Starting phenix.real_space_refine on Mon Aug 25 12:28:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z9r_39868/08_2025/8z9r_39868.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z9r_39868/08_2025/8z9r_39868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8z9r_39868/08_2025/8z9r_39868.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z9r_39868/08_2025/8z9r_39868.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z9r_39868/08_2025/8z9r_39868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z9r_39868/08_2025/8z9r_39868.map" } resolution = 2.58 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= 0.001 sd= 0.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 52 5.49 5 S 166 5.16 5 C 17607 2.51 5 N 4891 2.21 5 O 5359 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 28075 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 5021 Classifications: {'peptide': 621} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 589} Chain: "B" Number of atoms: 5422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5422 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 35, 'TRANS': 640} Chain breaks: 2 Chain: "C" Number of atoms: 6005 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 746, 5993 Classifications: {'peptide': 746} Link IDs: {'PTRANS': 44, 'TRANS': 701} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 746, 5991 Classifications: {'peptide': 746} Link IDs: {'PTRANS': 44, 'TRANS': 701} Chain breaks: 2 bond proxies already assigned to first conformer: 6111 Chain: "D" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 260 Classifications: {'RNA': 12} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna2p': 4, 'rna3p': 7} Chain: "E" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 83 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pyr': 1} Link IDs: {'rna2p': 2, 'rna3p': 1} Chain: "F" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 269 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 9} Link IDs: {'rna2p': 1, 'rna3p': 11} Chain: "G" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 226 Unusual residues: {'ATP': 1} Classifications: {'RNA': 9, 'undetermined': 1} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8, None: 1} Not linked: pdbres="ATP G 1 " pdbres=" G G 2 " Chain: "H" Number of atoms: 3616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3616 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 26, 'TRANS': 422} Chain: "I" Number of atoms: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 5021 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 33, 'TRANS': 594} Chain breaks: 5 Chain: "J" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1926 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 16, 'TRANS': 220} Chain breaks: 1 Chain: "K" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 226 Unusual residues: {'ATP': 1} Classifications: {'RNA': 9, 'undetermined': 1} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 4, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 5, None: 1} Not linked: pdbres="ATP K 1 " pdbres=" G K 2 " Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER C 336 " occ=0.73 ... (10 atoms not shown) pdb=" OG BSER C 336 " occ=0.27 Time building chain proxies: 6.32, per 1000 atoms: 0.23 Number of scatterers: 28075 At special positions: 0 Unit cell: (115.827, 144.053, 173.253, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 166 16.00 P 52 15.00 O 5359 8.00 N 4891 7.00 C 17607 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6394 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 37 sheets defined 47.3% alpha, 11.4% beta 12 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 3.10 Creating SS restraints... Processing helix chain 'A' and resid 9 through 16 Processing helix chain 'A' and resid 27 through 46 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 134 through 155 Processing helix chain 'A' and resid 157 through 167 Processing helix chain 'A' and resid 177 through 184 Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 233 through 237 removed outlier: 4.208A pdb=" N ASP A 236 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 257 removed outlier: 3.630A pdb=" N GLN A 257 " --> pdb=" O TRP A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 273 through 287 removed outlier: 3.669A pdb=" N LEU A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 302 Processing helix chain 'A' and resid 304 through 316 removed outlier: 3.861A pdb=" N GLU A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 removed outlier: 3.923A pdb=" N GLU A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG A 345 " --> pdb=" O MET A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 380 Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.971A pdb=" N GLN A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 492 Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 498 through 516 removed outlier: 3.501A pdb=" N ASN A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 