Starting phenix.real_space_refine on Tue Aug 26 09:19:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r3l_18872/08_2025/8r3l_18872.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r3l_18872/08_2025/8r3l_18872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8r3l_18872/08_2025/8r3l_18872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r3l_18872/08_2025/8r3l_18872.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r3l_18872/08_2025/8r3l_18872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r3l_18872/08_2025/8r3l_18872.map" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 S 126 5.16 5 C 11144 2.51 5 N 3117 2.21 5 O 3458 1.98 5 H 17553 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35431 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 11437 Classifications: {'peptide': 708} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 675} Chain breaks: 1 Chain: "B" Number of atoms: 11774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 11774 Classifications: {'peptide': 740} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 707} Chain breaks: 1 Chain: "C" Number of atoms: 10917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 10917 Classifications: {'peptide': 677} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 27, 'TRANS': 649} Chain: "R" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 438 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 1, 'rna3p_pyr': 9} Link IDs: {'rna2p': 4, 'rna3p': 10} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' U:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "V" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 527 Classifications: {'RNA': 16} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 10, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 12} Chain: "G" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 338 Classifications: {'peptide': 24} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 16} Time building chain proxies: 7.05, per 1000 atoms: 0.20 Number of scatterers: 35431 At special positions: 0 Unit cell: (105, 128.52, 144.48, 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 126 16.00 P 33 15.00 O 3458 8.00 N 3117 7.00 C 11144 6.00 H 17553 1.00 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: 3.61 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4058 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 23 sheets defined 49.2% alpha, 14.1% beta 5 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 7.37 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 Processing helix chain 'A' and resid 10 through 23 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: 3.689A 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 209 through 216 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 314 removed outlier: 3.718A pdb=" N PHE A 314 " --> pdb=" O CYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 350 removed outlier: 3.562A 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 Processing helix chain 'A' and resid 433 through 452 removed outlier: 3.956A 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: 3.684A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 582 through 602 removed outlier: 4.118A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 612 Processing helix chain 'A' and resid 633 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 4.123A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 removed outlier: 3.526A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 715 removed outlier: 3.514A 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 13 through 22 removed outlier: 3.653A pdb=" N ILE B 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 5.525A 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: 3.506A pdb=" N GLN B 115 " --> pdb=" O MET B 111 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.548A pdb=" N GLN B 124 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 162 through 176 Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 245 through 265 removed outlier: 3.657A pdb=" N ARG B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 291 removed outlier: 3.516A pdb=" N LYS B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.545A 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 376 removed outlier: 4.102A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE B 376 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 474 Processing helix chain 'B' and resid 505 through 512 Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 518 through 537 Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 612 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: 6.588A pdb=" N SER B 678 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 700 removed outlier: 4.155A pdb=" N LEU B 683 " --> pdb=" O GLN B 679 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 733 Processing helix chain 'B' and resid 736 through 756 removed outlier: 3.666A pdb=" N ARG B 755 " --> pdb=" O GLU B 751 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN B 756 " --> pdb=" O GLU B 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.848A 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 27 through 32 Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 60 through 66 Processing helix chain 'C' and resid 92 through 103 removed outlier: 4.140A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 115 removed outlier: 4.397A pdb=" N LYS C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 179 through 194 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 251 through 272 removed outlier: 4.061A pdb=" N VAL C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 285 Processing helix chain 'C' and resid 294 through 301 Processing helix chain 'C' and resid 305 through 316 Processing helix chain 'C' and resid 390 through 405 Processing helix chain 'C' and resid 407 through 413 Processing helix chain 'C' and resid 429 through 441 Processing helix chain 'C' and resid 442 through 448 Processing helix chain 'C' and resid 514 through 518 Processing helix chain 'C' and resid 541 through 556 Processing helix chain 'C' and resid 556 through 567 Processing helix chain 'C' and resid 567 through 573 removed outlier: 3.677A pdb=" N LEU C 571 " --> pdb=" O ASP C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 582 Processing helix chain 'C' and resid 585 through 606 removed outlier: 4.348A pdb=" N GLY C 590 " --> pdb=" O LYS C 586 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLN C 591 " --> pdb=" O ALA C 587 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE C 595 " --> pdb=" O GLN C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 619 Processing helix chain 'C' and resid 620 through 624 removed outlier: 3.909A pdb=" N ALA C 623 " --> pdb=" O PRO C 620 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA C 624 " --> pdb=" O PHE C 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 620 through 624' Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61 removed outlier: 4.010A pdb=" N LYS A 73 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.666A pdb=" N THR A 123 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 293 removed outlier: 6.279A pdb=" N ARG A 496 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N THR A 491 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N THR A 498 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N CYS A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 481 " --> pdb=" O LYS A 506 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 317 through 324 removed outlier: 11.609A pdb=" N LYS A 318 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 10.939A pdb=" N MET A 548 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N GLY A 546 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE A 322 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU A 544 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL A 542 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL A 565 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLU A 544 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU A 563 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG A 496 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N THR A 491 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N THR A 498 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N CYS A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 481 " --> pdb=" O LYS A 506 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 379 removed outlier: 5.710A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL A 379 " --> pdb=" O GLN B 367 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 628 through 632 removed outlier: 6.741A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 185 Processing sheet with id=AB2, first strand: chain 'B' and resid 240 through 244 removed outlier: 6.783A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 489 through 492 removed outlier: 4.539A pdb=" N PHE B 496 " --> pdb=" O VAL B 502 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 642 through 645 Processing sheet with