Starting phenix.real_space_refine on Sun Jun 15 02:08:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pm0_17755/06_2025/8pm0_17755.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pm0_17755/06_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_17755/06_2025/8pm0_17755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pm0_17755/06_2025/8pm0_17755.map" model { file = "/net/cci-nas-00/data/ceres_data/8pm0_17755/06_2025/8pm0_17755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pm0_17755/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.75, per 1000 atoms: 0.58 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: 4.72 Conformation dependent library (CDL) restraints added in 2.2 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: 5.71 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: 5.90 Time building geometry restraints manager: 5.30 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: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 43.520 Find NCS groups from input model: 0.230 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: 0.000 Load rotamer database and sin/cos tables:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.540 ------------------------------------------------------------------------------- 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 : 1.924 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: 1.3495 time to fit residues: 312.4160 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 : 1.730 ------------------------------------------------------------------------------- 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 = 0.3329 r_free = 0.3329 target = 0.112210 restraints weight = 22455.302| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.83 r_work: 0.3067 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 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 73.763 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 4.78842 ( 2262) covalent geometry : bond 0.00309 (17053) covalent geometry : angle 0.52020 (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 : 1.809 Fit side-chains revert: symmetry clash REVERT: A 111 ASP cc_start: 0.3038 (OUTLIER) cc_final: 0.2751 (p0) REVERT: A 155 MET cc_start: 0.3257 (tmt) cc_final: 0.2716 (ptm) REVERT: A 399 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8320 (pt0) REVERT: A 629 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8281 (mm-30) REVERT: B 211 ARG cc_start: 0.8170 (mtm180) cc_final: 0.7909 (mtt90) REVERT: B 227 MET cc_start: 0.8901 (pmm) cc_final: 0.8701 (pmm) REVERT: B 425 ASN cc_start: 0.9097 (OUTLIER) cc_final: 0.8870 (t0) REVERT: B 429 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8812 (mtmt) REVERT: B 446 ASP cc_start: 0.8013 (m-30) cc_final: 0.7477 (m-30) REVERT: B 656 GLU cc_start: 0.7539 (tt0) cc_final: 0.7312 (mm-30) REVERT: B 706 ARG cc_start: 0.8028 (ptp90) cc_final: 0.7678 (ptp90) REVERT: C 28 MET cc_start: 0.8710 (ttp) cc_final: 0.8316 (ttp) REVERT: C 146 ASP cc_start: 0.7903 (p0) cc_final: 0.7355 (p0) REVERT: C 368 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6557 (mtp-110) REVERT: C 396 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6989 (tt0) REVERT: C 473 MET cc_start: 0.6974 (tpp) cc_final: 0.6714 (tpp) outliers start: 49 outliers final: 17 residues processed: 232 average time/residue: 1.5064 time to fit residues: 385.6580 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 : 1.693 ------------------------------------------------------------------------------- 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: 0.9980 chunk 3 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 144 optimal weight: 0.8980 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: 0.0470 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.151942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.112064 restraints weight = 22457.298| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.28 r_work: 0.3074 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1208 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= 0.119 Angle : 0.481 6.280 23147 Z= 0.255 Chirality : 0.039 0.167 2574 Planarity : 0.004 0.057 2870 Dihedral : 10.582 80.259 2676 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.54 % Allowed : 24.80 % 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: 0.89 (0.19), residues: 1976 helix: 1.76 (0.18), residues: 890 sheet: -0.05 (0.32), residues: 241 loop : -0.44 (0.21), residues: 845 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 0.005 0.000 ARG C 17 Details of bonding type rmsd hydrogen bonds : bond 0.04090 ( 822) hydrogen bonds : angle 4.59356 ( 2262) covalent geometry : bond 0.00265 (17053) covalent