556 Processing helix chain 'A' and resid 559 through 580 removed outlier: 3.731A pdb=" N ARG A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ARG A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 604 through 617 removed outlier: 3.548A pdb=" N MET A 617 " --> pdb=" O GLY A 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 5 Processing helix chain 'B' and resid 13 through 19 removed outlier: 3.976A pdb=" N GLU B 17 " --> pdb=" O THR B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 47 Proline residue: B 44 - end of helix Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.567A pdb=" N ILE B 70 " --> pdb=" O PRO B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 94 Processing helix chain 'B' and resid 95 through 108 Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 114 through 121 Processing helix chain 'B' and resid 134 through 151 Processing helix chain 'B' and resid 157 through 169 Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 247 through 266 removed outlier: 4.023A pdb=" N GLY B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N PHE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE B 256 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 257 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 286 Processing helix chain 'B' and resid 310 through 325 removed outlier: 3.816A pdb=" N MET B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 344 removed outlier: 3.703A pdb=" N MET B 332 " --> pdb=" O PRO B 328 " (cutoff:3.500A) Proline residue: B 338 - end of helix Processing helix chain 'B' and resid 373 through 378 removed outlier: 4.525A pdb=" N ARG B 378 " --> pdb=" O ASP B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 409 removed outlier: 3.704A pdb=" N SER B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 450 removed outlier: 3.945A pdb=" N VAL B 450 " --> pdb=" O THR B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 459 removed outlier: 3.659A pdb=" N CYS B 459 " --> pdb=" O PRO B 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 456 through 459' Processing helix chain 'B' and resid 486 through 491 removed outlier: 4.294A pdb=" N VAL B 491 " --> pdb=" O PRO B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 514 Processing helix chain 'B' and resid 518 through 537 removed outlier: 3.509A pdb=" N TYR B 537 " --> pdb=" O TYR B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 552 Processing helix chain 'B' and resid 558 through 562 Processing helix chain 'B' and resid 575 through 583 Processing helix chain 'B' and resid 587 through 595 removed outlier: 3.690A pdb=" N ARG B 593 " --> pdb=" O GLU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 666 Processing helix chain 'B' and resid 667 through 671 Processing helix chain 'B' and resid 679 through 694 Processing helix chain 'B' and resid 698 through 708 removed outlier: 3.915A pdb=" N ARG B 708 " --> pdb=" O ARG B 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 27 removed outlier: 3.795A pdb=" N LEU C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 36 No H-bonds generated for 'chain 'C' and resid 34 through 36' Processing helix chain 'C' and resid 37 through 42 Processing helix chain 'C' and resid 52 through 55 Processing helix chain 'C' and resid 56 through 62 Processing helix chain 'C' and resid 102 through 109 removed outlier: 3.975A pdb=" N LYS C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 123 Processing helix chain 'C' and resid 123 through 136 removed outlier: 3.514A pdb=" N THR C 136 " --> pdb=" O ARG C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 165 No H-bonds generated for 'chain 'C' and resid 163 through 165' Processing helix chain 'C' and resid 166 through 176 Processing helix chain 'C' and resid 177 through 180 removed outlier: 3.503A pdb=" N THR C 180 " --> pdb=" O PRO C 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 180' Processing helix chain 'C' and resid 181 through 187 Processing helix chain 'C' and resid 189 through 204 Proline residue: C 202 - end of helix Processing helix chain 'C' and resid 208 through 220 Processing helix chain 'C' and resid 237 through 239 No H-bonds generated for 'chain 'C' and resid 237 through 239' Processing helix chain 'C' and resid 240 through 245 Processing helix chain 'C' and resid 260 through 276 Processing helix chain 'C' and resid 280 through 290 removed outlier: 4.066A pdb=" N THR C 284 " --> pdb=" O CYS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 306 Processing helix chain 'C' and resid 310 through 320 Processing helix chain 'C' and resid 403 through 415 removed outlier: 3.504A pdb=" N LEU C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 446 Processing helix chain 'C' and resid 448 through 455 Processing helix chain 'C' and resid 547 through 562 removed outlier: 3.796A pdb=" N HIS C 562 " --> pdb=" O SER C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 576 Processing helix chain 'C' and resid 581 through 589 Processing