id=AB5, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.571A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET C 90 " --> pdb=" O SER C 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 129 through 135 removed outlier: 5.918A pdb=" N PHE C 130 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR C 245 " --> pdb=" O PHE C 130 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 141 through 146 Processing sheet with id=AB8, first strand: chain 'C' and resid 292 through 293 Processing sheet with id=AB9, first strand: chain 'C' and resid 323 through 325 removed outlier: 6.930A pdb=" N GLU C 362 " --> pdb=" O THR C 333 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N THR C 371 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N VAL C 386 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE C 373 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU C 384 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG C 375 " --> pdb=" O ILE C 382 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 339 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 497 through 498 removed outlier: 6.810A pdb=" N VAL C 504 " --> pdb=" O LEU C 512 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 635 through 640 Processing sheet with id=AC5, first strand: chain 'C' and resid 657 through 659 removed outlier: 6.008A pdb=" N LEU C 665 " --> pdb=" O ALA C 672 " (cutoff:3.500A) 869 hydrogen bonds defined for protein. 2400 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 10.17 Time building geometry restraints manager: 4.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17521 1.03 - 1.23: 227 1.23 - 1.43: 7436 1.43 - 1.62: 10442 1.62 - 1.82: 220 Bond restraints: 35846 Sorted by residual: bond pdb=" N TYR G 3 " pdb=" H1 TYR G 3 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N MET A 1 " pdb=" H MET A 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.22e+00 bond pdb=" CA ILE C 147 " pdb=" CB ILE C 147 " ideal model delta sigma weight residual 1.528 1.543 -0.015 1.34e-02 5.57e+03 1.24e+00 bond pdb=" C SER B 444 " pdb=" O SER B 444 " ideal model delta sigma weight residual 1.243 1.235 0.009 9.50e-03 1.11e+04 8.18e-01 ... (remaining 35841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 64343 1.83 - 3.67: 403 3.67 - 5.50: 29 5.50 - 7.34: 3 7.34 - 9.17: 1 Bond angle restraints: 64779 Sorted by residual: angle pdb=" C SER B 444 " pdb=" CA SER B 444 " pdb=" CB SER B 444 " ideal model delta sigma weight residual 117.23 111.21 6.02 1.36e+00 5.41e-01 1.96e+01 angle pdb=" CB MET A 86 " pdb=" CG MET A 86 " pdb=" SD MET A 86 " ideal model delta sigma weight residual 112.70 121.87 -9.17 3.00e+00 1.11e-01 9.34e+00 angle pdb=" CA SER B 444 " pdb=" C SER B 444 " pdb=" N ASP B 445 " ideal model delta sigma weight residual 119.98 117.57 2.41 8.50e-01 1.38e+00 8.02e+00 angle pdb=" CG MET A 86 " pdb=" SD MET A 86 " pdb=" CE MET A 86 " ideal model delta sigma weight residual 100.90 105.89 -4.99 2.20e+00 2.07e-01 5.15e+00 angle pdb=" CB MET C 206 " pdb=" CG MET C 206 " pdb=" SD MET C 206 " ideal model delta sigma weight residual 112.70 118.94 -6.24 3.00e+00 1.11e-01 4.33e+00 ... (remaining 64774 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 14787 17.94 - 35.88: 1422 35.88 - 53.82: 487 53.82 - 71.76: 129 71.76 - 89.70: 35 Dihedral angle restraints: 16860 sinusoidal: 9597 harmonic: 7263 Sorted by residual: dihedral pdb=" CA PHE A 612 " pdb=" C PHE A 612 " pdb=" N GLU A 613 " pdb=" CA GLU A 613 " ideal model delta harmonic sigma weight residual 180.00 152.52 27.48 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA ASP A 386 " pdb=" CB ASP A 386 " pdb=" CG ASP A 386 " pdb=" OD1 ASP A 386 " ideal model delta sinusoidal sigma weight residual -30.00 -89.55 59.55 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CB GLU A 252 " pdb=" CG GLU A 252 " pdb=" CD GLU A 252 " pdb=" OE1 GLU A 252 " ideal model delta sinusoidal sigma weight residual 0.00 -89.70 89.70 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 16857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2393 0.052 - 0.104: 291 0.104 - 0.155: 71 0.155 - 0.207: 0 0.207 - 0.259: 1 Chirality restraints: 2756 Sorted by residual: chirality pdb=" P U R 18 " pdb=" OP1 U R 18 " pdb=" OP2 U R 18 " pdb=" O5' U R 18 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ILE A 354 " pdb=" N ILE A 354 " pdb=" C ILE A 354 " pdb=" CB ILE A 354 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA ILE C 647 " pdb=" N ILE C 647 " pdb=" C ILE C 647 " pdb=" CB ILE C 647 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 