Starting phenix.real_space_refine on Sun May 18 09:20:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pm0_17755/05_2025/8pm0_17755.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pm0_17755/05_2025/8pm0_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8pm0_17755/05_2025/8pm0_17755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pm0_17755/05_2025/8pm0_17755.map" model { file = "/net/cci-nas-00/data/ceres_data/8pm0_17755/05_2025/8pm0_17755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pm0_17755/05_2025/8pm0_17755.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.35, per 1000 atoms: 0.56 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: 4.52 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 5.40 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: 5.81 Time building geometry restraints manager: 5.20 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=" CA GLY B 354 " pdb=" C GLY B 354 " ideal model delta sigma weight residual 1.522 1.511 0.011 1.30e-02 5.92e+03 7.60e-01 ... (remaining 17048 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 22846 1.62 - 3.24: 238 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=" CB MET B 407 " pdb=" CG MET B 407 " pdb=" SD MET B 407 " ideal model delta sigma weight residual 112.70 120.80 -8.10 3.00e+00 1.11e-01 7.30e+00 angle pdb=" N ILE B 248 " pdb=" CA ILE B 248 " pdb=" C ILE B 248 " ideal model delta sigma weight residual 113.20 110.89 2.31 9.60e-01 1.09e+00 5.77e+00 angle pdb=" CA GLY B 500 " pdb=" C GLY B 500 " pdb=" N PHE B 501 " ideal model delta sigma weight residual 115.62 117.36 -1.74 7.60e-01 1.73e+00 5.25e+00 angle pdb=" CB GLU B 267 " pdb=" CG GLU B 267 " pdb=" CD GLU B 267 " ideal model delta sigma weight residual 112.60 116.46 -3.86 1.70e+00 3.46e-01 5.15e+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 - 0.028: 1625 0.028 - 0.057: 681 0.057 - 0.085: 138 0.085 - 0.114: 95 0.114 - 0.142: 35 Chirality restraints: 2574 Sorted by residual: 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 chirality pdb=" CA ILE B 667 " pdb=" N ILE B 667 " pdb=" C ILE B 667 " pdb=" CB ILE B 667 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 40.800 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 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= 0.121 Angle : 0.475 8.104 23147 Z= 0.251 Chirality : 0.037 0.142 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (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 TRP 0.007 0.001 TRP B 438 HIS 0.002 0.001 HIS C 151 PHE 0.010 0.001 PHE C 119 TYR 0.013 0.001 TYR B 555 ARG 0.002 0.000 ARG C 3 Details of bonding type rmsd hydrogen bonds : bond 0.13966 ( 822) hydrogen bonds : angle 6.04662 ( 2262) covalent geometry : bond 0.00268 (17053) covalent geometry : angle 0.47503 (23147) *********************** 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 : 1.949 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: 1.3462 time to fit residues: 310.8836 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 : 1.724 ------------------------------------------------------------------------------- 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 168 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 60 optimal weight: 0.0470 chunk 94 optimal weight: 0.3980 chunk 116 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS A 499 ASN A 510 HIS B 105 ASN B 184 HIS B 312 ASN B 687 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.151528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.112452 restraints weight = 22455.266| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.16 r_work: 0.3088 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17053 Z= 0.137 Angle : 0.520 6.777 23147 Z= 0.276 Chirality : 0.041 0.170 2574 Planarity : 0.004 0.054 2870 Dihedral : 10.878 73.762 2707 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.76 % Allowed : 23.56 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.19), residues: 1976 helix: 1.63 (0.17), residues: 899 sheet: 0.04 (0.33), residues: 239 loop : -0.41 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 438 HIS 0.012 0.001 HIS B 649 PHE 0.010 0.001 PHE A 520 TYR 0.014 0.001 TYR B 555 ARG 0.007 0.000 ARG C 15 Details of bonding type rmsd hydrogen bonds : bond 0.04514 ( 822) hydrogen bonds : angle 4.78839 ( 2262) covalent geometry : bond 0.00309 (17053) covalent geometry : angle 0.52019 (23147) *********************** 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 247 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 198 time to evaluate : 1.837 Fit side-chains revert: symmetry clash REVERT: A 111 ASP cc_start: 0.3027 (OUTLIER) cc_final: 0.2742 (p0) REVERT: A 155 MET cc_start: 0.3263 (tmt) cc_final: 0.2726 (ptm) REVERT: A 399 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8279 (pt0) REVERT: A 629 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8237 (mm-30) REVERT: B 211 ARG cc_start: 0.8172 (mtm180) cc_final: 0.7890 (mtt90) REVERT: B 227 MET cc_start: 0.8882 (pmm) cc_final: 0.8680 (pmm) REVERT: B 425 ASN cc_start: 0.9088 (OUTLIER) cc_final: 0.8863 (t0) REVERT: B 429 