helix chain 'C' and resid 594 through 609 Processing helix chain 'C' and resid 615 through 630 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 737 through 754 removed outlier: 3.512A pdb=" N ARG C 754 " --> pdb=" O ARG C 750 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 185 removed outlier: 3.625A pdb=" N THR H 181 " --> pdb=" O THR H 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 257 Processing helix chain 'H' and resid 272 through 286 removed outlier: 4.121A pdb=" N CYS H 276 " --> pdb=" O SER H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 298 Processing helix chain 'H' and resid 304 through 317 Processing helix chain 'H' and resid 335 through 344 removed outlier: 3.936A pdb=" N GLU H 339 " --> pdb=" O PRO H 335 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 380 Processing helix chain 'H' and resid 382 through 403 removed outlier: 3.755A pdb=" N GLN H 401 " --> pdb=" O ARG H 397 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N HIS H 403 " --> pdb=" O PHE H 399 " (cutoff:3.500A) Processing helix chain 'H' and resid 484 through 493 removed outlier: 3.533A pdb=" N ASN H 493 " --> pdb=" O TYR H 489 " (cutoff:3.500A) Processing helix chain 'H' and resid 494 through 497 Processing helix chain 'H' and resid 498 through 515 Processing helix chain 'H' and resid 540 through 557 Processing helix chain 'H' and resid 559 through 581 removed outlier: 4.380A pdb=" N ARG H 571 " --> pdb=" O ALA H 567 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU H 572 " --> pdb=" O ASN H 568 " (cutoff:3.500A) Processing helix chain 'H' and resid 592 through 599 removed outlier: 4.354A pdb=" N LYS H 596 " --> pdb=" O ARG H 592 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL H 597 " --> pdb=" O PRO H 593 " (cutoff:3.500A) Processing helix chain 'H' and resid 604 through 617 removed outlier: 3.670A pdb=" N MET H 617 " --> pdb=" O GLY H 613 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 5 removed outlier: 3.729A pdb=" N THR I 5 " --> pdb=" O ASN I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 16 removed outlier: 3.661A pdb=" N THR I 15 " --> pdb=" O ASN I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 19 No H-bonds generated for 'chain 'I' and resid 17 through 19' Processing helix chain 'I' and resid 33 through 47 Proline residue: I 44 - end of helix Processing helix chain 'I' and resid 53 through 58 removed outlier: 3.547A pdb=" N ALA I 57 " --> pdb=" O ASN I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 94 Processing helix chain 'I' and resid 95 through 108 Processing helix chain 'I' and resid 109 through 113 removed outlier: 3.894A pdb=" N LEU I 113 " --> pdb=" O LEU I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 120 removed outlier: 3.649A pdb=" N GLU I 117 " --> pdb=" O LYS I 114 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU I 118 " --> pdb=" O TYR I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 151 Processing helix chain 'I' and resid 157 through 169 removed outlier: 3.623A pdb=" N TYR I 161 " --> pdb=" O THR I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 224 Processing helix chain 'I' and resid 247 through 266 removed outlier: 4.112A pdb=" N GLY I 252 " --> pdb=" O MET I 248 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N PHE I 253 " --> pdb=" O LEU I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 280 through 286 Processing helix chain 'I' and resid 310 through 326 removed outlier: 3.813A pdb=" N MET I 314 " --> pdb=" O ASP I 310 " (cutoff:3.500A) Processing helix chain 'I' and resid 328 through 343 Proline residue: I 338 - end of helix Processing helix chain 'I' and resid 373 through 378 removed outlier: 4.476A pdb=" N ARG I 378 " --> pdb=" O ASP I 375 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 432 through 450 removed outlier: 3.775A pdb=" N VAL I 450 " --> pdb=" O THR I 446 " (cutoff:3.500A) Processing helix chain 'I' and resid 496 through 514 Processing helix chain 'I' and resid 518 through 537 Processing helix chain 'I' and resid 543 through 552 Processing helix chain 'I' and resid 575 through 583 removed outlier: 3.800A pdb=" N HIS I 582 " --> pdb=" O ALA I 578 " (cutoff:3.500A) Processing helix chain 'I' and resid 587 through 595 Processing helix chain 'I' and resid 648 through 662 removed outlier: 3.541A pdb=" N GLU I 652 " --> pdb=" O LEU I 648 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU I 653 " --> pdb=" O LEU I 649 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE I 662 " --> pdb=" O VAL I 658 " (cutoff:3.500A) Processing helix chain 'I' and resid 684 through 693 removed outlier: 3.606A pdb=" N LEU I 688 " --> pdb=" O LEU I 684 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 27 removed outlier: 3.637A pdb=" N LEU J 16 " --> pdb=" O THR J 12 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL J 17 " --> pdb=" O LEU J 13 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU J 19 " --> pdb=" O ALA J 15 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR J 20 " --> pdb=" O LEU J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 36 No H-bonds generated for 'chain 'J' and resid 34 through 36' Processing helix chain 'J' and resid 37 through 42 Processing helix chain 'J' and resid 52 through 55 Processing helix chain 'J' and resid 56 through 63 Processing helix chain 'J' and resid 102 through 111 removed outlier: 3.542A pdb=" N TYR J 106 " --> pdb=" O VAL J 102 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS J 109 " --> pdb=" O ASP J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 124 removed outlier: 3.606A pdb=" N VAL J 119 " --> pdb=" O SER J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 135 removed outlier: 3.629A pdb=" N GLN J 131 " --> pdb=" O ASP J 127 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG J 132 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE J 133 " --> pdb=" O LYS J 129 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 176 Processing helix chain 'J' and resid 181 through 187 Processing helix chain 'J' and resid 192 through 201 removed outlier: 3.588A pdb=" N LEU J 196 " --> pdb=" O ALA J 192 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS J 197 " --> pdb=" O VAL J 193 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG J 198 " --> pdb=" O GLU J 194 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL J 199 " --> pdb=" O LYS J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 209 removed outlier: 3.673A pdb=" N GLN J 209 " --> pdb=" O VAL J 206 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 221 removed outlier: 3.760A pdb=" N ILE J 215 " --> pdb=" O SER J 211 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU J 219 " --> pdb=" O ILE J 215 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE J 220 " --> pdb=" O ALA J 216 " (cutoff:3.500A) Processing helix chain 'J' and resid 234 through 239 removed outlier: 3.607A pdb=" N GLU J 239 " --> pdb=" O PRO J 235 " (cutoff:3.500A) Processing helix chain 'J' and resid 240 through 245 removed outlier: 3.632A pdb=" N LEU J 244 " --> pdb=" O MET J 240 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N CYS J 245 " --> pdb=" O ALA J 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 240 through 245' Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 59 removed outlier: 3.534A pdb=" N ASP A 89 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL A 94 " --> pdb=" O ASP A 89 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA A 95 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU A 117 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS A 97 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N PHE A 119 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 99 " --> pdb=" O PHE A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 211 Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 211 removed outlier: 4.590A pdb=" N ASN B 453 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 242 removed outlier: 7.398A pdb=" N TRP A 426 " --> pdb=" O ILE A 450 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 442 through 451 current: chain 'A' and resid 290 through 291 Processing sheet with id=AA5, first strand: chain 'A' and resid 259 through 262 removed outlier: 3.879A pdb=" N LEU A 475 " --> pdb=" O MET A 451 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N TRP A 426 " --> pdb=" O ILE A 450 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA7, first strand: chain 'A' and resid 405 through 406 removed outlier: 3.720A pdb=" N ARG A 406 " --> pdb=" O HIS A 434 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 526 through 530 Processing sheet with id=AA9, first strand: chain 'B' and resid 124 through 126 removed outlier: 3.606A pdb=" N ARG B 131 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 173 through 178 removed outlier: 3.716A pdb=" N GLY B 178 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR B 210 " --> pdb=" O GLY B 178 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 242 through 245 removed outlier: 7.393A pdb=" N LEU B 226 " --> pdb=" O ASP B 348 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 468 through 470 Processing sheet with id=AB4, first strand: chain 'B' and resid 608 through 611 Processing sheet with id=AB5, first strand: chain 'B' and resid 633 through 634 removed outlier: 4.560A pdb=" N THR B 633 " --> pdb=" O SER C 68 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AB7, first strand: chain 'C' and resid 141 through 143 Processing sheet with id=AB8, first strand: chain 'C' and resid 149 through 154 Processing sheet with id=AB9, first strand: chain 'C' and resid 297 through 298 Processing sheet with id=AC1, first strand: chain 'C' and resid 328 through 330 removed outlier: 3.651A pdb=" N MET C 328 " --> pdb=" O PHE C 335 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LYS C 371 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N SER C 340 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LYS C 