2753 not shown) Planarity restraints: 5157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 571 " 0.214 9.50e-02 1.11e+02 7.16e-02 6.37e+00 pdb=" NE ARG B 571 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 571 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 571 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 571 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG B 571 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG B 571 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG B 571 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG B 571 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 148 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO C 149 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 149 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 149 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " -0.022 2.00e-02 2.50e+03 9.09e-03 2.68e+00 pdb=" N9 A V 4 " 0.022 2.00e-02 2.50e+03 pdb=" C8 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A V 4 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A V 4 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A V 4 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A V 4 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A V 4 " -0.002 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 " 0.003 2.00e-02 2.50e+03 pdb=" H8 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" H2 A V 4 " 0.001 2.00e-02 2.50e+03 ... (remaining 5154 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 1110 2.14 - 2.75: 65361 2.75 - 3.37: 102646 3.37 - 3.98: 132126 3.98 - 4.60: 207843 Nonbonded interactions: 509086 Sorted by model distance: nonbonded pdb=" OE1 GLU A 610 " pdb=" H GLU A 610 " model vdw 1.519 2.450 nonbonded pdb=" OE1 GLU A 243 " pdb=" H GLU A 243 " model vdw 1.521 2.450 nonbonded pdb=" OE1 GLU A 206 " pdb=" H GLU A 206 " model vdw 1.582 2.450 nonbonded pdb=" OD1 ASN C 148 " pdb=" H LYS C 214 " model vdw 1.587 2.450 nonbonded pdb=" O MET B 409 " pdb=" H22 G R 16 " model vdw 1.592 2.450 ... (remaining 509081 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: 4.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.230 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 44.340 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 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 : 0.002 0.034 18293 Z= 0.115 Angle : 0.475 9.170 24830 Z= 0.250 Chirality : 0.038 0.259 2756 Planarity : 0.003 0.095 3092 Dihedral : 17.480 89.696 7198 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.21 % Allowed : 17.91 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.19), residues: 2131 helix: 1.60 (0.17), residues: 956 sheet: 0.23 (0.31), residues: 271 loop : -0.66 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 571 TYR 0.011 0.001 TYR G 17 PHE 0.021 0.001 PHE A 612 TRP 0.012 0.001 TRP C 557 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00249 (18293) covalent geometry : angle 0.47501 (24830) hydrogen bonds : bond 0.14120 ( 879) hydrogen bonds : angle 6.06290 ( 2428) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 194 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 744 MET cc_start: 0.5051 (tpp) cc_final: 0.4190 (ptm) REVERT: C 483 MET cc_start: 0.4067 (mmt) cc_final: 0.3698 (mmm) REVERT: C 493 ARG cc_start: 0.5071 (mmt-90) cc_final: 0.4690 (mtm-85) outliers start: 4 outliers final: 3 residues processed: 198 average time/residue: 0.3832 time to fit residues: 111.6807 Evaluate side-chains 190 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 187 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain C residue 537 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 ASN C 556 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.139194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.100905 restraints weight = 89828.859| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.16 r_work: 0.3193 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.0670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18293 Z= 0.196 Angle : 0.523 5.565 24830 Z= 0.280 Chirality : 0.040 0.164 2756 Planarity : 0.004 0.050 3092 Dihedral : 10.182 74.316 2829 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.26 % Allowed : 16.91 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.18), residues: 2131 helix: 1.54 (0.17), residues: 973 sheet: 0.08 (0.31), residues: 265 loop : -0.85 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 571 TYR 0.014 0.001 TYR G 17 PHE 0.027 0.001 PHE A 612 TRP 0.007 0.001 TRP C 78 HIS 0.006 0.001 HIS C 27 Details of bonding type rmsd covalent geometry : bond 0.00423 (18293) covalent geometry : angle 0.52345 (24830) hydrogen bonds : bond 0.04986 ( 879) hydrogen bonds : angle 4.91735 ( 2428) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8265 (pp) REVERT: B 409 MET cc_start: 0.6327 (pmm) cc_final: 0.6034 (pmm) REVERT: B 707 ARG cc_start: 0.7619 (mtm110) cc_final: 0.7248 (mtt180) REVERT: C 522 GLN cc_start: 0.6092 (mt0) cc_final: 0.5447 (mp10) outliers start: 24 outliers final: 16 residues processed: 209 average time/residue: 0.3603 time to fit residues: 112.5005 Evaluate side-chains 197 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 TRP Chi-restraints excluded: chain G residue 4 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 121 optimal weight: 0.6980 chunk 184 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 ASN A 703 ASN B 306 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.138488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.100319 restraints weight = 89885.076| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.29 r_work: 0.3173 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18293 Z= 0.184 Angle : 0.511 6.286 24830 Z= 0.270 Chirality : 0.039 0.174 2756 Planarity : 0.004 0.038 3092 Dihedral : 10.201 74.173 2827 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.68 % Allowed : 17.17 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.18), residues: 2131 helix: 1.46 (0.17), residues: 973 sheet: -0.05 (0.32), residues: 251 loop : -1.06 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 571 TYR 0.016 0.001 TYR G 17 PHE 0.031 0.001 PHE A 612 TRP 0.012 0.001 TRP C 537 HIS 0.006 0.001 HIS C 27 Details of bonding type rmsd covalent geometry : bond 0.00412 (18293) covalent geometry : angle 0.51056 (24830) hydrogen bonds : bond 0.04601 ( 879) hydrogen bonds : angle 4.71217 ( 2428) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.5149 (ttm-80) cc_final: 0.4867 (ptm160) REVERT: A 292 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8309 (pp) REVERT: B 409 MET cc_start: 0.6396 (pmm) cc_final: 0.5708 (pmm) REVERT: B 522 ASP cc_start: 0.8516 (m-30) cc_final: 0.8074 (m-30) REVERT: B 688 MET cc_start: 0.8386 (mmm) cc_final: 0.8147 (mmp) REVERT: B 707 ARG cc_start: 0.7640 (mtm110) cc_final: 0.7235 (mtt180) REVERT: C 64 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8329 (mtp) REVERT: C 483 MET cc_start: 0.4087 (mmt) cc_final: 0.3759 (mmm) REVERT: C 493 ARG cc_start: 0.5052 (mmt-90) cc_final: 0.4486 (mtm-85) REVERT: C 522 GLN cc_start: 0.6370 (mt0) cc_final: 0.5669 (mp10) outliers start: 32 outliers final: 22 residues processed: 212 average time/residue: 0.3658 time to fit residues: 114.4332 Evaluate side-chains 207 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 737 LYS Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 TRP Chi-restraints excluded: chain G residue 13 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 48 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 171 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 641 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.139673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.102396 restraints weight = 89019.983| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.35 r_work: 0.3204 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18293 Z= 0.117 Angle : 0.473 6.315 24830 Z= 0.248 Chirality : 0.038 0.159 2756 Planarity : 0.003 0.038 3092 Dihedral : 10.116 73.744 2827 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.68 % Allowed : 17.75 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.18), residues: 2131 helix: 1.63 (0.17), residues: 972 sheet: 0.06 (0.33), residues: 251 loop : -1.00 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 571 TYR 0.013 0.001 TYR G 17 PHE 0.028 0.001 PHE A 612 TRP 0.006 0.001 TRP C 557 HIS 0.003 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00260 (18293) covalent geometry : angle 0.47257 (24830) hydrogen bonds : bond 0.03981 ( 879) hydrogen bonds : angle 4.51468 ( 2428) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.5135 (ttm-80) cc_final: 0.4880 (ptm160) REVERT: A 292 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8297 (pp) REVERT: B 409 MET cc_start: 0.6464 (pmm) cc_final: 0.5976 (pmm) REVERT: B 707 ARG cc_start: 0.7607 (mtm110) cc_final: 0.7244 (mtt180) REVERT: B 744 MET cc_start: 0.5091 (tpt) cc_final: 0.4534 (ptm) REVERT: C 10 LEU cc_start: 0.8160 (tp) cc_final: 0.7957 (tp) REVERT: C 64 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8294 (mtp) REVERT: C 522 GLN cc_start: 0.6424 (mt0) cc_final: 0.5715 (mp10) REVERT: C 595 PHE cc_start: 0.7576 (OUTLIER) cc_final: 0.7364 (t80) outliers start: 32 outliers final: 25 residues processed: 207 average time/residue: 0.3800 time to fit residues: 115.8617 Evaluate side-chains 210 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 TRP Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 595 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 155 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 195 optimal weight: 0.9990 chunk 196 optimal weight: 0.9990 chunk 210 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 199 optimal weight: 0.6980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.139325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.101963 restraints weight = 89300.372| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.36 r_work: 0.3197 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18293 Z= 0.123 Angle : 0.468 4.509 24830 Z= 0.246 Chirality : 0.038 0.153 2756 Planarity : 0.003 0.037 3092 Dihedral : 10.077 73.761 2827 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.94 % Allowed : 17.70 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.18), residues: 2131 helix: 1.67 (0.17), residues: 973 sheet: 0.03 (0.33), residues: 251 loop : -1.00 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 721 TYR 0.013 0.001 TYR G 17 PHE 0.026 0.001 PHE A 612 TRP 0.006 0.001 TRP A 577 HIS 0.003 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00274 (18293) covalent geometry : angle 0.46818 (24830) hydrogen bonds : bond 0.03912 ( 879) hydrogen bonds : angle 4.42732 ( 2428) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.5163 (ttm-80) cc_final: 0.4914 (ptm160) REVERT: B 522 ASP cc_start: 0.8495 (m-30) cc_final: 0.8047 (m-30) REVERT: B 707 ARG cc_start: 0.7632 (mtm110) cc_final: 0.7265 (mtt180) REVERT: C 10 LEU cc_start: 0.8170 (tp) cc_final: 0.7965 (tp) REVERT: C 64 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8306 (mtp) REVERT: C 458 MET cc_start: 0.2301 (OUTLIER) cc_final: 0.2025 (tpp) REVERT: C 522 GLN cc_start: 0.6460 (mt0) cc_final: 0.5702 (mp10) REVERT: C 525 GLU cc_start: 0.6594 (pm20) cc_final: 0.6242 (pm20) REVERT: C 595 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.7339 (t80) outliers start: 37 outliers final: 29 residues processed: 215 average time/residue: 0.3367 time to fit residues: 105.7895 Evaluate side-chains 216 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 TRP Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 595 PHE Chi-restraints excluded: chain G residue 4 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 145 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.138877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.100909 restraints weight = 89248.389| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.24 r_work: 0.3193 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18293 Z= 0.147 Angle : 0.481 5.128 24830 Z= 0.253 Chirality : 0.038 0.161 2756 Planarity : 0.003 0.037 3092 Dihedral : 10.083 73.664 2827 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.04 % Allowed : 17.49 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.18), residues: 2131 helix: 1.65 (0.17), residues: 974 sheet: -0.01 (0.33), residues: 251 loop : -1.03 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 269 TYR 0.014 0.001 TYR G 17 PHE 0.028 0.001 PHE A 612 TRP 0.006 0.001 TRP A 577 HIS 0.003 0.001 HIS C 27 Details of bonding type rmsd covalent geometry : bond 0.00329 (18293) covalent geometry : angle 0.48079 (24830) hydrogen bonds : bond 0.04001 ( 879) hydrogen bonds : angle 4.43105 ( 2428) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8267 (pp) REVERT: B 314 ASN cc_start: 0.8125 (t0) cc_final: 0.7793 (m110) REVERT: B 522 ASP cc_start: 0.8517 (m-30) cc_final: 0.8069 (m-30) REVERT: B 707 ARG cc_start: 0.7651 (mtm110) cc_final: 0.7276 (mtt180) REVERT: B 744 MET cc_start: 0.5357 (tpp) cc_final: 0.4445 (ptm) REVERT: C 64 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8299 (mtp) REVERT: C 458 MET cc_start: 0.2290 (OUTLIER) cc_final: 0.1959 (tpp) REVERT: C 493 ARG cc_start: 0.5179 (mmt-90) cc_final: 0.4748 (mtm-85) REVERT: C 522 GLN cc_start: 0.6462 (mt0) cc_final: 0.5679 (mp10) REVERT: C 595 PHE cc_start: 0.7614 (OUTLIER) cc_final: 0.7408 (t80) outliers start: 39 outliers final: 28 residues processed: 213 average time/residue: 0.3075 time to fit residues: 97.6733 Evaluate side-chains 213 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 TRP Chi-restraints excluded: chain C residue 595 PHE Chi-restraints excluded: chain G residue 4 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 102 optimal weight: 0.0980 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 200 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 166 optimal weight: 0.5980 chunk 214 optimal weight: 0.0070 chunk 74 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.139753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.102483 restraints weight = 89304.650| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.41 r_work: 0.3207 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18293 Z= 0.105 Angle : 0.463 4.931 24830 Z= 0.242 Chirality : 0.038 0.150 2756 Planarity : 0.003 0.036 3092 Dihedral : 10.043 73.646 2827 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.83 % Allowed : 17.49 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.18), residues: 2131 helix: 1.77 (0.17), residues: 973 sheet: 0.02 (0.33), residues: 253 loop : -0.96 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 493 TYR 0.013 0.001 TYR G 17 PHE 0.026 0.001 PHE A 612 TRP 0.006 0.001 TRP A 368 HIS 0.002 0.000 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00234 (18293) covalent geometry : angle 0.46303 (24830) hydrogen bonds : bond 0.03754 ( 879) hydrogen bonds : angle 4.33239 ( 2428) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 522 ASP cc_start: 0.8492 (m-30) cc_final: 0.8047 (m-30) REVERT: B 707 ARG cc_start: 0.7567 (mtm110) cc_final: 0.7231 (mtt180) REVERT: B 744 MET cc_start: 0.5324 (tpp) cc_final: 0.4421 (ptm) REVERT: C 64 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8275 (mtp) REVERT: C 458 MET cc_start: 0.2286 (OUTLIER) cc_final: 0.1949 (tpp) REVERT: C 522 GLN cc_start: 0.6435 (mt0) cc_final: 0.5668 (mp10) outliers start: 35 outliers final: 29 residues processed: 208 average time/residue: 0.3283 time to fit residues: 101.2882 Evaluate side-chains 211 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 TRP Chi-restraints excluded: chain G residue 11 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 61 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 211 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.139502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.101745 restraints weight = 89044.085| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.28 r_work: 0.3203 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18293 Z= 0.117 Angle : 0.467 5.789 24830 Z= 0.244 Chirality : 0.038 0.155 2756 Planarity : 0.003 0.037 3092 Dihedral : 9.957 73.573 2823 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.68 % Allowed : 17.91 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.18), residues: 2131 helix: 1.81 (0.17), residues: 974 sheet: -0.14 (0.32), residues: 266 loop : -0.97 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 269 TYR 0.013 0.001 TYR G 17 PHE 0.027 0.001 PHE A 612 TRP 0.007 0.001 TRP B 309 HIS 0.002 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00262 (18293) covalent geometry : angle 0.46695 (24830) hydrogen bonds : bond 0.03745 ( 879) hydrogen bonds : angle 4.30692 ( 2428) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8275 (pp) REVERT: B 148 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7104 (mp0) REVERT: B 522 ASP cc_start: 0.8501 (m-30) cc_final: 0.8048 (m-30) REVERT: B 707 ARG cc_start: 0.7591 (mtm110) cc_final: 0.7236 (mtt180) REVERT: B 744 MET cc_start: 0.5497 (tpp) cc_final: 0.4574 (ptm) REVERT: C 1 MET cc_start: 0.4600 (tpp) cc_final: 0.4240 (tpp) REVERT: C 64 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8284 (mtp) REVERT: C 522 GLN cc_start: 0.6437 (mt0) cc_final: 0.5672 (mp10) outliers start: 32 outliers final: 27 residues processed: 206 average time/residue: 0.3375 time to fit residues: 102.6617 Evaluate side-chains 212 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 TRP Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain G residue 11 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 81 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 184 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.138506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.101262 restraints weight = 88914.759| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.54 r_work: 0.3185 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18293 Z= 0.152 Angle : 0.485 5.864 24830 Z= 0.255 Chirality : 0.039 0.170 2756 Planarity : 0.004 0.038 3092 Dihedral : 10.006 73.473 2823 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.73 % Allowed : 17.64 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.18), residues: 2131 helix: 1.74 (0.17), residues: 973 sheet: -0.13 (0.32), residues: 263 loop : -1.06 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 269 TYR 0.015 0.001 TYR G 17 PHE 0.031 0.001 PHE A 612 TRP 0.007 0.001 TRP A 406 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00342 (18293) covalent geometry : angle 0.48529 (24830) hydrogen bonds : bond 0.03955 ( 879) hydrogen bonds : angle 4.37433 ( 2428) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8244 (pp) REVERT: B 522 ASP cc_start: 0.8499 (m-30) cc_final: 0.8047 (m-30) REVERT: B 707 ARG cc_start: 0.7644 (mtm110) cc_final: 0.7260 (mtt180) REVERT: B 744 MET cc_start: 0.5520 (tpp) cc_final: 0.4532 (ptm) REVERT: C 64 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8262 (mtp) REVERT: C 522 GLN cc_start: 0.6563 (mt0) cc_final: 0.5761 (mp10) outliers start: 33 outliers final: 26 residues processed: 210 average time/residue: 0.3438 time to fit residues: 106.7066 Evaluate side-chains 210 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 TRP Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain G residue 11 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 96 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 179 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 581 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.138311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.100624 restraints weight = 89443.727| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.28 r_work: 0.3180 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18293 Z= 0.145 Angle : 0.487 6.408 24830 Z= 0.255 Chirality : 0.039 0.168 2756 Planarity : 0.003 0.037 3092 Dihedral : 10.016 73.481 2823 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.52 % Allowed : 17.91 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.18), residues: 2131 helix: 1.74 (0.17), residues: 976 sheet: -0.17 (0.32), residues: 263 loop : -1.07 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 269 TYR 0.015 0.001 TYR G 17 PHE 0.031 0.001 PHE A 612 TRP 0.006 0.001 TRP A 577 HIS 0.003 0.001 HIS C 27 Details of bonding type rmsd covalent geometry : bond 0.00326 (18293) covalent geometry : angle 0.48669 (24830) hydrogen bonds : bond 0.03934 ( 879) hydrogen bonds : angle 4.37183 ( 2428) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8236 (pp) REVERT: B 522 ASP cc_start: 0.8540 (m-30) cc_final: 0.8080 (m-30) REVERT: B 707 ARG cc_start: 0.7649 (mtm110) cc_final: 0.7261 (mtt180) REVERT: B 744 MET cc_start: 0.5506 (tpp) cc_final: 0.4523 (ptm) REVERT: C 64 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8271 (mtp) REVERT: C 493 ARG cc_start: 0.5190 (mmt-90) cc_final: 0.4623 (mtm-85) REVERT: C 522 GLN cc_start: 0.6626 (mt0) cc_final: 0.5848 (mp10) outliers start: 29 outliers final: 26 residues processed: 201 average time/residue: 0.3056 time to fit residues: 92.2223 Evaluate side-chains 208 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 TRP Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain G residue 11 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 203 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 chunk 165 optimal weight: 0.5980 chunk 181 optimal weight: 8.9990 chunk 18 optimal weight: 0.0270 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 26 optimal weight: 0.2980 chunk 92 optimal weight: 1.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.139757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.102377 restraints weight = 88768.011| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.50 r_work: 0.3209 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18293 Z= 0.099 Angle : 0.464 6.417 24830 Z= 0.242 Chirality : 0.038 0.152 2756 Planarity : 0.003 0.036 3092 Dihedral : 9.927 73.521 2823 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.26 % Allowed : 18.17 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.18), residues: 2131 helix: 1.90 (0.17), residues: 977 sheet: -0.09 (0.32), residues: 261 loop : -0.98 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 571 TYR 0.012 0.001 TYR G 17 PHE 0.027 0.001 PHE A 612 TRP 0.010 0.001 TRP B 309 HIS 0.002 0.000 HIS C 27 Details of bonding type rmsd covalent geometry : bond 0.00219 (18293) covalent geometry : angle 0.46441 (24830) hydrogen bonds : bond 0.03597 ( 879) hydrogen bonds : angle 4.25397 ( 2428) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8737.48 seconds wall clock time: 148 minutes 52.72 seconds (8932.72 seconds total)