi-restraints excluded: chain H residue 888 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 223 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 255 optimal weight: 0.7980 chunk 207 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 chunk 268 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 570 HIS C 674 GLN F 210 HIS F 248 HIS ** G 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25878 Z= 0.194 Angle : 0.559 10.852 35106 Z= 0.282 Chirality : 0.044 0.333 3834 Planarity : 0.004 0.052 4494 Dihedral : 5.163 61.749 3426 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.48 % Allowed : 8.33 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.42 (0.15), residues: 3120 helix: 1.61 (0.19), residues: 818 sheet: -0.15 (0.18), residues: 806 loop : -0.13 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 337 HIS 0.007 0.001 HIS F 101 PHE 0.017 0.001 PHE B 239 TYR 0.013 0.001 TYR H 755 ARG 0.004 0.000 ARG H 566 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 178 time to evaluate : 2.720 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 136 CYS cc_start: 0.8755 (OUTLIER) cc_final: 0.7777 (m) REVERT: A 138 MET cc_start: 0.8661 (tmm) cc_final: 0.8364 (ptm) REVERT: B 332 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8098 (mt) REVERT: B 354 PHE cc_start: 0.7733 (m-80) cc_final: 0.7340 (m-80) REVERT: B 555 GLN cc_start: 0.8766 (tp40) cc_final: 0.8415 (tp-100) REVERT: B 681 MET cc_start: 0.9470 (tpt) cc_final: 0.9055 (tpp) REVERT: B 685 ARG cc_start: 0.8916 (mmm-85) cc_final: 0.7917 (mtp85) REVERT: C 312 HIS cc_start: 0.8111 (m-70) cc_final: 0.7788 (m-70) REVERT: C 387 TRP cc_start: 0.7867 (m-10) cc_final: 0.7362 (m-10) REVERT: C 737 MET cc_start: 0.8979 (mmt) cc_final: 0.8611 (mmt) REVERT: F 116 TYR cc_start: 0.8063 (m-80) cc_final: 0.7788 (m-10) REVERT: F 138 MET cc_start: 0.7784 (ptm) cc_final: 0.7078 (ptm) REVERT: F 198 HIS cc_start: 0.9021 (p-80) cc_final: 0.8682 (p-80) REVERT: G 89 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8690 (mt) REVERT: G 103 VAL cc_start: 0.8687 (m) cc_final: 0.8273 (p) REVERT: G 200 LEU cc_start: 0.8488 (mp) cc_final: 0.8208 (tp) REVERT: G 665 MET cc_start: 0.8665 (ttt) cc_final: 0.8233 (tmm) REVERT: G 681 MET cc_start: 0.9433 (tpp) cc_final: 0.9149 (tpp) REVERT: G 688 MET cc_start: 0.9181 (mmm) cc_final: 0.8849 (mmt) REVERT: G 696 TYR cc_start: 0.9406 (t80) cc_final: 0.9110 (t80) REVERT: G 743 PHE cc_start: 0.8483 (m-80) cc_final: 0.8195 (m-80) REVERT: G 805 TRP cc_start: 0.8678 (p-90) cc_final: 0.8331 (p-90) REVERT: H 489 LYS cc_start: 0.7519 (mmmt) cc_final: 0.7066 (pttt) REVERT: H 523 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7630 (tp-100) REVERT: H 546 MET cc_start: 0.8510 (mmm) cc_final: 0.8246 (mmm) REVERT: H 566 ARG cc_start: 0.8796 (ptm-80) cc_final: 0.8563 (ptp90) REVERT: H 888 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8426 (ttm) outliers start: 41 outliers final: 24 residues processed: 210 average time/residue: 0.3580 time to fit residues: 120.8694 Evaluate side-chains 198 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 169 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 358 GLN Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 523 GLN Chi-restraints excluded: chain C residue 824 HIS Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 669 LEU Chi-restraints excluded: chain G residue 771 LEU Chi-restraints excluded: chain H residue 523 GLN Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 648 GLU Chi-restraints excluded: chain H residue 653 ILE Chi-restraints excluded: chain H residue 670 VAL Chi-restraints excluded: chain H residue 725 ILE Chi-restraints excluded: chain H residue 810 LEU Chi-restraints excluded: chain H residue 847 ASP Chi-restraints excluded: chain H residue 866 VAL Chi-restraints excluded: chain H residue 888 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 0.6980 chunk 269 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 299 optimal weight: 0.5980 chunk 248 optimal weight: 0.3980 chunk 138 optimal weight: 0.0570 chunk 24 optimal weight: 4.9990 chunk 99 optimal weight: 0.0470 chunk 157 optimal weight: 4.