369 " --> pdb=" O SER C 340 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N THR C 386 " --> pdb=" O ILE C 390 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ILE C 390 " --> pdb=" O THR C 386 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N THR C 482 " --> pdb=" O ASP C 391 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE C 393 " --> pdb=" O THR C 482 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 345 through 351 removed outlier: 3.809A pdb=" N LYS C 349 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL C 359 " --> pdb=" O PHE C 351 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 456 through 457 Processing sheet with id=AC4, first strand: chain 'C' and resid 498 through 500 removed outlier: 6.784A pdb=" N VAL C 506 " --> pdb=" O LEU C 517 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 645 through 647 Processing sheet with id=AC6, first strand: chain 'C' and resid 664 through 666 removed outlier: 7.071A pdb=" N ILE C 671 " --> pdb=" O VAL C 678 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 694 through 695 removed outlier: 7.080A pdb=" N TYR C 702 " --> pdb=" O CYS C 719 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N HIS C 721 " --> pdb=" O TYR C 702 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 210 through 211 removed outlier: 3.525A pdb=" N VAL I 294 " --> pdb=" O CYS I 430 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 240 through 242 removed outlier: 7.428A pdb=" N TRP H 426 " --> pdb=" O ILE H 450 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU H 475 " --> pdb=" O MET H 451 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL H 464 " --> pdb=" O ILE H 263 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 240 through 242 removed outlier: 5.412A pdb=" N PHE H 425 " --> pdb=" O THR H 416 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N THR H 416 " --> pdb=" O PHE H 425 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY H 427 " --> pdb=" O ILE H 414 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 322 through 323 Processing sheet with id=AD3, first strand: chain 'H' and resid 526 through 531 Processing sheet with id=AD4, first strand: chain 'I' and resid 124 through 125 Processing sheet with id=AD5, first strand: chain 'I' and resid 173 through 175 Processing sheet with id=AD6, first strand: chain 'I' and resid 242 through 245 Processing sheet with id=AD7, first strand: chain 'I' and resid 380 through 381 Processing sheet with id=AD8, first strand: chain 'I' and resid 467 through 470 Processing sheet with id=AD9, first strand: chain 'J' and resid 141 through 143 Processing sheet with id=AE1, first strand: chain 'J' and resid 149 through 154 1209 hydrogen bonds defined for protein. 3354 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 5.11 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8558 1.34 - 1.45: 4212 1.45 - 1.57: 15650 1.57 - 1.69: 99 1.69 - 1.81: 270 Bond restraints: 28789 Sorted by residual: bond pdb=" C ASP H 418 " pdb=" N PRO H 419 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.21e+00 bond pdb=" C VAL J 103 " pdb=" N PRO J 104 " ideal model delta sigma weight residual 1.334 1.368 -0.035 2.34e-02 1.83e+03 2.18e+00 bond pdb=" CA ASP C 666 " pdb=" CB ASP C 666 " ideal model delta sigma weight residual 1.536 1.592 -0.056 4.10e-02 5.95e+02 1.87e+00 bond pdb=" CA GLU H 325 " pdb=" CB GLU H 325 " ideal model delta sigma weight residual 1.527 1.544 -0.017 1.61e-02 3.86e+03 1.06e+00 bond pdb=" CB GLU H 325 " pdb=" CG GLU H 325 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.44e-01 ... (remaining 28784 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 38384 1.59 - 3.17: 668 3.17 - 4.76: 108 4.76 - 6.35: 22 6.35 - 7.93: 6 Bond angle restraints: 39188 Sorted by residual: angle pdb=" N ALA H 513 " pdb=" CA ALA H 513 " pdb=" C ALA H 513 " ideal model delta sigma weight residual 114.62 107.48 7.14 1.14e+00 7.69e-01 3.92e+01 angle pdb=" N LEU I 665 " pdb=" CA LEU I 665 " pdb=" C LEU I 665 " ideal model delta sigma weight residual 113.12 108.37 4.75 1.25e+00 6.40e-01 1.44e+01 angle pdb=" CA ALA H 513 " pdb=" C ALA H 513 " pdb=" N ALA H 514 " ideal model delta sigma weight residual 119.71 115.58 4.13 1.17e+00 7.31e-01 1.25e+01 angle pdb=" C PRO C 235 " pdb=" N ARG C 236 " pdb=" CA ARG C 236 " ideal model delta sigma weight residual 121.54 127.89 -6.35 1.91e+00 2.74e-01 1.11e+01 angle pdb=" N VAL I 566 " pdb=" CA VAL I 566 " pdb=" C VAL I 566 " ideal model delta sigma weight residual 113.39 108.78 4.61 1.47e+00 4.63e-01 9.85e+00 ... (remaining 39183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 16097 18.00 - 35.99: 1222 35.99 - 53.99: 217 53.99 - 71.98: 78 71.98 - 89.98: 36 Dihedral angle restraints: 17650 sinusoidal: 7798 harmonic: 9852 Sorted by residual: dihedral pdb=" CA ASP C 751 " pdb=" C ASP C 751 " pdb=" N LEU C 752 " pdb=" CA LEU C 752 " ideal model delta harmonic sigma weight residual 180.00 156.37 23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA ILE H 299 " pdb=" C ILE H 299 " pdb=" N ALA H 300 " pdb=" CA ALA H 300 " ideal model delta harmonic sigma weight residual 180.00 160.60 19.40 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA GLU C 418 " pdb=" C GLU C 418 " pdb=" N PRO C 419 " pdb=" CA PRO C 419 " ideal model delta harmonic sigma weight residual 180.00 160.76 19.24 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 17647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3619 0.051 - 0.102: 651 0.102 - 0.153: 117 0.153 - 0.204: 2 0.204 - 0.255: 1 Chirality restraints: 4390 Sorted by residual: chirality pdb=" CB ILE H 299 " pdb=" CA ILE H 299 " pdb=" CG1 ILE H 299 " pdb=" CG2 ILE H 299 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA GLU C 405 " pdb=" N GLU C 405 " pdb=" C GLU C 405 " pdb=" CB GLU C 405 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.63e-01 chirality pdb=" CA SER B 463 " pdb=" N SER B 463 " pdb=" C SER B 463 " pdb=" CB SER B 463 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.98e-01 ... (remaining 4387 not shown) Planarity restraints: 4843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 418 " 0.044 5.00e-02 4.00e+02 6.66e-02 7.11e+00 pdb=" N PRO C 419 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 419 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 419 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 27 " 0.042 5.00e-02 4.00e+02 6.35e-02 6.44e+00 pdb=" N PRO C 28 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO C 28 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 28 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 559 " -0.041 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO A 560 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 560 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 560 " -0.035 5.00e-02 4.00e+02 ... (remaining 4840 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 575 2.68 - 3.23: 27207 3.23 - 3.79: 45548 3.79 - 4.34: 63581 4.34 - 4.90: 102622 Nonbonded interactions: 239533 Sorted by model distance: nonbonded pdb=" OH TYR I 22 " pdb=" O ALA I 484 " model vdw 2.121 3.040 nonbonded pdb=" OD2 ASP I 500 " pdb=" OH TYR I 537 " model vdw 2.126 3.040 nonbonded pdb=" OG1 THR B 228 " pdb=" O ASP B 348 " model vdw 2.168 3.040 nonbonded pdb=" OG1 THR B 401 " pdb=" O SER B 420 " model vdw 2.174 3.040 nonbonded pdb=" OD1 ASP A 365 " pdb=" OG SER B 570 " model vdw 2.189 3.040 ... (remaining 239528 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 1 through 177 or resid 210 through 274 or resid 279 throug \ h 602 or resid 622 through 635 or resid 645 through 680 or resid 682 through 693 \ )) selection = chain 'I' } ncs_group { reference = chain 'G' selection = chain 'K' } 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=0.27 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: 4.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.500 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28791 Z= 0.111 Angle : 0.529 7.934 39188 Z= 0.275 Chirality : 0.040 0.255 4390 Planarity : 0.005 0.067 4843 Dihedral : 13.831 89.976 11256 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.23 (0.15), residues: 3331 helix: 1.22 (0.14), residues: 1429 sheet: -0.17 (0.31), residues: 302 loop : -0.73 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 755 TYR 0.016 0.001 TYR H 621 PHE 0.026 0.001 PHE C 41 TRP 0.021 0.001 TRP I 330 HIS 0.008 0.001 HIS A 573 Details of bonding type rmsd covalent geometry : bond 0.00250 (28789) covalent geometry : angle 0.52933 (39188) hydrogen bonds : bond 0.16639 ( 1221) hydrogen bonds : angle 6.34153 ( 3412) Misc. bond : bond 0.00034 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 ASN cc_start: 0.7154 (m-40) cc_final: 0.6786 (m110) REVERT: B 169 MET cc_start: 0.9038 (mmp) cc_final: 0.8794 (mmm) REVERT: B 266 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8420 (mt-10) REVERT: C 142 ARG cc_start: 0.7458 (tpm170) cc_final: 0.7030 (tpp-160) REVERT: C 145 ARG cc_start: 0.8175 (tpp-160) cc_final: 0.7626 (tpp-160) REVERT: C 309 GLU cc_start: 0.7345 (tp30) cc_final: 0.6770 (tm-30) REVERT: I 213 LYS cc_start: 0.8693 (ptmm) cc_final: 0.8423 (ptmm) outliers start: 0 outliers final: 0 residues processed: 410 average time/residue: 0.8320 time to fit residues: 383.2615 Evaluate side-chains 262 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.0770 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN ** B 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN C 442 HIS ** C 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 669 ASN ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 741 ASN H 327 GLN ** H 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 542 GLN I 16 GLN ** I 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.132873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.091801 restraints weight = 53471.292| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.63 r_work: 0.3132 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 