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8808 (mtmt) REVERT: B 446 ASP cc_start: 0.7983 (m-30) cc_final: 0.7448 (m-30) REVERT: B 656 GLU cc_start: 0.7509 (tt0) cc_final: 0.7277 (mm-30) REVERT: B 706 ARG cc_start: 0.8000 (ptp90) cc_final: 0.7639 (ptp90) REVERT: C 28 MET cc_start: 0.8690 (ttp) cc_final: 0.8286 (ttp) REVERT: C 146 ASP cc_start: 0.7885 (p0) cc_final: 0.7331 (p0) REVERT: C 368 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6545 (mtp-110) REVERT: C 396 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6952 (tt0) REVERT: C 473 MET cc_start: 0.6969 (tpp) cc_final: 0.6708 (tpp) outliers start: 49 outliers final: 17 residues processed: 232 average time/residue: 1.3865 time to fit residues: 355.7469 Evaluate side-chains 199 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 2.015 ------------------------------------------------------------------------------- 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 A residue 607 LEU 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 716 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 173 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 144 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 195 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 HIS B 562 HIS ** B 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.149877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.108438 restraints weight = 22490.021| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.85 r_work: 0.3041 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17053 Z= 0.158 Angle : 0.513 6.470 23147 Z= 0.272 Chirality : 0.041 0.182 2574 Planarity : 0.004 0.057 2870 Dihedral : 10.680 83.112 2676 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.10 % Allowed : 24.13 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.19), residues: 1976 helix: 1.59 (0.17), residues: 896 sheet: -0.01 (0.33), residues: 239 loop : -0.54 (0.20), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 438 HIS 0.006 0.001 HIS C 151 PHE 0.011 0.001 PHE A 520 TYR 0.015 0.001 TYR B 555 ARG 0.004 0.000 ARG C 17 Details of bonding type rmsd hydrogen bonds : bond 0.04580 ( 822) hydrogen bonds : angle 4.67711 ( 2262) covalent geometry : bond 0.00364 (17053) covalent geometry : angle 0.51341 (23147) *********************** 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 243 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 188 time to evaluate : 1.990 Fit side-chains revert: symmetry clash REVERT: A 111 ASP cc_start: 0.3089 (OUTLIER) cc_final: 0.2674 (p0) REVERT: A 155 MET cc_start: 0.3112 (tmt) cc_final: 0.2604 (ptm) REVERT: A 294 ASP cc_start: 0.7931 (t0) cc_final: 0.7502 (t0) REVERT: A 399 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8327 (pt0) REVERT: A 533 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8201 (tt0) REVERT: A 599 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7836 (mm-30) REVERT: A 629 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8266 (mm-30) REVERT: B 211 ARG cc_start: 0.8249 (mtm180) cc_final: 0.7909 (mtt90) REVERT: B 429 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8826 (mtmt) REVERT: B 446 ASP cc_start: 0.8026 (m-30) cc_final: 0.7449 (m-30) REVERT: B 656 GLU cc_start: 0.7566 (tt0) cc_final: 0.7350 (mm-30) REVERT: B 744 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6877 (tmm) REVERT: C 28 MET cc_start: 0.8728 (ttp) cc_final: 0.8417 (ttp) REVERT: C 146 ASP cc_start: 0.7966 (p0) cc_final: 0.7441 (p0) REVERT: C 257 GLN cc_start: 0.6697 (OUTLIER) cc_final: 0.6390 (mt0) REVERT: C 368 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6553 (mtp-110) REVERT: C 473 MET cc_start: 0.7022 (tpp) cc_final: 0.6776 (tpp) outliers start: 55 outliers final: 17 residues processed: 225 average time/residue: 1.3367 time to fit residues: 332.5770 Evaluate side-chains 195 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 1.766 ------------------------------------------------------------------------------- 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 533 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 152 SER Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 744 MET 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 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 101 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 162 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 13 optimal weight: 0.0970 chunk 46 optimal weight: 0.0020 chunk 11 optimal weight: 7.9990 chunk 24 optimal weight: 0.2980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 HIS B 671 ASN B 687 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.152052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.112626 restraints weight = 22499.762| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.04 r_work: 0.3084 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17053 Z= 0.112 Angle : 0.475 6.768 23147 Z= 0.252 Chirality : 0.039 0.167 2574 Planarity : 0.004 0.057 2870 Dihedral : 10.477 73.522 2671 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.42 % Allowed : 24.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.19), residues: 1976 helix: 1.75 (0.18), residues: 890 sheet: -0.02 (0.33), residues: 239 loop : -0.51 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 438 HIS 0.006 0.001 HIS C 151 PHE 0.010 0.001 PHE A 520 TYR 0.014 0.001 TYR B 555 ARG 0.004 0.000 ARG C 17 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 822) hydrogen bonds : angle 4.53368 ( 2262) covalent geometry : bond 0.00247 (17053) covalent geometry : angle 0.47539 (23147) *********************** 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 236 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 193 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2498 (ppp) cc_final: 0.1212 (ptm) REVERT: A 111 ASP cc_start: 0.3048 (OUTLIER) cc_final: 0.2644 (p0) REVERT: A 155 MET cc_start: 0.3106 (tmt) cc_final: 0.2647 (ptm) REVERT: A 294 ASP cc_start: 0.7932 (t0) cc_final: 0.7530 (t0) REVERT: A 335 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.9017 (tt) REVERT: A 599 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7658 (mm-30) REVERT: A 629 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8233 (mm-30) REVERT: B 124 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7976 (mt0) REVERT: B 211 ARG cc_start: 0.8267 (mtm180) cc_final: 0.7911 (mtt90) REVERT: B 429 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8740 (mtmt) REVERT: B 446 ASP cc_start: 0.7867 (m-30) cc_final: 0.7411 (m-30) REVERT: B 744 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6810 (tmm) REVERT: C 28 MET cc_start: 0.8648 (ttp) cc_final: 0.8359 (ttp) REVERT: C 146 ASP cc_start: 0.7947 (p0) cc_final: 0.7415 (p0) REVERT: C 252 ASN cc_start: 0.5985 (OUTLIER) cc_final: 0.5736 (m110) REVERT: C 257 GLN cc_start: 0.6719 (OUTLIER) cc_final: 0.6440 (mt0) REVERT: C 318 ARG cc_start: 0.7294 (mmt-90) cc_final: 0.7057 (mpt180) REVERT: C 396 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7129 (tt0) REVERT: C 473 MET cc_start: 0.7078 (tpp) cc_final: 0.6836 (tpp) outliers start: 43 outliers final: 15 residues processed: 222 average time/residue: 1.4407 time to fit residues: 352.7305 Evaluate side-chains 205 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 335 LEU 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 223 THR Chi-restraints excluded: chain B residue 260 ARG 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 744 MET Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 252 ASN 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 396 GLU 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 90 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 104 optimal weight: 0.4980 chunk 191 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 194 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN A 670 GLN B 184 HIS B 687 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.150669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.111410 restraints weight = 22680.884| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.26 r_work: 0.3068 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17053 Z= 0.146 Angle : 0.507 11.056 23147 Z= 0.266 Chirality : 0.040 0.180 2574 Planarity : 0.004 0.056 2870 Dihedral : 10.518 84.553 2670 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.99 % Allowed : 24.35 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.19), residues: 1976 helix: 1.67 (0.17), residues: 890 sheet: -0.02 (0.32), residues: 247 loop : -0.52 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 438 HIS 0.006 0.001 HIS C 151 PHE 0.011 0.001 PHE A 520 TYR 0.016 0.001 TYR B 555 ARG 0.004 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.04298 ( 822) hydrogen bonds : angle 4.54373 ( 2262) covalent geometry : bond 0.00336 (17053) covalent geometry : angle 0.50694 (23147) *********************** 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 240 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 187 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2517 (ppp) cc_final: 0.1322 (ptm) REVERT: A 111 ASP cc_start: 0.3175 (OUTLIER) cc_final: 0.2792 (p0) REVERT: A 155 MET cc_start: 0.3071 (tmt) cc_final: 0.2596 (ptp) REVERT: A 294 ASP cc_start: 0.8024 (t0) cc_final: 0.7574 (t0) REVERT: A 382 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.8029 (pt0) REVERT: A 599 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7601 (mm-30) REVERT: A 629 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8232 (mm-30) REVERT: B 108 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7815 (mp) REVERT: B 124 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7932 (mt0) REVERT: B 211 ARG cc_start: 0.8305 (mtm180) cc_final: 0.7936 (mtt90) REVERT: B 429 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8894 (mttp) REVERT: B 446 ASP cc_start: 0.7887 (m-30) cc_final: 0.7450 (m-30) REVERT: B 744 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.6791 (tmm) REVERT: C 28 MET cc_start: 0.8648 (ttp) cc_final: 0.8371 (ttp) REVERT: C 146 ASP cc_start: 0.7961 (p0) cc_final: 0.7421 (p0) REVERT: C 257 GLN cc_start: 0.6718 (OUTLIER) cc_final: 0.6412 (mt0) REVERT: C 431 MET cc_start: 0.7452 (mtt) cc_final: 0.7192 (mtt) outliers start: 53 outliers final: 23 residues processed: 225 average time/residue: 1.4183 time to fit residues: 351.8850 Evaluate side-chains 208 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 1.774 ------------------------------------------------------------------------------- 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 119 GLU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 382 GLU 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 124 GLN Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 260 ARG 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 709 VAL Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 744 MET 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 215 THR Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 333 THR 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 76 optimal weight: 0.0670 chunk 193 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 197 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 HIS B 687 GLN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.150666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.111270 restraints weight = 22588.627| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.25 r_work: 0.3056 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17053 Z= 0.142 Angle : 0.498 8.013 23147 Z= 0.262 Chirality : 0.040 0.180 2574 Planarity : 0.004 0.058 2870 Dihedral : 10.451 73.550 2670 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.66 % Allowed : 23.84 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.18), residues: 1976 helix: 1.66 (0.17), residues: 891 sheet: 0.04 (0.32), residues: 238 loop : -0.57 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 438 HIS 0.006 0.001 HIS C 151 PHE 0.011 0.001 PHE A 520 TYR 0.015 0.001 TYR B 555 ARG 0.004 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.04226 ( 822) hydrogen bonds : angle 4.53174 ( 2262) covalent geometry : bond 0.00325 (17053) covalent geometry : angle 0.49751 (23147) *********************** 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 254 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 189 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2568 (ppp) cc_final: 0.1421 (ptm) REVERT: A 111 ASP cc_start: 0.3205 (OUTLIER) cc_final: 0.2826 (p0) REVERT: A 155 MET cc_start: 0.3047 (tmt) cc_final: 0.2587 (ptp) REVERT: A 294 ASP cc_start: 0.7999 (t0) cc_final: 0.7522 (t0) REVERT: A 382 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8046 (pt0) REVERT: A 399 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8288 (pt0) REVERT: A 599 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7465 (mm-30) REVERT: A 629 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8253 (mm-30) REVERT: B 108 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7784 (mp) REVERT: B 124 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7952 (mt0) REVERT: B 211 ARG cc_start: 0.8311 (mtm180) cc_final: 0.7941 (mtt90) REVERT: B 429 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8889 (mttp) REVERT: B 446 ASP cc_start: 0.7880 (m-30) cc_final: 0.7461 (m-30) REVERT: B 716 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6496 (tp30) REVERT: B 744 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6697 (tmm) REVERT: C 5 LYS cc_start: 0.7954 (mtmm) cc_final: 0.7735 (mtmp) REVERT: C 28 MET cc_start: 0.8643 (ttp) cc_final: 0.8366 (ttp) REVERT: C 146 ASP cc_start: 0.7987 (p0) cc_final: 0.7461 (p0) REVERT: C 216 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7397 (mtm180) REVERT: C 257 GLN cc_start: 0.6706 (OUTLIER) cc_final: 0.6404 (mt0) REVERT: C 473 MET cc_start: 0.6936 (tpp) cc_final: 0.6667 (tpp) outliers start: 65 outliers final: 30 residues processed: 233 average time/residue: 1.4081 time to fit residues: 362.6342 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 : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 382 GLU 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 152 SER Chi-restraints excluded: chain B residue 260 ARG 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 709 VAL Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 716 GLU Chi-restraints excluded: chain B residue 744 MET 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 215 THR Chi-restraints excluded: chain C residue 216 ARG 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 483 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 170 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 172 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 133 optimal weight: 0.4980 chunk 165 optimal weight: 0.0670 chunk 154 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 153 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN A 499 ASN B 184 HIS B 687 GLN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.151920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.111511 restraints weight = 22511.199| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.71 r_work: 0.3080 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17053 Z= 0.112 Angle : 0.490 11.567 23147 Z= 0.256 Chirality : 0.039 0.168 2574 Planarity : 0.004 0.056 2870 Dihedral : 10.436 82.368 2670 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.93 % Allowed : 24.80 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.19), residues: 1976 helix: 1.75 (0.18), residues: 890 sheet: 0.07 (0.32), residues: 250 loop : -0.50 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 438 HIS 0.007 0.001 HIS C 151 PHE 0.010 0.001 PHE A 520 TYR 0.014 0.001 TYR B 555 ARG 0.004 0.000 ARG C 17 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 822) hydrogen bonds : angle 4.45421 ( 2262) covalent geometry : bond 0.00249 (17053) covalent geometry : angle 0.49024 (23147) *********************** 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: 52 poor density : 191 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2392 (ppp) cc_final: 0.0894 (tmm) REVERT: A 111 ASP cc_start: 0.3187 (OUTLIER) cc_final: 0.2836 (p0) REVERT: A 155 MET cc_start: 0.3000 (tmt) cc_final: 0.2566 (ptp) REVERT: A 294 ASP cc_start: 0.7988 (t0) cc_final: 0.7512 (t0) REVERT: A 382 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8049 (pt0) REVERT: A 597 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7819 (mm-30) REVERT: A 599 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7350 (mm-30) REVERT: A 629 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8257 (mm-30) REVERT: B 108 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7792 (mp) REVERT: B 211 ARG cc_start: 0.8266 (mtm180) cc_final: 0.7904 (mtt90) REVERT: B 260 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7855 (ttp-110) REVERT: B 353 LYS cc_start: 0.8584 (mtmt) cc_final: 0.8028 (mtmm) REVERT: B 429 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8871 (mttp) REVERT: B 446 ASP cc_start: 0.7843 (m-30) cc_final: 0.7435 (m-30) REVERT: B 744 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.6662 (tmm) REVERT: C 5 LYS cc_start: 0.7957 (mtmm) cc_final: 0.7743 (mtmp) REVERT: C 28 MET cc_start: 0.8592 (ttp) cc_final: 0.8328 (ttp) REVERT: C 146 ASP cc_start: 0.7962 (p0) cc_final: 0.7445 (p0) REVERT: C 216 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7348 (mtm180) REVERT: C 257 GLN cc_start: 0.6675 (OUTLIER) cc_final: 0.6377 (mt0) REVERT: C 368 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6513 (mtp-110) REVERT: C 473 MET cc_start: 0.6974 (tpp) cc_final: 0.6705 (tpp) outliers start: 52 outliers final: 28 residues processed: 227 average time/residue: 1.4511 time to fit residues: 363.3841 Evaluate side-chains 221 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 1.884 ------------------------------------------------------------------------------- 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 286 ASP Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 388 ASN 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 152 SER 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 546 MET Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 744 MET 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 172 VAL 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 311 CYS 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 444 VAL Chi-restraints excluded: chain C residue 460 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 63 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 173 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN B 184 HIS B 687 GLN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.151610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.109696 restraints weight = 22515.665| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.03 r_work: 0.3061 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1675 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= 0.125 Angle : 0.504 11.957 23147 Z= 0.263 Chirality : 0.040 0.171 2574 Planarity : 0.004 0.057 2870 Dihedral : 10.396 73.502 2670 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.87 % Allowed : 25.31 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.19), residues: 1976 helix: 1.71 (0.17), residues: 891 sheet: 0.11 (0.33), residues: 240 loop : -0.53 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 438 HIS 0.006 0.001 HIS C 151 PHE 0.016 0.001 PHE B 344 TYR 0.015 0.001 TYR B 555 ARG 0.006 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 822) hydrogen bonds : angle 4.44528 ( 2262) covalent geometry : bond 0.00283 (17053) covalent geometry : angle 0.50427 (23147) *********************** 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 238 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 187 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2193 (ppp) cc_final: 0.0945 (tmt) REVERT: A 111 ASP cc_start: 0.3259 (OUTLIER) cc_final: 0.2897 (p0) REVERT: A 132 LEU cc_start: 0.2816 (OUTLIER) cc_final: 0.2611 (tm) REVERT: A 155 MET cc_start: 0.2952 (tmt) cc_final: 0.2515 (ptp) REVERT: A 294 ASP cc_start: 0.8019 (t0) cc_final: 0.7528 (t0) REVERT: A 382 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8065 (pt0) REVERT: A 599 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7407 (mm-30) REVERT: A 629 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8275 (mm-30) REVERT: B 108 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7754 (mp) REVERT: B 124 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8070 (mt0) REVERT: B 211 ARG cc_start: 0.8311 (mtm180) cc_final: 0.7944 (mtt90) REVERT: B 429 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8882 (mttp) REVERT: B 446 ASP cc_start: 0.7862 (m-30) cc_final: 0.7459 (m-30) REVERT: C 28 MET cc_start: 0.8658 (ttp) cc_final: 0.8389 (ttp) REVERT: C 146 ASP cc_start: 0.8044 (p0) cc_final: 0.7489 (p0) REVERT: C 216 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7354 (mtm180) REVERT: C 257 GLN cc_start: 0.6674 (OUTLIER) cc_final: 0.6358 (mt0) REVERT: C 368 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6511 (mtp-110) REVERT: C 431 MET cc_start: 0.7463 (mtt) cc_final: 0.7139 (mtt) REVERT: C 473 MET cc_start: 0.6952 (tpp) cc_final: 0.6595 (tpp) outliers start: 51 outliers final: 29 residues processed: 225 average time/residue: 1.3916 time to fit residues: 346.1746 Evaluate side-chains 221 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG 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 132 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 388 ASN 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 124 GLN Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 260 ARG 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 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 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 311 CYS 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 444 VAL Chi-restraints excluded: chain C residue 460 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 177 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 159 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 180 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 HIS ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 GLN 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 = 0.3773 r_free = 0.3773 target = 0.149725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.110638 restraints weight = 22546.988| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.22 r_work: 0.3056 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17053 Z= 0.174 Angle : 0.552 12.876 23147 Z= 0.286 Chirality : 0.041 0.188 2574 Planarity : 0.004 0.060 2870 Dihedral : 10.507 81.229 2670 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.87 % Allowed : 25.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.18), residues: 1976 helix: 1.60 (0.17), residues: 889 sheet: 0.14 (0.33), residues: 238 loop : -0.61 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 438 HIS 0.006 0.001 HIS C 151 PHE 0.012 0.001 PHE B 551 TYR 0.016 0.001 TYR B 555 ARG 0.006 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.04537 ( 822) hydrogen bonds : angle 4.54493 ( 2262) covalent geometry : bond 0.00405 (17053) covalent geometry : angle 0.55156 (23147) *********************** 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 237 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 186 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.1920 (ppp) cc_final: 0.0827 (tmt) REVERT: A 111 ASP cc_start: 0.3192 (OUTLIER) cc_final: 0.2772 (p0) REVERT: A 132 LEU cc_start: 0.2837 (OUTLIER) cc_final: 0.2610 (tm) REVERT: A 294 ASP cc_start: 0.8024 (t0) cc_final: 0.7566 (t0) REVERT: A 382 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8063 (pt0) REVERT: A 399 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8238 (pt0) REVERT: A 599 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7417 (mm-30) REVERT: A 629 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8237 (mm-30) REVERT: B 108 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7810 (mp) REVERT: B 124 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8072 (mt0) REVERT: B 211 ARG cc_start: 0.8294 (mtm180) cc_final: 0.7937 (mtt90) REVERT: B 429 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8888 (mttp) REVERT: B 446 ASP cc_start: 0.7920 (m-30) cc_final: 0.7433 (m-30) REVERT: C 28 MET cc_start: 0.8678 (ttp) cc_final: 0.8411 (ttp) REVERT: C 146 ASP cc_start: 0.8078 (p0) cc_final: 0.7491 (p0) REVERT: C 257 GLN cc_start: 0.6664 (OUTLIER) cc_final: 0.6325 (mt0) REVERT: C 368 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.6483 (mtp-110) REVERT: C 369 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.7009 (mtp180) REVERT: C 431 MET cc_start: 0.7454 (mtt) cc_final: 0.7141 (mtt) REVERT: C 473 MET cc_start: 0.6970 (tpp) cc_final: 0.6567 (tpp) outliers start: 51 outliers final: 28 residues processed: 221 average time/residue: 1.4305 time to fit residues: 351.5264 Evaluate side-chains 217 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG 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 132 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 388 ASN 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 B residue 108 LEU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 260 ARG 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 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 215 THR Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 368 ARG Chi-restraints excluded: chain C residue 369 ARG Chi-restraints excluded: chain C residue 393 SER 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 164 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 190 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 103 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 135 optimal weight: 0.0070 chunk 183 optimal weight: 3.