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 HIS F 248 HIS G 704 ASN ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25878 Z= 0.146 Angle : 0.525 10.675 35106 Z= 0.264 Chirality : 0.042 0.260 3834 Planarity : 0.004 0.046 4494 Dihedral : 4.833 61.924 3426 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.45 % Allowed : 8.91 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.61 (0.15), residues: 3120 helix: 1.78 (0.19), residues: 818 sheet: -0.01 (0.18), residues: 816 loop : -0.03 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 770 HIS 0.007 0.001 HIS F 101 PHE 0.014 0.001 PHE H 391 TYR 0.020 0.001 TYR G 353 ARG 0.004 0.000 ARG H 566 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 189 time to evaluate : 3.338 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 136 CYS cc_start: 0.8728 (OUTLIER) cc_final: 0.7823 (m) REVERT: A 138 MET cc_start: 0.8627 (tmm) cc_final: 0.8360 (ptm) REVERT: B 332 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8174 (mt) REVERT: B 555 GLN cc_start: 0.8792 (tp40) cc_final: 0.8439 (tp-100) REVERT: B 681 MET cc_start: 0.9483 (tpt) cc_final: 0.9167 (tpp) REVERT: B 685 ARG cc_start: 0.8896 (mmm-85) cc_final: 0.8052 (ttm-80) REVERT: C 312 HIS cc_start: 0.8074 (m-70) cc_final: 0.7745 (m-70) REVERT: C 319 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7525 (mt-10) REVERT: C 387 TRP cc_start: 0.7824 (m-10) cc_final: 0.7341 (m-10) REVERT: C 737 MET cc_start: 0.8963 (mmt) cc_final: 0.8737 (mmt) REVERT: F 102 MET cc_start: 0.7135 (mtm) cc_final: 0.6709 (mtm) REVERT: F 116 TYR cc_start: 0.8090 (m-80) cc_final: 0.7793 (m-10) REVERT: F 138 MET cc_start: 0.7777 (ptm) cc_final: 0.7076 (ptm) REVERT: F 198 HIS cc_start: 0.8986 (p-80) cc_final: 0.8703 (p90) REVERT: G 50 MET cc_start: 0.5847 (ptt) cc_final: 0.5635 (ptt) REVERT: G 89 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8665 (mt) REVERT: G 103 VAL cc_start: 0.8681 (m) cc_final: 0.8273 (p) REVERT: G 200 LEU cc_start: 0.8497 (mp) cc_final: 0.8256 (tp) REVERT: G 665 MET cc_start: 0.8693 (ttt) cc_final: 0.8252 (tmm) REVERT: G 681 MET cc_start: 0.9429 (tpp) cc_final: 0.9148 (tpp) REVERT: G 688 MET cc_start: 0.9162 (mmm) cc_final: 0.8564 (mmt) REVERT: G 696 TYR cc_start: 0.9418 (t80) cc_final: 0.9113 (t80) REVERT: G 805 TRP cc_start: 0.8683 (p-90) cc_final: 0.8427 (p-90) REVERT: G 808 ARG cc_start: 0.8781 (mtt90) cc_final: 0.8248 (ttm110) REVERT: H 523 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7640 (tp-100) REVERT: H 546 MET cc_start: 0.8451 (mmm) cc_final: 0.8238 (mmm) REVERT: H 815 MET cc_start: 0.8392 (mmm) cc_final: 0.7848 (tmm) REVERT: H 888 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8448 (ttm) outliers start: 40 outliers final: 20 residues processed: 217 average time/residue: 0.3676 time to fit residues: 129.3710 Evaluate side-chains 200 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 175 time to evaluate : 3.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 358 GLN Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 725 ILE Chi-restraints excluded: chain C residue 824 HIS Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 669 LEU Chi-restraints excluded: chain G residue 771 LEU Chi-restraints excluded: chain G residue 814 CYS Chi-restraints excluded: chain H residue 523 GLN Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 648 GLU Chi-restraints excluded: chain H residue 847 ASP Chi-restraints excluded: chain H residue 866 VAL Chi-restraints excluded: chain H residue 888 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 219 optimal weight: 0.9990 chunk 169 optimal weight: 5.9990 chunk 252 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 298 optimal weight: 0.9980 chunk 186 optimal weight: 0.7980 chunk 182 optimal weight: 0.9990 chunk 137 optimal weight: 0.2980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: