Starting phenix.real_space_refine on Thu Aug 6 18:49:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pm0_17755/08_2026/8pm0_17755.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pm0_17755/08_2026/8pm0_17755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pm0_17755/08_2026/8pm0_17755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pm0_17755/08_2026/8pm0_17755.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pm0_17755/08_2026/8pm0_17755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pm0_17755/08_2026/8pm0_17755.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 141 atoms to isotropic. 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 P 33 5.49 5 Mg 1 5.21 5 S 120 5.16 5 C 10367 2.51 5 N 2906 2.21 5 O 3242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16669 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 5748 Classifications: {'peptide': 708} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 675} Chain breaks: 1 Chain: "B" Number of atoms: 5850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5850 Classifications: {'peptide': 735} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 702} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4283 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 19, 'TRANS': 517} Chain: "V" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 659 Classifications: {'RNA': 31} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 11, 'rna3p_pyr': 13} Link IDs: {'rna2p': 7, 'rna3p': 23} Chain breaks: 1 Chain: "P" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 73 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 2, 'TRANS': 6} Chain: "G" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 2, 'TRANS': 4} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.74, per 1000 atoms: 0.22 Number of scatterers: 16669 At special positions: 0 Unit cell: (96.6, 122.64, 145.32, 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) S 120 16.00 P 33 15.00 Mg 1 11.99 O 3242 8.00 N 2906 7.00 C 10367 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 839.8 milliseconds 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3770 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 21 sheets defined 50.0% alpha, 14.1% beta 6 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 Processing helix chain 'A' and resid 10 through 24 removed outlier: 3.812A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 50 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 139 removed outlier: 3.644A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 186 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 330 through 350 removed outlier: 3.636A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.663A pdb=" N SER A 409 " --> pdb=" O CYS A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 452 removed outlier: 4.295A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 529 through 538 Proline residue: A 534 - end of helix removed outlier: 3.815A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 583 through 601 removed outlier: 3.508A pdb=" N GLN A 587 " --> pdb=" O ARG A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 615 removed outlier: 3.616A pdb=" N LYS A 615 " --> pdb=" O PHE A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 4.043A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 697 through 715 removed outlier: 3.631A pdb=" N LEU A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 14 through 22 removed outlier: 5.849A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 removed outlier: 3.772A pdb=" N GLN B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 124 Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 156 through 161 removed outlier: 3.899A pdb=" N SER B 160 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 175 removed outlier: 3.693A pdb=" N ASP B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 248 through 265 removed outlier: 3.786A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 291 Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.512A pdb=" N GLN B 313 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.537A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 414 through 426 Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 473 Processing helix chain 'B' and resid 505 through 512 Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 518 through 536 Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 613 through 616 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 636 through 640 Processing helix chain 'B' and resid 672 through 678 removed outlier: 6.361A pdb=" N SER B 678 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 700 removed outlier: 4.057A pdb=" N LEU B 683 " --> pdb=" O GLN B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 705 removed outlier: 3.791A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 732 Processing helix chain 'B' and resid 736 through 756 removed outlier: 3.833A pdb=" N ARG B 755 " --> pdb=" O GLU B 751 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN B 756 " --> pdb=" O GLU B 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.983A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 24 through 32 removed outlier: 4.019A pdb=" N ALA C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.827A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 128 Processing helix chain 'C' and resid 155 through 168 Processing helix chain 'C' and resid 169 through 172 removed outlier: 3.520A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 172' Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 250 through 273 removed outlier: 3.861A pdb=" N VAL C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER C 273 " --> pdb=" O ARG C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 286 Processing helix chain 'C' and resid 294 through 299 Processing helix chain 'C' and resid 305 through 316 removed outlier: 3.651A pdb=" N MET C 315 " --> pdb=" O CYS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 406 removed outlier: 3.748A pdb=" N GLN C 406 " --> pdb=" O MET C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 412 Processing helix chain 'C' and resid 429 through 441 removed outlier: 3.581A pdb=" N ASP C 441 " --> pdb=" O HIS C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 448 Processing helix chain 'C' and resid 514 through 518 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.328A pdb=" N PHE A 117 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY A 121 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 293 removed outlier: 7.322A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N VAL A 557 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU A 549 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL A 542 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLY A 546 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N GLU A 319 " --> pdb=" O GLY A 546 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N MET A 548 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 9.892A pdb=" N TRP A 317 " --> pdb=" O MET A 548 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 293 removed outlier: 6.670A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 378 removed outlier: 5.838A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 627 through 631 removed outlier: 6.211A pdb=" N GLY A 631 " --> pdb=" O PRO A 620 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA9, first strand: chain 'B' and resid 178 through 183 Processing sheet with id=AB1, first strand: chain 'B' and resid 240 through 244 removed outlier: 6.930A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 489 through 492 Processing sheet with id=AB3, first strand: chain 'B' and resid 642 through 645 Processing sheet with id=AB4, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.585A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N MET C 90 " --> pdb=" O SER C 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 129 through 135 removed outlier: 5.615A pdb=" N PHE C 130 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR C 245 " --> pdb=" O PHE C 130 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 141 through 145 Processing sheet with id=AB7, first strand: chain 'C' and resid 292 through 293 Processing sheet with id=AB8, first strand: chain 'C' and resid 319 through 320 Processing sheet with id=AB9, first strand: chain 'C' and resid 323 through 325 removed outlier: 6.745A pdb=" N GLU C 362 " --> pdb=" O THR C 333 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ALA C 377 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU C 381 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ARG C 479 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU C 384 " --> pdb=" O ARG C 479 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER C 481 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL C 386 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL C 478 " --> pdb=" O ILE C 463 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ILE C 463 " --> pdb=" O VAL C 478 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 338 through 345 Processing sheet with id=AC2, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AC3, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.777A pdb=" N LEU C 513 " --> pdb=" O VAL C 504 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASP C 506 " --> pdb=" O VAL C 511 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL C 511 " --> pdb=" O ASP C 506 " (cutoff:3.500A) 811 hydrogen bonds defined for protein. 2232 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5352 1.34 - 1.46: 2954 1.46 - 1.58: 8471 1.58 - 1.70: 68 1.70 - 1.82: 208 Bond restraints: 17053 Sorted by residual: bond pdb=" N MET C 1 " pdb=" CA MET C 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.66e+00 bond pdb=" CB GLU B 267 " pdb=" CG GLU B 267 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.05e+00 bond pdb=" C LYS B 353 " pdb=" N GLY B 354 " ideal model delta sigma weight residual 1.335 1.328 0.007 7.50e-03 1.78e+04 8.80e-01 bond pdb=" N9 A V 8 " pdb=" C4 A V 8 " ideal model delta sigma weight residual 1.374 1.368 0.006 6.00e-03 2.78e+04 8.61e-01 ... (remaining 17048 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 22771 1.62 - 3.24: 313 3.24 - 4.86: 61 4.86 - 6.48: 1 6.48 - 8.10: 1 Bond angle restraints: 23147 Sorted by residual: angle pdb=" N ILE A 323 " pdb=" CA ILE A 323 " pdb=" C ILE A 323 " ideal model delta sigma weight residual 111.56 108.63 2.93 8.60e-01 1.35e+00 1.16e+01 angle pdb=" O4' A V 7 " pdb=" C1' A V 7 " pdb=" N9 A V 7 " ideal model delta sigma weight