geometry : angle 0.48085 (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 240 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 195 time to evaluate : 1.989 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.2508 (ppp) cc_final: 0.1184 (ptm) REVERT: A 111 ASP cc_start: 0.3007 (OUTLIER) cc_final: 0.2703 (p0) REVERT: A 155 MET cc_start: 0.2833 (tmt) cc_final: 0.2414 (ptm) REVERT: A 294 ASP cc_start: 0.7899 (t0) cc_final: 0.7454 (t0) REVERT: A 599 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7845 (mm-30) REVERT: A 629 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8258 (mm-30) REVERT: B 211 ARG cc_start: 0.8268 (mtm180) cc_final: 0.7929 (mtt90) REVERT: B 429 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8801 (mtmt) REVERT: B 446 ASP cc_start: 0.7945 (m-30) cc_final: 0.7354 (m-30) REVERT: B 744 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6807 (tmm) REVERT: C 28 MET cc_start: 0.8735 (ttp) cc_final: 0.8446 (ttp) REVERT: C 61 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7789 (mtpt) REVERT: C 146 ASP cc_start: 0.7913 (p0) cc_final: 0.7381 (p0) REVERT: C 147 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7932 (pp) REVERT: C 257 GLN cc_start: 0.6715 (OUTLIER) cc_final: 0.6444 (mt0) REVERT: C 396 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7049 (tt0) REVERT: C 473 MET cc_start: 0.7063 (tpp) cc_final: 0.6826 (tpp) outliers start: 45 outliers final: 12 residues processed: 223 average time/residue: 1.4651 time to fit residues: 360.3184 Evaluate side-chains 200 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 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 223 THR 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 716 GLU Chi-restraints excluded: chain B residue 744 MET Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 396 GLU 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: 2.9990 chunk 81 optimal weight: 5.9990 chunk 111 optimal weight: 0.2980 chunk 146 optimal weight: 2.9990 chunk 162 optimal weight: 0.0060 chunk 57 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 13 optimal weight: 0.1980 chunk 46 optimal weight: 0.0370 chunk 11 optimal weight: 6.9990 chunk 24 optimal weight: 0.2980 overall best weight: 0.1674 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.154759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.114805 restraints weight = 22449.676| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.64 r_work: 0.3139 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1538 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= 0.091 Angle : 0.452 6.164 23147 Z= 0.239 Chirality : 0.038 0.151 2574 Planarity : 0.003 0.057 2870 Dihedral : 10.324 73.571 2670 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.03 % Allowed : 25.08 % Favored : 72.89 % 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: 1.03 (0.19), residues: 1976 helix: 1.88 (0.18), residues: 894 sheet: 0.05 (0.33), residues: 235 loop : -0.39 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 438 HIS 0.004 0.001 HIS C 151 PHE 0.009 0.001 PHE C 330 TYR 0.013 0.001 TYR B 555 ARG 0.005 0.000 ARG C 17 Details of bonding type rmsd hydrogen bonds : bond 0.03366 ( 822) hydrogen bonds : angle 4.41033 ( 2262) covalent geometry : bond 0.00190 (17053) covalent geometry : angle 0.45176 (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 245 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 209 time to evaluate : 1.852 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.2434 (ppp) cc_final: 0.1058 (ttm) REVERT: A 111 ASP cc_start: 0.3058 (OUTLIER) cc_final: 0.2699 (p0) REVERT: A 155 MET cc_start: 0.3236 (tmt) cc_final: 0.2746 (ptp) REVERT: A 294 ASP cc_start: 0.7912 (t0) cc_final: 0.7495 (t0) REVERT: A 599 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7361 (mm-30) REVERT: A 629 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8283 (mm-30) REVERT: B 124 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7833 (mt0) REVERT: B 211 ARG cc_start: 0.8192 (mtm180) cc_final: 0.7902 (mtt90) REVERT: B 353 LYS cc_start: 0.8431 (mtmt) cc_final: 0.7863 (mtmm) REVERT: B 429 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8733 (mtmt) REVERT: B 446 ASP cc_start: 0.7888 (m-30) cc_final: 0.7403 (m-30) REVERT: C 5 LYS cc_start: 0.7697 (mtpp) cc_final: 0.7468 (mtmp) REVERT: C 28 MET cc_start: 0.8623 (ttp) cc_final: 0.8367 (ttp) REVERT: C 146 ASP cc_start: 0.7895 (p0) cc_final: 0.7345 (p0) REVERT: C 147 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7885 (pp) REVERT: C 191 LYS cc_start: 0.8136 (mmtm) cc_final: 0.7556 (tmmm) REVERT: C 215 THR cc_start: 0.7955 (OUTLIER) cc_final: 0.7204 (p) REVERT: C 216 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7225 (mtm180) REVERT: C 252 ASN cc_start: 0.5751 (OUTLIER) cc_final: 0.5431 (m110) REVERT: C 473 MET cc_start: 0.7132 (tpp) cc_final: 0.6905 (tpp) outliers start: 36 outliers final: 13 residues processed: 232 average time/residue: 1.4397 time to fit residues: 368.0957 Evaluate side-chains 204 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 1.749 ------------------------------------------------------------------------------- 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 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 429 LYS Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 716 GLU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 147 ILE 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 252 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 393 SER 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: 0.5980 chunk 75 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 59 optimal weight: 0.2980 chunk 18 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 191 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 194 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 670 GLN B 184 HIS B 687 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.152646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.113897 restraints weight = 22666.702| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.18 r_work: 0.3101 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17053 Z= 0.119 Angle : 0.485 10.880 23147 Z= 0.253 Chirality : 0.039 0.160 2574 Planarity : 0.004 0.056 2870 Dihedral : 10.332 73.570 2670 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.87 % Allowed : 24.80 % 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: 1.03 (0.19), residues: 1976 helix: 1.88 (0.18), residues: 889 sheet: 0.05 (0.32), residues: 243 loop : -0.38 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 438 HIS 0.005 0.001 HIS C 151 PHE 0.010 0.001 PHE C 119 TYR 0.015 0.001 TYR B 555 ARG 0.004 0.000 ARG B 151 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 822) hydrogen bonds : angle 4.40101 ( 2262) covalent geometry : bond 0.00268 (17053) covalent geometry : angle 0.48510 (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: 51 poor density : 189 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2396 (ppp) cc_final: 0.1095 (ttm) REVERT: A 111 ASP cc_start: 0.3145 (OUTLIER) cc_final: 0.2857 (p0) REVERT: A 155 MET cc_start: 0.2868 (tmt) cc_final: 0.2481 (ptp) REVERT: A 294 ASP cc_start: 0.7935 (t0) cc_final: 0.7456 (t0) REVERT: A 311 MET cc_start: 0.9063 (mmp) cc_final: 0.8747 (mmm) REVERT: A 599 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7368 (mm-30) REVERT: A 629 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8310 (mm-30) REVERT: B 124 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7915 (mt0) REVERT: B 211 ARG cc_start: 0.8260 (mtm180) cc_final: 0.7896 (mtt90) REVERT: B 353 LYS cc_start: 0.8519 (mtmt) cc_final: 0.7926 (mtmm) REVERT: B 429 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8715 (mtmt) REVERT: B 446 ASP cc_start: 0.7836 (m-30) cc_final: 0.7409 (m-30) REVERT: B 716 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6500 (tp30) REVERT: C 5 LYS cc_start: 0.7665 (mtpp) cc_final: 0.7393 (mtmm) REVERT: C 28 MET cc_start: 0.8605 (ttp) cc_final: 0.8346 (ttp) REVERT: C 146 ASP cc_start: 0.7921 (p0) cc_final: 0.7380 (p0) REVERT: C 215 THR cc_start: 0.8168 (OUTLIER) cc_final: 0.7380 (p) REVERT: C 216 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7170 (mtm180) REVERT: C 252 ASN cc_start: 0.5820 (OUTLIER) cc_final: 0.5301 (m110) REVERT: C 257 GLN cc_start: 0.6666 (OUTLIER) cc_final: 0.6430 (mt0) REVERT: C 283 MET cc_start: 0.6803 (mmt) cc_final: 0.6546 (mmt) REVERT: C 341 GLU cc_start: 0.5728 (OUTLIER) cc_final: 0.5511 (tp30) REVERT: C 431 MET cc_start: 0.7479 (mtt) cc_final: 0.7144 (mtt) REVERT: C 473 MET cc_start: 0.7136 (tpp) cc_final: 0.6928 (tpp) outliers start: 51 outliers final: 18 residues processed: 224 average time/residue: 1.3786 time to fit residues: 341.9701 Evaluate side-chains 211 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 1.772 ------------------------------------------------------------------------------- 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 394 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 429 LYS 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 716 GLU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 216 ARG 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 341 GLU Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 460 MET 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: 3.9990 chunk 193 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 197 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 190 optimal weight: 0.9980 chunk 52 optimal weight: 0.2980 chunk 24 optimal weight: 0.0030 chunk 50 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.153159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.114064 restraints weight = 22557.285| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.06 r_work: 0.3116 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17053 Z= 0.110 Angle : 0.470 8.031 23147 Z= 0.247 Chirality : 0.039 0.157 2574 Planarity : 0.004 0.055 2870 Dihedral : 10.393 80.674 2670 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.54 % Allowed : 24.75 % Favored : 72.72 % 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: 0.98 (0.19), residues: 1976 helix: 1.83 (0.18), residues: 895 sheet: 0.03 (0.32), residues: 249 loop : -0.41 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 438 HIS 0.005 0.001 HIS C 151 PHE 0.010 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 0.03698 ( 822) hydrogen bonds : angle 4.37610 ( 2262) covalent geometry : bond 0.00244 (17053) covalent geometry : angle 0.46955 (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 239 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 194 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2117 (ppp) cc_final: 0.1170 (ttp) REVERT: A 111 ASP cc_start: 0.3147 (OUTLIER) cc_final: 0.2896 (p0) REVERT: A 155 MET cc_start: 0.2814 (tmt) cc_final: 0.2435 (ptp) REVERT: A 294 ASP cc_start: 0.7940 (t0) cc_final: 0.7449 (t0) REVERT: A 311 MET cc_start: 0.9038 (mmp) cc_final: 0.8735 (mmm) REVERT: A 599 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7294 (mm-30) REVERT: A 629 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8276 (mm-30) REVERT: B 124 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7875 (mt0) REVERT: B 211 ARG cc_start: 0.8213 (mtm180) cc_final: 0.7881 (mtt90) REVERT: B 353 LYS cc_start: 0.8490 (mtmt) cc_final: 0.7896 (mtmm) REVERT: B 429 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8865 (mtmt) REVERT: B 446 ASP cc_start: 0.7783 (m-30) cc_final: 0.7350 (m-30) REVERT: C 5 LYS cc_start: 0.7625 (mtpp) cc_final: 0.7400 (mtmm) REVERT: C 28 MET cc_start: 0.8578 (ttp) cc_final: 0.8337 (ttp) REVERT: C 146 ASP cc_start: 0.7917 (p0) cc_final: 0.7378 (p0) REVERT: C 186 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8027 (m) REVERT: C 191 LYS cc_start: 0.8222 (mmtm) cc_final: 0.7577 (tmmm) REVERT: C 215 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7365 (p) REVERT: C 216 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7198 (mtm180) REVERT: C 252 ASN cc_start: 0.5890 (OUTLIER) cc_final: 0.5376 (m110) REVERT: C 283 MET cc_start: 0.7033 (mmt) cc_final: 0.6563 (mmt) REVERT: C 431 MET cc_start: 0.7467 (mtt) cc_final: 0.7139 (mtt) REVERT: C 536 MET cc_start: 0.3956 (tpt) cc_final: 0.3747 (tmm) outliers start: 45 outliers final: 20 residues processed: 224 average time/residue: 1.4125 time to fit residues: 350.0090 Evaluate side-chains 212 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 1.745 ------------------------------------------------------------------------------- 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 394 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 429 LYS 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 116 LYS Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 460 MET 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: 10.0000 chunk 37 optimal weight: 0.0370 chunk 172 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 154 optimal weight: 0.6980 chunk 157 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- 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 419 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.151402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.111801 restraints weight = 22513.312| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.25 r_work: 0.3092 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1657 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= 0.135 Angle : 0.496 8.860 23147 Z= 0.260 Chirality : 0.040 0.169 2574 Planarity : 0.004 0.054 2870 Dihedral : 10.369 73.553 2670 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.82 % Allowed : 24.46 % Favored : 72.72 % 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: 0.95 (0.19), residues: 1976 helix: 1.78 (0.17), residues: 892 sheet: 0.11 (0.32), residues: 248 loop : -0.42 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 438 HIS 0.005 0.001 HIS C 151 PHE 0.016 0.001 PHE B 344 TYR 0.016 0.001 TYR B 555 ARG 0.005 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.04045 ( 822) hydrogen bonds : angle 4.42151 ( 2262) covalent geometry : bond 0.00307 (17053) covalent geometry : angle 0.49561 (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 238 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 188 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2170 (ppp) cc_final: 0.1023 (tmt) REVERT: A 111 ASP cc_start: 0.3103 (OUTLIER) cc_final: 0.2847 (p0) REVERT: A 155 MET cc_start: 0.2856 (tmt) cc_final: 0.2490 (ptp) REVERT: A 294 ASP cc_start: 0.7963 (t0) cc_final: 0.7443 (t0) REVERT: A 311 MET cc_start: 0.9062 (mmp) cc_final: 0.8764 (mmm) REVERT: A 382 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8022 (pt0) REVERT: A 399 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8219 (pt0) REVERT: A 599 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7358 (mm-30) REVERT: A 629 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8239 (mm-30) REVERT: B 108 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7783 (mp) REVERT: B 124 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7917 (mt0) REVERT: B 211 ARG cc_start: 0.8280 (mtm180) cc_final: 0.7892 (mtt90) REVERT: B 353 LYS cc_start: 0.8526 (mtmt) cc_final: 0.7949 (mtmm) REVERT: B 429 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8863 (mttp) REVERT: B 446 ASP cc_start: 0.7823 (m-30) cc_final: 0.7416 (m-30) REVERT: B 744 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.6635 (tmm) REVERT: C 5 LYS cc_start: 0.7577 (mtpp) cc_final: 0.7370 (mtmm) REVERT: C 28 MET cc_start: 0.8588 (ttp) cc_final: 0.8316 (ttp) REVERT: C 90 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.7854 (mpp) REVERT: C 146 ASP cc_start: 0.7931 (p0) cc_final: 0.7399 (p0) REVERT: C 216 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7304 (mtm180) REVERT: C 252 ASN cc_start: 0.5962 (OUTLIER) cc_final: 0.5603 (m110) REVERT: C 257 GLN cc_start: 0.6635 (OUTLIER) cc_final: 0.6388 (mt0) REVERT: C 283 MET cc_start: 0.6980 (mmt) cc_final: 0.6496 (mmt) REVERT: C 467 MET cc_start: 0.6479 (mpp) cc_final: 0.5712 (mpp) REVERT: C 473 MET cc_start: 0.6840 (tpp) cc_final: 0.6534 (tpp) REVERT: C 536 MET cc_start: 0.3978 (tpt) cc_final: 0.3769 (tmm) outliers start: 50 outliers final: 21 residues processed: 220 average time/residue: 1.3935 time to fit residues: 338.5346 Evaluate side-chains 212 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 1.703 ------------------------------------------------------------------------------- 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 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 356 MET Chi-restraints excluded: chain B residue 429 LYS 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 90 MET Chi-restraints excluded: chain C residue 116 LYS 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 252 ASN Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 346 THR 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: 0.8980 chunk 25 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 173 optimal weight: 0.0670 chunk 37 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 21 optimal weight: 0.4980 chunk 142 optimal weight: 0.7980 chunk 158 optimal weight: 7.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN B 184 HIS B 687 GLN C 419 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.152379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.112882 restraints weight = 22494.285| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.18 r_work: 0.3106 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17053 Z= 0.112 Angle : 0.481 10.989 23147 Z= 0.252 Chirality : 0.039 0.163 2574 Planarity : 0.004 0.054 2870 Dihedral : 10.389 81.748 2670 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.25 % Allowed : 25.14 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.96 (0.19), residues: 1976 helix: 1.79 (0.17), residues: 896 sheet: 0.18 (0.33), residues: 240 loop : -0.45 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 438 HIS 0.004 0.001 HIS C 151 PHE 0.014 0.001 PHE B 344 TYR 0.014 0.001 TYR B 555 ARG 0.004 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.03741 ( 822) hydrogen bonds : angle 4.37294 ( 2262) covalent geometry : bond 0.00250 (17053) covalent geometry : angle 0.48114 (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 227 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.1973 (ppp) cc_final: 0.1082 (tmm) REVERT: A 111 ASP cc_start: 0.3175 (OUTLIER) cc_final: 0.2889 (p0) REVERT: A 155 MET cc_start: 0.2940 (tmt) cc_final: 0.2511 (ptp) REVERT: A 294 ASP cc_start: 0.7955 (t0) cc_final: 0.7468 (t0) REVERT: A 311 MET cc_start: 0.9002 (mmp) cc_final: 0.8798 (mmm) REVERT: A 382 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.8023 (pt0) REVERT: A 599 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7291 (mm-30) REVERT: B 108 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7786 (mp) REVERT: B 124 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.8137 (mt0) REVERT: B 211 ARG cc_start: 0.8204 (mtm180) cc_final: 0.7897 (mtt90) REVERT: B 353 LYS cc_start: 0.8458 (mtmt) cc_final: 0.7891 (mtmm) REVERT: B 429 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8863 (mttp) REVERT: B 446 ASP cc_start: 0.7839 (m-30) cc_final: 0.7419 (m-30) REVERT: C 28 MET cc_start: 0.8556 (ttp) cc_final: 0.8344 (ttp) REVERT: C 90 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7859 (mpp) REVERT: C 146 ASP cc_start: 0.8000 (p0) cc_final: 0.7444 (p0) REVERT: C 191 LYS cc_start: 0.8206 (mmtm) cc_final: 0.7543 (tmmm) REVERT: C 216 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7341 (mtm180) REVERT: C 257 GLN cc_start: 0.6686 (OUTLIER) cc_final: 0.6422 (mt0) REVERT: C 283 MET cc_start: 0.6945 (mmt) cc_final: 0.6417 (mmt) REVERT: C 368 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6492 (mtp-110) REVERT: C 473 MET cc_start: 0.6855 (tpp) cc_final: 0.6516 (tpp) outliers start: 40 outliers final: 21 residues processed: 212 average time/residue: 1.3986 time to fit residues: 327.8287 Evaluate side-chains 215 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 1.683 ------------------------------------------------------------------------------- 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 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 356 MET Chi-restraints excluded: chain B residue 429 LYS 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 90 MET Chi-restraints excluded: chain C residue 116 LYS 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 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: 2.9990 chunk 39 optimal weight: 0.5980 chunk 159 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 180 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN B 184 HIS B 687 GLN C 419 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.148914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.107553 restraints weight = 22516.506| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.90 r_work: 0.3053 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17053 Z= 0.203 Angle : 0.572 12.833 23147 Z= 0.297 Chirality : 0.042 0.196 2574 Planarity : 0.004 0.057 2870 Dihedral : 10.494 74.213 2670 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.31 % Allowed : 25.14 % Favored : 72.55 % 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: 0.73 (0.18), residues: 1976 helix: 1.58 (0.17), residues: 890 sheet: 0.16 (0.32), residues: 246 loop : -0.57 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 438 HIS 0.004 0.001 HIS C 127 PHE 0.014 0.002 PHE B 551 TYR 0.018 0.002 TYR B 555 ARG 0.007 0.001 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.04840 ( 822) hydrogen bonds : angle 4.57356 ( 2262) covalent geometry : bond 0.00475 (17053) covalent geometry : angle 0.57220 (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 222 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 2.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.1728 (ppp) cc_final: 0.0963 (tmm) REVERT: A 6 ARG cc_start: 0.4158 (OUTLIER) cc_final: 0.3295 (mtp180) REVERT: A 111 ASP cc_start: 0.3142 (OUTLIER) cc_final: 0.2746 (p0) REVERT: A 294 ASP cc_start: 0.8002 (t0) cc_final: 0.7520 (t0) REVERT: A 311 MET cc_start: 0.9071 (mmp) cc_final: 0.8798 (mmm) REVERT: A 382 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8041 (pt0) REVERT: A 399 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8210 (pt0) REVERT: A 599 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7427 (mm-30) REVERT: B 108 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7829 (mp) REVERT: B 124 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7939 (mt0) REVERT: B 211 ARG cc_start: 0.8286 (mtm180) cc_final: 0.7945 (mtt90) REVERT: B 429 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8729 (ttpt) REVERT: B 446 ASP cc_start: 0.7938 (m-30) cc_final: 0.7454 (m-30) REVERT: B 744 MET cc_start: 0.6876 (OUTLIER) cc_final: 0.6605 (tmm) REVERT: C 28 MET cc_start: 0.8667 (ttp) cc_final: 0.8410 (ttp) REVERT: C 146 ASP cc_start: 0.8097 (p0) cc_final: 0.7512 (p0) REVERT: C 257 GLN cc_start: 0.6695 (OUTLIER) cc_final: 0.6407 (mt0) REVERT: C 283 MET cc_start: 0.6714 (mmt) cc_final: 0.6501 (mmt) REVERT: C 431 MET cc_start: 0.7423 (mtt) cc_final: 0.7098 (mtt) REVERT: C 473 MET cc_start: 0.6859 (tpp) cc_final: 0.6604 (tpp) outliers start: 41 outliers final: 15 residues processed: 209 average time/residue: 1.7322 time to fit residues: 402.5238 Evaluate side-chains 197 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 