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 HIS B 679 GLN C 110 HIS ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.152194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.113328 restraints weight = 22519.341| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.10 r_work: 0.3101 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17053 Z= 0.109 Angle : 0.499 12.061 23147 Z= 0.260 Chirality : 0.039 0.168 2574 Planarity : 0.004 0.057 2870 Dihedral : 10.374 73.516 2670 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.97 % Allowed : 26.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.19), residues: 1976 helix: 1.72 (0.18), residues: 892 sheet: 0.12 (0.33), residues: 240 loop : -0.55 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 438 HIS 0.006 0.001 HIS C 151 PHE 0.014 0.001 PHE B 344 TYR 0.013 0.001 TYR B 555 ARG 0.006 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 822) hydrogen bonds : angle 4.43677 ( 2262) covalent geometry : bond 0.00242 (17053) covalent geometry : angle 0.49912 (23147) ********************** 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 219 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.1762 (ppp) cc_final: 0.0916 (tmt) REVERT: A 111 ASP cc_start: 0.3224 (OUTLIER) cc_final: 0.2868 (p0) REVERT: A 132 LEU cc_start: 0.2820 (OUTLIER) cc_final: 0.2603 (tm) REVERT: A 155 MET cc_start: 0.2814 (tmt) cc_final: 0.2407 (ptp) REVERT: A 294 ASP cc_start: 0.7987 (t0) cc_final: 0.7527 (t0) REVERT: A 382 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8022 (pt0) REVERT: A 399 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8272 (pt0) REVERT: A 599 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7295 (mm-30) REVERT: A 629 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8249 (mm-30) REVERT: B 124 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7988 (mt0) REVERT: B 211 ARG cc_start: 0.8243 (mtm180) cc_final: 0.7892 (mtt90) REVERT: B 260 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7868 (ttp-110) REVERT: B 429 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8869 (mttp) REVERT: B 446 ASP cc_start: 0.7828 (m-30) cc_final: 0.7417 (m-30) REVERT: C 28 MET cc_start: 0.8645 (ttp) cc_final: 0.8387 (ttp) REVERT: C 146 ASP cc_start: 0.7992 (p0) cc_final: 0.7458 (p0) REVERT: C 191 LYS cc_start: 0.8238 (mmtm) cc_final: 0.7556 (tmmm) REVERT: C 368 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.6468 (mtp-110) REVERT: C 431 MET cc_start: 0.7446 (mtt) cc_final: 0.7134 (mtt) REVERT: C 473 MET cc_start: 0.6981 (tpp) cc_final: 0.6552 (tpp) outliers start: 35 outliers final: 19 residues processed: 209 average time/residue: 1.3464 time to fit residues: 311.9971 Evaluate side-chains 206 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 1.787 ------------------------------------------------------------------------------- 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 132 LEU Chi-restraints excluded: chain A residue 382 GLU 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 124 GLN Chi-restraints excluded: chain B residue 260 ARG 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 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 215 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 311 CYS 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 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 103 optimal weight: 0.1980 chunk 127 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 109 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 168 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN B 184 HIS B 679 GLN B 687 GLN C 110 HIS ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.151422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.112679 restraints weight = 22543.187| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.93 r_work: 0.3070 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17053 Z= 0.126 Angle : 0.519 11.734 23147 Z= 0.267 Chirality : 0.040 0.172 2574 Planarity : 0.004 0.057 2870 Dihedral : 10.440 81.873 2670 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.09 % Allowed : 26.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.19), residues: 1976 helix: 1.71 (0.18), residues: 890 sheet: 0.11 (0.32), residues: 240 loop : -0.55 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 438 HIS 0.006 0.001 HIS B 649 PHE 0.012 0.001 PHE B 344 TYR 0.015 0.001 TYR B 555 ARG 0.006 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 822) hydrogen bonds : angle 4.43506 ( 2262) covalent geometry : bond 0.00287 (17053) covalent geometry : angle 0.51866 (23147) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12986.17 seconds wall clock time: 224 minutes 5.16 seconds (13445.16 seconds total)