residual 108.20 110.93 -2.73 8.00e-01 1.56e+00 1.16e+01 angle pdb=" O5' U V 46 " pdb=" C5' U V 46 " pdb=" C4' U V 46 " ideal model delta sigma weight residual 109.40 111.99 -2.59 8.00e-01 1.56e+00 1.05e+01 angle pdb=" O5' A V 7 " pdb=" C5' A V 7 " pdb=" C4' A V 7 " ideal model delta sigma weight residual 109.40 111.86 -2.46 8.00e-01 1.56e+00 9.45e+00 angle pdb=" C2' A V 4 " pdb=" C1' A V 4 " pdb=" N9 A V 4 " ideal model delta sigma weight residual 112.00 115.31 -3.31 1.10e+00 8.26e-01 9.07e+00 ... (remaining 23142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 8851 17.82 - 35.65: 1110 35.65 - 53.47: 382 53.47 - 71.29: 123 71.29 - 89.11: 41 Dihedral angle restraints: 10507 sinusoidal: 4690 harmonic: 5817 Sorted by residual: dihedral pdb=" CB GLU A 457 " pdb=" CG GLU A 457 " pdb=" CD GLU A 457 " pdb=" OE1 GLU A 457 " ideal model delta sinusoidal sigma weight residual 0.00 89.11 -89.11 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU A 56 " pdb=" CG GLU A 56 " pdb=" CD GLU A 56 " pdb=" OE1 GLU A 56 " ideal model delta sinusoidal sigma weight residual 0.00 -88.18 88.18 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU B 78 " pdb=" CG GLU B 78 " pdb=" CD GLU B 78 " pdb=" OE1 GLU B 78 " ideal model delta sinusoidal sigma weight residual 0.00 -87.11 87.11 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 10504 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1660 0.030 - 0.059: 641 0.059 - 0.089: 127 0.089 - 0.119: 125 0.119 - 0.149: 21 Chirality restraints: 2574 Sorted by residual: chirality pdb=" C1' A V 4 " pdb=" O4' A V 4 " pdb=" C2' A V 4 " pdb=" N9 A V 4 " both_signs ideal model delta sigma weight residual False 2.47 2.32 0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA ILE C 385 " pdb=" N ILE C 385 " pdb=" C ILE C 385 " pdb=" CB ILE C 385 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA ILE B 450 " pdb=" N ILE B 450 " pdb=" C ILE B 450 " pdb=" CB ILE B 450 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 2571 not shown) Planarity restraints: 2870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " -0.028 2.00e-02 2.50e+03 1.26e-02 4.37e+00 pdb=" N9 A V 4 " 0.029 2.00e-02 2.50e+03 pdb=" C8 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A V 4 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A V 4 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A V 4 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A V 4 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A V 4 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 514 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO C 515 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 515 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 515 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 587 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C GLN A 587 " -0.027 2.00e-02 2.50e+03 pdb=" O GLN A 587 " 0.010 2.00e-02 2.50e+03 pdb=" N SER A 588 " 0.009 2.00e-02 2.50e+03 ... (remaining 2867 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 156 2.58 - 3.16: 13863 3.16 - 3.74: 26554 3.74 - 4.32: 37627 4.32 - 4.90: 62291 Nonbonded interactions: 140491 Sorted by model distance: nonbonded pdb=" O PHE B 700 " pdb=" OG SER B 703 " model vdw 1.995 3.040 nonbonded pdb=" O ARG B 334 " pdb=" OG SER B 338 " model vdw 2.044 3.040 nonbonded pdb=" O MET C 11 " pdb=" NH1 ARG C 17 " model vdw 2.053 3.120 nonbonded pdb=" OG SER B 19 " pdb=" OG SER B 506 " model vdw 2.066 3.040 nonbonded pdb=" O MET B 409 " pdb=" N2 G V 49 " model vdw 2.085 3.120 ... (remaining 140486 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.120 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:7.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 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 0.033 17053 Z= 0.131 Angle : 0.490 8.104 23147 Z= 0.276 Chirality : 0.039 0.149 2574 Planarity : 0.003 0.046 2870 Dihedral : 19.028 89.113 6737 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.14 % Allowed : 25.54 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.19), residues: 1976 helix: 1.73 (0.18), residues: 885 sheet: 0.04 (0.33), residues: 237 loop : -0.35 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 3 TYR 0.013 0.001 TYR B 555 PHE 0.010 0.001 PHE C 119 TRP 0.007 0.001 TRP B 438 HIS 0.002 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (17053) covalent geometry : angle 0.48997 / 0.28 (23147) hydrogen bonds : bond 0.13966 / 8.86 ( 822) hydrogen bonds : angle 6.04662 / 4.29 ( 2262) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.2632 (tmt) cc_final: 0.2256 (ptm) REVERT: B 227 MET cc_start: 0.8830 (pmm) cc_final: 0.8332 (pmm) REVERT: C 536 MET cc_start: 0.4509 (mmm) cc_final: 0.4292 (mmm) outliers start: 38 outliers final: 30 residues processed: 208 average time/residue: 0.5146 time to fit residues: 119.0045 Evaluate side-chains 196 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 27 HIS Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 455 ASP Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 530 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 HIS A 326 HIS A 499 ASN A 510 HIS A 670 GLN B 105 ASN B 184 HIS B 312 ASN B 687 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.149068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.108088 restraints weight = 