1.994 ------------------------------------------------------------------------------- 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 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 429 LYS 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 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 346 THR 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: 0.5980 chunk 190 optimal weight: 2.9990 chunk 39 optimal weight: 0.0870 chunk 162 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 HIS C 110 HIS C 419 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.151428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.112666 restraints weight = 22510.847| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.15 r_work: 0.3089 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17053 Z= 0.119 Angle : 0.501 12.161 23147 Z= 0.262 Chirality : 0.039 0.173 2574 Planarity : 0.004 0.057 2870 Dihedral : 10.449 82.531 2670 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.52 % Allowed : 26.44 % Favored : 72.04 % 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: 1.69 (0.17), residues: 890 sheet: 0.15 (0.33), residues: 242 loop : -0.52 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 438 HIS 0.004 0.001 HIS C 110 PHE 0.017 0.001 PHE B 412 TYR 0.013 0.001 TYR B 555 ARG 0.005 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 822) hydrogen bonds : angle 4.45165 ( 2262) covalent geometry : bond 0.00268 (17053) covalent geometry : angle 0.50123 (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 215 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.1790 (ppp) cc_final: 0.1176 (tmm) REVERT: A 111 ASP cc_start: 0.3250 (OUTLIER) cc_final: 0.2894 (p0) REVERT: A 155 MET cc_start: 0.2891 (tmt) cc_final: 0.2492 (ptp) REVERT: A 294 ASP cc_start: 0.7981 (t0) cc_final: 0.7501 (t0) REVERT: A 311 MET cc_start: 0.9015 (mmp) cc_final: 0.8776 (mmm) REVERT: A 599 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7323 (mm-30) REVERT: B 429 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8859 (mttp) REVERT: B 446 ASP cc_start: 0.7855 (m-30) cc_final: 0.7439 (m-30) REVERT: C 5 LYS cc_start: 0.7836 (mtmm) cc_final: 0.7466 (mtpp) REVERT: C 28 MET cc_start: 0.8604 (ttp) cc_final: 0.8371 (ttp) REVERT: C 146 ASP cc_start: 0.8066 (p0) cc_final: 0.7490 (p0) REVERT: C 283 MET cc_start: 0.6921 (mmt) cc_final: 0.6386 (mmt) REVERT: C 431 MET cc_start: 0.7446 (mtt) cc_final: 0.7123 (mtt) REVERT: C 473 MET cc_start: 0.6914 (tpp) cc_final: 0.6571 (tpp) outliers start: 27 outliers final: 16 residues processed: 208 average time/residue: 1.3415 time to fit residues: 309.4964 Evaluate side-chains 197 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 1.739 ------------------------------------------------------------------------------- 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 286 ASP 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 152 SER Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 592 SER 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 281 LEU Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 346 THR 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 103 optimal weight: 0.0000 chunk 127 optimal weight: 0.4980 chunk 16 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 chunk 184 optimal weight: 0.8980 chunk 198 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 135 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- 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 110 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.152064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.113315 restraints weight = 22521.629| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.23 r_work: 0.3101 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1850 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= 0.113 Angle : 0.508 11.235 23147 Z= 0.262 Chirality : 0.039 0.167 2574 Planarity : 0.004 0.056 2870 Dihedral : 10.353 73.477 2670 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.47 % Allowed : 26.66 % Favored : 71.87 % 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: 0.88 (0.19), residues: 1976 helix: 1.73 (0.17), residues: 895 sheet: 0.17 (0.33), residues: 242 loop : -0.52 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 438 HIS 0.003 0.001 HIS C 151 PHE 0.011 0.001 PHE B 344 TYR 0.014 0.001 TYR B 555 ARG 0.005 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 822) hydrogen bonds : angle 4.38646 ( 2262) covalent geometry : bond 0.00253 (17053) covalent geometry : angle 0.50805 (23147) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13752.89 seconds wall clock time: 237 minutes 55.64 seconds (14275.64 seconds total)