22496.990| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.66 r_work: 0.3034 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17053 Z= 0.223 Angle : 0.597 7.561 23147 Z= 0.316 Chirality : 0.044 0.188 2574 Planarity : 0.005 0.055 2870 Dihedral : 11.033 73.194 2707 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.27 % Allowed : 23.73 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.18), residues: 1976 helix: 1.38 (0.17), residues: 904 sheet: 0.01 (0.33), residues: 241 loop : -0.58 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 17 TYR 0.015 0.002 TYR B 497 PHE 0.013 0.002 PHE C 119 TRP 0.012 0.002 TRP B 438 HIS 0.006 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.22 (17053) covalent geometry : angle 0.59651 / 0.32 (23147) hydrogen bonds : bond 0.05503 / 3.68 ( 822) hydrogen bonds : angle 4.98827 / 3.52 ( 2262) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 184 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 111 ASP cc_start: 0.2991 (OUTLIER) cc_final: 0.2691 (p0) REVERT: A 155 MET cc_start: 0.3202 (tmt) cc_final: 0.2730 (ptm) REVERT: A 399 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8277 (pt0) REVERT: A 629 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8213 (mm-30) REVERT: B 211 ARG cc_start: 0.8195 (mtm180) cc_final: 0.7928 (mtt90) REVERT: B 425 ASN cc_start: 0.9131 (OUTLIER) cc_final: 0.8913 (t0) REVERT: B 429 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8860 (mtmt) REVERT: B 649 HIS cc_start: 0.7979 (m-70) cc_final: 0.7765 (m90) REVERT: B 656 GLU cc_start: 0.7549 (tt0) cc_final: 0.7223 (mm-30) REVERT: C 28 MET cc_start: 0.8715 (ttp) cc_final: 0.8391 (ttp) REVERT: C 368 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6568 (mtp-110) REVERT: C 437 HIS cc_start: 0.7983 (t-170) cc_final: 0.7629 (t70) outliers start: 58 outliers final: 21 residues processed: 223 average time/residue: 0.5789 time to fit residues: 142.6035 Evaluate side-chains 196 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 716 GLU Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 368 ARG Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 447 GLN Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 483 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 52 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 197 optimal weight: 9.9990 chunk 108 optimal weight: 0.9980 chunk 162 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 184 HIS B 562 HIS B 671 ASN B 687 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.150341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.111093 restraints weight = 22831.600| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.14 r_work: 0.3076 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17053 Z= 0.137 Angle : 0.503 6.104 23147 Z= 0.269 Chirality : 0.040 0.145 2574 Planarity : 0.004 0.056 2870 Dihedral : 10.796 93.957 2681 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.82 % Allowed : 24.58 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.18), residues: 1976 helix: 1.50 (0.17), residues: 901 sheet: -0.01 (0.33), residues: 243 loop : -0.59 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 17 TYR 0.014 0.001 TYR B 555 PHE 0.010 0.001 PHE A 520 TRP 0.011 0.001 TRP B 438 HIS 0.005 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (17053) covalent geometry : angle 0.50329 / 0.27 (23147) hydrogen bonds : bond 0.04519 / 3.02 ( 822) hydrogen bonds : angle 4.74334 / 3.34 ( 2262) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 188 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 111 ASP cc_start: 0.2992 (OUTLIER) cc_final: 0.2632 (p0) REVERT: A 155 MET cc_start: 0.3165 (tmt) cc_final: 0.2764 (ptm) REVERT: A 294 ASP cc_start: 0.7883 (t0) cc_final: 0.7481 (t0) REVERT: A 599 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7670 (mm-30) REVERT: A 629 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8213 (mm-30) REVERT: B 211 ARG cc_start: 0.8177 (mtm180) cc_final: 0.7895 (mtt90) REVERT: B 429 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8848 (mttp) REVERT: B 656 GLU cc_start: 0.7540 (tt0) cc_final: 0.7311 (mm-30) REVERT: B 718 MET cc_start: 0.7149 (mtt) cc_final: 0.6769 (mtt) REVERT: C 28 MET cc_start: 0.8705 (ttp) cc_final: 0.8380 (ttp) REVERT: C 146 ASP cc_start: 0.7901 (p0) cc_final: 0.7363 (p0) REVERT: C 257 GLN cc_start: 0.6568 (OUTLIER) cc_final: 0.6253 (mt0) REVERT: C 368 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6551 (mtp-110) REVERT: C 473 MET cc_start: 0.6941 (tpp) cc_final: 0.6611 (tpp) outliers start: 50 outliers final: 19 residues processed: 222 average time/residue: 0.5740 time to fit residues: 140.7331 Evaluate side-chains 195 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 716 GLU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 368 ARG Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 483 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 153 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 115 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 175 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 105 optimal weight: 0.0370 chunk 72 optimal weight: 1.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 184 HIS B 687 GLN C 419 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.151195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.112078 restraints weight = 22592.664| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.02 r_work: 0.3082 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17053 Z= 0.121 Angle : 0.487 8.619 23147 Z= 0.260 Chirality : 0.039 0.144 2574 Planarity : 0.004 0.057 2870 Dihedral : 10.604 80.116 2674 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.82 % Allowed : 24.97 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.18), residues: 1976 helix: 1.60 (0.17), residues: 896 sheet: 0.00 (0.33), residues: 235 loop : -0.57 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 17 TYR 0.013 0.001 TYR B 555 PHE 0.011 0.001 PHE A 520 TRP 0.011 0.001 TRP B 438 HIS 0.008 0.001 HIS B 649 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (17053) covalent geometry : angle 0.48731 / 0.26 (23147) hydrogen bonds : bond 0.04194 / 2.82 ( 822) hydrogen bonds : angle 4.62958 / 3.26 ( 2262) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 190 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 111 ASP cc_start: 0.3115 (OUTLIER) cc_final: 0.2717 (p0) REVERT: A 155 MET cc_start: 0.3073 (tmt) cc_final: 0.2597 (ptm) REVERT: A 294 ASP cc_start: 0.7927 (t0) cc_final: 0.7501 (t0) REVERT: A 335 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.9030 (tt) REVERT: A 399 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8259 (pt0) REVERT: A 599 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7782 (mm-30) REVERT: A 629 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8227 (mm-30) REVERT: B 108 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7840 (mp) REVERT: B 211 ARG cc_start: 0.8213 (mtm180) cc_final: 0.7903 (mtt90) REVERT: B 429 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8847 (mttp) REVERT: B 446 ASP cc_start: 0.7973 (m-30) cc_final: 0.7380 (m-30) REVERT: B 656 GLU cc_start: 0.7554 (tt0) cc_final: 0.7332 (mm-30) REVERT: C 28 MET cc_start: 0.8693 (ttp) cc_final: 0.8384 (ttp) REVERT: C 146 ASP cc_start: 0.7914 (p0) cc_final: 0.7367 (p0) REVERT: C 216 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7240 (mtm180) REVERT: C 257 GLN cc_start: 0.6641 (OUTLIER) cc_final: 0.6323 (mt0) REVERT: C 312 LYS cc_start: 0.7193 (OUTLIER) cc_final: 0.6945 (mtmm) REVERT: C 396 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7001 (tt0) REVERT: C 473 MET cc_start: 0.6881 (tpp) cc_final: 0.6667 (tpp) REVERT: C 536 MET cc_start: 0.4383 (mmm) cc_final: 0.4148 (mmm) outliers start: 50 outliers final: 25 residues processed: 225 average time/residue: 0.6635 time to fit residues: 165.6630 Evaluate side-chains 212 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 716 GLU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 483 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 13 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 191 optimal weight: 7.9990 chunk 117 optimal weight: 0.8980 chunk 165 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 184 HIS ** B 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 GLN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.150778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.110294 restraints weight = 22547.445| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.19 r_work: 0.3052 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17053 Z= 0.136 Angle : 0.497 8.680 23147 Z= 0.264 Chirality : 0.040 0.150 2574 Planarity : 0.004 0.057 2870 Dihedral : 10.590 97.177 2671 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.21 % Allowed : 24.46 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.18), residues: 1976 helix: 1.63 (0.17), residues: 891 sheet: -0.03 (0.32), residues: 247 loop : -0.55 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 706 TYR 0.014 0.001 TYR B 555 PHE 0.011 0.001 PHE A 520 TRP 0.011 0.001 TRP B 438 HIS 0.006 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (17053) covalent geometry : angle 0.49694 / 0.26 (23147) hydrogen bonds : bond 0.04262 / 2.87 ( 822) hydrogen bonds : angle 4.59897 / 3.24 ( 2262) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 185 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.3124 (OUTLIER) cc_final: 0.2753 (p0) REVERT: A 155 MET cc_start: 0.3078 (tmt) cc_final: 0.2642 (ptm) REVERT: A 294 ASP cc_start: 0.7979 (t0) cc_final: 0.7565 (t0) REVERT: A 335 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.9037 (tt) REVERT: A 399 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8299 (pt0) REVERT: A 599 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7742 (mm-30) REVERT: A 629 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8266 (mm-30) REVERT: B 108 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7828 (mp) REVERT: B 124 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8085 (mt0) REVERT: B 211 ARG cc_start: 0.8290 (mtm180) cc_final: 0.7941 (mtp85) REVERT: B 425 ASN cc_start: 0.9114 (OUTLIER) cc_final: 0.8877 (t0) REVERT: B 429 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8870 (mttp) REVERT: B 446 ASP cc_start: 0.8007 (m-30) cc_final: 0.7515 (m-30) REVERT: C 28 MET cc_start: 0.8721 (ttp) cc_final: 0.8448 (ttp) REVERT: C 146 ASP cc_start: 0.7952 (p0) cc_final: 0.7403 (p0) REVERT: C 257 GLN cc_start: 0.6690 (OUTLIER) cc_final: 0.6366 (mt0) REVERT: C 368 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6531 (mtp-110) REVERT: C 473 MET cc_start: 0.6900 (tpp) cc_final: 0.6660 (tpp) outliers start: 57 outliers final: 28 residues processed: 224 average time/residue: 0.6264 time to fit residues: 155.9469 Evaluate side-chains 215 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 716 GLU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 368 ARG Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 483 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 177 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN B 184 HIS ** B 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 GLN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.148596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.108556 restraints weight = 22615.130| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.17 r_work: 0.3034 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17053 Z= 0.209 Angle : 0.553 8.635 23147 Z= 0.292 Chirality : 0.043 0.166 2574 Planarity : 0.005 0.063 2870 Dihedral : 10.609 82.202 2671 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.95 % Allowed : 23.96 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.18), residues: 1976 helix: 1.42 (0.17), residues: 895 sheet: -0.03 (0.32), residues: 247 loop : -0.69 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 476 TYR 0.017 0.002 TYR B 555 PHE 0.014 0.002 PHE A 520 TRP 0.013 0.002 TRP B 438 HIS 0.007 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.21 (17053) covalent geometry : angle 0.55321 / 0.29 (23147) hydrogen bonds : bond 0.04990 / 3.38 ( 822) hydrogen bonds : angle 4.70853 / 3.31 ( 2262) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 190 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.2918 (tmt) cc_final: 0.2594 (ptm) REVERT: A 294 ASP cc_start: 0.7961 (t0) cc_final: 0.7491 (t0) REVERT: A 335 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9061 (tt) REVERT: A 599 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7753 (mm-30) REVERT: A 629 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8226 (mm-30) REVERT: B 108 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7838 (mp) REVERT: B 124 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8076 (mt0) REVERT: B 211 ARG cc_start: 0.8297 (mtm180) cc_final: 0.7922 (mtp85) REVERT: B 425 ASN cc_start: 0.9116 (OUTLIER) cc_final: 0.8890 (t0) REVERT: B 429 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8889 (mttp) REVERT: B 649 HIS cc_start: 0.7982 (m90) cc_final: 0.7710 (m90) REVERT: C 28 MET cc_start: 0.8657 (ttp) cc_final: 0.8390 (ttp) REVERT: C 146 ASP cc_start: 0.8019 (p0) cc_final: 0.7465 (p0) REVERT: C 257 GLN cc_start: 0.6711 (OUTLIER) cc_final: 0.6403 (mt0) REVERT: C 368 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6523 (mtp-110) REVERT: C 396 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6959 (tt0) REVERT: C 473 MET cc_start: 0.6943 (tpp) cc_final: 0.6738 (tpp) outliers start: 70 outliers final: 31 residues processed: 239 average time/residue: 0.5830 time to fit residues: 154.5263 Evaluate side-chains 220 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 368 ARG Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 532 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 101 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 92 optimal weight: 0.3980 chunk 67 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 499 ASN B 184 HIS ** B 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 GLN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.150201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.111184 restraints weight = 22540.035| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.33 r_work: 0.3060 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17053 Z= 0.133 Angle : 0.506 9.166 23147 Z= 0.268 Chirality : 0.040 0.165 2574 Planarity : 0.004 0.060 2870 Dihedral : 10.523 73.640 2671 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.16 % Allowed : 25.37 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.18), residues: 1976 helix: 1.56 (0.17), residues: 890 sheet: 0.04 (0.33), residues: 238 loop : -0.68 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 706 TYR 0.014 0.001 TYR B 555 PHE 0.011 0.001 PHE A 520 TRP 0.010 0.001 TRP B 438 HIS 0.007 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (17053) covalent geometry : angle 0.50559 / 0.27 (23147) hydrogen bonds : bond 0.04318 / 2.92 ( 822) hydrogen bonds : angle 4.60789 / 3.24 ( 2262) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 187 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.3012 (OUTLIER) cc_final: 0.2600 (p0) REVERT: A 155 MET cc_start: 0.3028 (tmt) cc_final: 0.2598 (ptp) REVERT: A 294 ASP cc_start: 0.8009 (t0) cc_final: 0.7534 (t0) REVERT: A 335 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9040 (tt) REVERT: A 524 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7985 (mt-10) REVERT: A 599 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7531 (mm-30) REVERT: A 629 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8243 (mm-30) REVERT: B 108 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7798 (mp) REVERT: B 124 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7985 (mt0) REVERT: B 211 ARG cc_start: 0.8307 (mtm180) cc_final: 0.7941 (mtp85) REVERT: B 425 ASN cc_start: 0.9086 (OUTLIER) cc_final: 0.8838 (t0) REVERT: B 429 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8868 (mttp) REVERT: C 28 MET cc_start: 0.8635 (ttp) cc_final: 0.8366 (ttp) REVERT: C 146 ASP cc_start: 0.8002 (p0) cc_final: 0.7449 (p0) REVERT: C 257 GLN cc_start: 0.6724 (OUTLIER) cc_final: 0.6419 (mt0) REVERT: C 396 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6942 (tt0) REVERT: C 536 MET cc_start: 0.4290 (mmm) cc_final: 0.4061 (mmm) outliers start: 56 outliers final: 28 residues processed: 228 average time/residue: 0.6425 time to fit residues: 162.5355 Evaluate side-chains 217 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 532 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 34 optimal weight: 0.0170 chunk 37 optimal weight: 0.2980 chunk 151 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.0622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 184 HIS ** B 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 GLN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.149987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.109375 restraints weight = 22554.730| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.66 r_work: 0.3056 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17053 Z= 0.149 Angle : 0.517 9.342 23147 Z= 0.273 Chirality : 0.041 0.166 2574 Planarity : 0.004 0.059 2870 Dihedral : 10.555 92.622 2671 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.33 % Allowed : 25.25 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.18), residues: 1976 helix: 1.56 (0.17), residues: 890 sheet: 0.07 (0.33), residues: 238 loop : -0.68 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 380 TYR 0.014 0.001 TYR B 555 PHE 0.012 0.001 PHE A 520 TRP 0.011 0.001 TRP B 438 HIS 0.007 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (17053) covalent geometry : angle 0.51749 / 0.27 (23147) hydrogen bonds : bond 0.04396 / 2.98 ( 822) hydrogen bonds : angle 4.60376 / 3.24 ( 2262) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 191 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2189 (ppp) cc_final: 0.0739 (ptm) REVERT: A 111 ASP cc_start: 0.3012 (OUTLIER) cc_final: 0.2638 (p0) REVERT: A 155 MET cc_start: 0.3014 (tmt) cc_final: 0.2566 (ptp) REVERT: A 294 ASP cc_start: 0.8013 (t0) cc_final: 0.7565 (t0) REVERT: A 324 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8732 (tmtt) REVERT: A 335 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.9045 (tt) REVERT: A 599 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7435 (mm-30) REVERT: A 629 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8251 (mm-30) REVERT: B 108 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7822 (mp) REVERT: B 211 ARG cc_start: 0.8267 (mtm180) cc_final: 0.7957 (mtp85) REVERT: B 425 ASN cc_start: 0.9099 (OUTLIER) cc_final: 0.8860 (t0) REVERT: B 429 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8886 (mttp) REVERT: C 28 MET cc_start: 0.8614 (ttp) cc_final: 0.8347 (ttp) REVERT: C 146 ASP cc_start: 0.8010 (p0) cc_final: 0.7468 (p0) REVERT: C 257 GLN cc_start: 0.6757 (OUTLIER) cc_final: 0.6416 (mt0) REVERT: C 396 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6993 (tt0) REVERT: C 473 MET cc_start: 0.6853 (tpp) cc_final: 0.6537 (tpp) REVERT: C 536 MET cc_start: 0.4330 (mmm) cc_final: 0.4121 (mmm) outliers start: 59 outliers final: 32 residues processed: 234 average time/residue: 0.6141 time to fit residues: 160.1795 Evaluate side-chains 220 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 179 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 532 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 160 optimal weight: 5.9990 chunk 161 optimal weight: 0.6980 chunk 137 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 15 optimal weight: 0.0060 chunk 173 optimal weight: 0.5980 chunk 130 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 184 HIS ** B 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 GLN C 110 HIS ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.151808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.112068 restraints weight = 22520.344| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.35 r_work: 0.3082 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17053 Z= 0.110 Angle : 0.494 12.275 23147 Z= 0.260 Chirality : 0.039 0.150 2574 Planarity : 0.004 0.056 2870 Dihedral : 10.446 75.171 2671 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.20 % Allowed : 26.61 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.19), residues: 1976 helix: 1.66 (0.18), residues: 891 sheet: 0.10 (0.33), residues: 238 loop : -0.60 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 706 TYR 0.013 0.001 TYR B 555 PHE 0.011 0.001 PHE C 323 TRP 0.009 0.001 TRP B 438 HIS 0.007 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (17053) covalent geometry : angle 0.49431 / 0.26 (23147) hydrogen bonds : bond 0.03882 / 2.63 ( 822) hydrogen bonds : angle 4.51523 / 3.18 ( 2262) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 187 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2491 (ppp) cc_final: 0.1171 (ptm) REVERT: A 111 ASP cc_start: 0.3194 (OUTLIER) cc_final: 0.2818 (p0) REVERT: A 155 MET cc_start: 0.2991 (tmt) cc_final: 0.2586 (ptp) REVERT: A 294 ASP cc_start: 0.8013 (t0) cc_final: 0.7546 (t0) REVERT: A 324 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8777 (tmtt) REVERT: A 599 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7356 (mm-30) REVERT: A 629 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8270 (mm-30) REVERT: B 124 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8015 (mt0) REVERT: B 211 ARG cc_start: 0.8280 (mtm180) cc_final: 0.7923 (mtt90) REVERT: B 260 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7923 (ttp-110) REVERT: B 425 ASN cc_start: 0.9076 (OUTLIER) cc_final: 0.8845 (t0) REVERT: B 429 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8871 (mttp) REVERT: B 554 ASP cc_start: 0.8767 (t0) cc_final: 0.8351 (m-30) REVERT: C 28 MET cc_start: 0.8626 (ttp) cc_final: 0.8377 (ttp) REVERT: C 146 ASP cc_start: 0.7955 (p0) cc_final: 0.7432 (p0) REVERT: C 257 GLN cc_start: 0.6698 (OUTLIER) cc_final: 0.6370 (mt0) REVERT: C 473 MET cc_start: 0.6899 (tpp) cc_final: 0.6629 (tpp) outliers start: 39 outliers final: 21 residues processed: 216 average time/residue: 0.5886 time to fit residues: 140.9465 Evaluate side-chains 210 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 444 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 117 optimal weight: 0.9990 chunk 109 optimal weight: 0.4980 chunk 145 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 184 HIS ** B 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 GLN B 687 GLN C 110 HIS ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.150096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.111196 restraints weight = 22599.984| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.19 r_work: 0.3068 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17053 Z= 0.148 Angle : 0.525 13.238 23147 Z= 0.274 Chirality : 0.040 0.203 2574 Planarity : 0.004 0.059 2870 Dihedral : 10.424 73.535 2670 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.09 % Allowed : 26.78 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.18), residues: 1976 helix: 1.63 (0.17), residues: 888 sheet: 0.09 (0.32), residues: 246 loop : -0.60 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 706 TYR 0.014 0.001 TYR B 555 PHE 0.016 0.001 PHE B 344 TRP 0.011 0.001 TRP B 438 HIS 0.007 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (17053) covalent geometry : angle 0.52459 / 0.27 (23147) hydrogen bonds : bond 0.04255 / 2.89 ( 822) hydrogen bonds : angle 4.54686 / 3.20 ( 2262) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2467 (ppp) cc_final: 0.1187 (ptm) REVERT: A 111 ASP cc_start: 0.3179 (OUTLIER) cc_final: 0.2831 (p0) REVERT: A 132 LEU cc_start: 0.2813 (OUTLIER) cc_final: 0.2597 (tm) REVERT: A 155 MET cc_start: 0.2958 (tmt) cc_final: 0.2534 (ptp) REVERT: A 294 ASP cc_start: 0.8021 (t0) cc_final: 0.7546 (t0) REVERT: A 324 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8740 (tmtt) REVERT: A 599 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7426 (mm-30) REVERT: A 629 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8244 (mm-30) REVERT: B 124 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8058 (mt0) REVERT: B 211 ARG cc_start: 0.8293 (mtm180) cc_final: 0.7894 (mtp85) REVERT: B 425 ASN cc_start: 0.9097 (OUTLIER) cc_final: 0.8886 (t0) REVERT: B 429 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8894 (mttp) REVERT: B 649 HIS cc_start: 0.7824 (m90) cc_final: 0.7601 (m90) REVERT: C 28 MET cc_start: 0.8651 (ttp) cc_final: 0.8393 (ttp) REVERT: C 146 ASP cc_start: 0.8003 (p0) cc_final: 0.7456 (p0) REVERT: C 257 GLN cc_start: 0.6691 (OUTLIER) cc_final: 0.6370 (mt0) REVERT: C 473 MET cc_start: 0.6934 (tpp) cc_final: 0.6651 (tpp) outliers start: 37 outliers final: 22 residues processed: 212 average time/residue: 0.5888 time to fit residues: 138.0832 Evaluate side-chains 211 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 460 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 56 optimal weight: 0.7980 chunk 71 optimal weight: 0.2980 chunk 159 optimal weight: 4.9990 chunk 26 optimal weight: 0.0020 chunk 109 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 171 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 182 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 184 HIS ** B 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 GLN B 687 GLN C 110 HIS ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.151532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.112424 restraints weight = 22438.264| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.19 r_work: 0.3085 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17053 Z= 0.115 Angle : 0.507 13.390 23147 Z= 0.265 Chirality : 0.039 0.183 2574 Planarity : 0.004 0.057 2870 Dihedral : 10.496 98.862 2670 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.48 % Allowed : 25.99 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 1976 helix: 1.68 (0.18), residues: 890 sheet: 0.12 (0.32), residues: 246 loop : -0.59 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 706 TYR 0.014 0.001 TYR B 555 PHE 0.019 0.001 PHE B 344 TRP 0.009 0.001 TRP B 438 HIS 0.006 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (17053) covalent geometry : angle 0.50678 / 0.27 (23147) hydrogen bonds : bond 0.03941 / 2.67 ( 822) hydrogen bonds : angle 4.49196 / 3.17 ( 2262) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5660.52 seconds wall clock time: 97 minutes 17.63 seconds (5837.63 seconds total)