28791 Z= 0.132 Angle : 0.572 7.593 39188 Z= 0.295 Chirality : 0.041 0.179 4390 Planarity : 0.005 0.063 4843 Dihedral : 10.274 86.434 4419 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.36 % Allowed : 9.10 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.15), residues: 3331 helix: 1.32 (0.14), residues: 1440 sheet: -0.22 (0.31), residues: 302 loop : -0.73 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 754 TYR 0.019 0.001 TYR I 533 PHE 0.020 0.001 PHE C 41 TRP 0.018 0.001 TRP A 70 HIS 0.013 0.001 HIS C 442 Details of bonding type rmsd covalent geometry : bond 0.00299 (28789) covalent geometry : angle 0.57155 (39188) hydrogen bonds : bond 0.04222 ( 1221) hydrogen bonds : angle 4.97218 ( 3412) Misc. bond : bond 0.00040 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 302 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7614 (mp10) cc_final: 0.7389 (mp10) REVERT: B 169 MET cc_start: 0.9074 (mmp) cc_final: 0.8759 (mmm) REVERT: B 213 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.8993 (tppp) REVERT: B 369 MET cc_start: 0.8696 (mtp) cc_final: 0.8412 (mtp) REVERT: B 609 MET cc_start: 0.9312 (OUTLIER) cc_final: 0.8945 (tpp) REVERT: C 145 ARG cc_start: 0.8426 (tpp-160) cc_final: 0.7932 (tpp-160) REVERT: C 187 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8377 (mtpm) REVERT: C 279 ARG cc_start: 0.8574 (ttp80) cc_final: 0.8307 (ttt180) REVERT: C 309 GLU cc_start: 0.7642 (tp30) cc_final: 0.6952 (tm-30) REVERT: H 229 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7579 (mtm180) REVERT: H 582 ARG cc_start: 0.8377 (mmp80) cc_final: 0.8089 (tpp-160) REVERT: I 210 TYR cc_start: 0.5864 (OUTLIER) cc_final: 0.4885 (p90) REVERT: I 213 LYS cc_start: 0.8548 (ptmm) cc_final: 0.8240 (ptmm) REVERT: I 469 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7582 (pp20) REVERT: J 142 ARG cc_start: 0.8281 (ttp-170) cc_final: 0.8019 (ttp-170) outliers start: 41 outliers final: 13 residues processed: 329 average time/residue: 0.7391 time to fit residues: 276.2086 Evaluate side-chains 278 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 259 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 604 GLU Chi-restraints excluded: chain H residue 200 ASN Chi-restraints excluded: chain H residue 204 ILE Chi-restraints excluded: chain H residue 229 ARG Chi-restraints excluded: chain I residue 210 TYR Chi-restraints excluded: chain I residue 469 GLU Chi-restraints excluded: chain I residue 472 SER Chi-restraints excluded: chain J residue 117 GLU Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 211 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 129 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 295 optimal weight: 0.0370 chunk 190 optimal weight: 6.9990 chunk 228 optimal weight: 1.9990 chunk 326 optimal weight: 20.0000 chunk 317 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 175 optimal weight: 7.9990 overall best weight: 1.3264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 304 ASN ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 306 ASN B 567 HIS C 154 GLN C 442 HIS C 614 GLN C 691 GLN H 257 GLN H 327 GLN H 434 HIS H 542 GLN ** I 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.129415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.087701 restraints weight = 52171.120| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.59 r_work: 0.3075 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28791 Z= 0.166 Angle : 0.570 7.296 39188 Z= 0.294 Chirality : 0.042 0.182 4390 Planarity : 0.005 0.063 4843 Dihedral : 10.145 87.988 4419 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.86 % Allowed : 11.10 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.29 (0.15), residues: 3331 helix: 1.37 (0.14), residues: 1436 sheet: -0.39 (0.30), residues: 307 loop : -0.77 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 750 TYR 0.020 0.001 TYR I 533 PHE 0.021 0.002 PHE C 41 TRP 0.014 0.001 TRP I 330 HIS 0.012 0.001 HIS C 442 Details of bonding type rmsd covalent geometry : bond 0.00392 (28789) covalent geometry : angle 0.57026 (39188) hydrogen bonds : bond 0.04120 ( 1221) hydrogen bonds : angle 4.67213 ( 3412) Misc. bond : bond 0.00025 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 296 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.8325 (ptm-80) cc_final: 0.8051 (ptm-80) REVERT: A 307 GLN cc_start: 0.7766 (mp10) cc_final: 0.7451 (mp10) REVERT: A 485 ARG cc_start: 0.8409 (mtp180) cc_final: 0.8066 (ttm-80) REVERT: B 169 MET cc_start: 0.9110 (mmp) cc_final: 0.8817 (mmm) REVERT: B 351 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8666 (pm20) REVERT: B 363 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.6909 (mtp180) REVERT: B 369 MET cc_start: 0.8700 (mtp) cc_final: 0.8351 (mtp) REVERT: B 609 MET cc_start: 0.9233 (OUTLIER) cc_final: 0.8905 (tpp) REVERT: B 651 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8293 (ttpp) REVERT: C 100 ASN cc_start: 0.8219 (t0) cc_final: 0.7894 (t0) REVERT: C 145 ARG cc_start: 0.8490 (tpp-160) cc_final: 0.8278 (tpt90) REVERT: C 146 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7234 (mtt) REVERT: C 187 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8092 (mtpm) REVERT: C 279 ARG cc_start: 0.8587 (ttp80) cc_final: 0.8310 (ttt180) REVERT: H 190 ASP cc_start: 0.7687 (p0) cc_final: 0.7454 (p0) REVERT: H 229 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7485 (mtm180) REVERT: H 325 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8033 (tm-30) REVERT: H 456 GLU cc_start: 0.8116 (tp30) cc_final: 0.7102 (mp0) REVERT: H 468 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7915 (mmtt) REVERT: H 539 THR cc_start: 0.8505 (p) cc_final: 0.8163 (t) REVERT: H 586 PHE cc_start: 0.8793 (m-80) cc_final: 0.8527 (m-80) REVERT: H 596 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.6892 (mtpp) REVERT: I 210 TYR cc_start: 0.6055 (OUTLIER) cc_final: 0.4990 (p90) REVERT: I 213 LYS cc_start: 0.8497 (ptmm) cc_final: 0.8239 (ptmm) REVERT: J 107 TRP cc_start: 0.7547 (t-100) cc_final: 0.7341 (t-100) outliers start: 56 outliers final: 14 residues processed: 334 average time/residue: 0.7517 time to fit residues: 285.8372 Evaluate side-chains 284 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 260 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 651 LYS Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 604 GLU Chi-restraints excluded: chain H residue 200 ASN Chi-restraints excluded: chain H residue 204 ILE Chi-restraints excluded: chain H residue 229 ARG Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain H residue 468 LYS Chi-restraints excluded: chain H residue 482 SER Chi-restraints excluded: chain H residue 596 LYS Chi-restraints excluded: chain I residue 210 TYR Chi-restraints excluded: chain I residue 472 SER Chi-restraints excluded: chain J residue 117 GLU Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 211 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 192 optimal weight: 2.9990 chunk 141 optimal weight: 0.5980 chunk 162 optimal weight: 4.9990 chunk 285 optimal weight: 8.9990 chunk 218 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 202 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 176 optimal weight: 4.9990 chunk 158 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN C 169 HIS C 442 HIS H 327 GLN H 542 GLN I 132 ASN I 227 ASN ** I 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 567 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.131118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.090029 restraints weight = 53799.348| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.61 r_work: 0.3107 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 28791 Z= 0.117 Angle : 0.530 7.449 39188 Z= 0.274 Chirality : 0.040 0.186 4390 Planarity : 0.005 0.064 4843 Dihedral : 9.996 89.246 4419 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.73 % Allowed : 12.79 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.29 (0.15), residues: 3331 helix: 1.39 (0.14), residues: 1450 sheet: -0.37 (0.30), residues: 301 loop : -0.81 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 750 TYR 0.019 0.001 TYR I 533 PHE 0.020 0.001 PHE C 41 TRP 0.012 0.001 TRP I 330 HIS 0.012 0.001 HIS C 442 Details of bonding type rmsd covalent geometry : bond 0.00272 (28789) covalent geometry : angle 0.53036 (39188) hydrogen bonds : bond 0.03579 ( 1221) hydrogen bonds : angle 4.50490 ( 3412) Misc. bond : bond 0.00034 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 277 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8148 (mmp80) REVERT: A 307 GLN cc_start: 0.7733 (mp10) cc_final: 0.7416 (mp10) REVERT: A 485 ARG cc_start: 0.8461 (mtp180) cc_final: 0.8097 (ttm-80) REVERT: A 515 GLU cc_start: 0.8553 (tt0) cc_final: 0.8088 (tm-30) REVERT: A 538 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7739 (ttm) REVERT: B 169 MET cc_start: 0.8989 (mmp) cc_final: 0.8743 (mmm) REVERT: B 609 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.8918 (tpp) REVERT: B 651 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8301 (ttpp) REVERT: B 653 GLU cc_start: 0.8079 (tp30) cc_final: 0.7861 (mt-10) REVERT: B 704 ARG cc_start: 0.8230 (ttp-110) cc_final: 0.8029 (ttm-80) REVERT: C 100 ASN cc_start: 0.8042 (t0) cc_final: 0.7751 (t0) REVERT: C 142 ARG cc_start: 0.7105 (tpm170) cc_final: 0.6403 (tpt-90) REVERT: C 145 ARG cc_start: 0.8453 (tpp-160) cc_final: 0.7477 (tmm-80) REVERT: C 146 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.7152 (mtt) REVERT: C 187 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8085 (mtpm) REVERT: C 279 ARG cc_start: 0.8588 (ttp80) cc_final: 0.8327 (ttt180) REVERT: H 190 ASP cc_start: 0.7699 (p0) cc_final: 0.7368 (p0) REVERT: H 325 GLU cc_start: 0.8511 (tm-30) cc_final: 0.7971 (tm-30) REVERT: H 456 GLU cc_start: 0.8084 (tp30) cc_final: 0.7162 (mp0) REVERT: H 468 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7945 (mmtt) REVERT: H 539 THR cc_start: 0.8551 (p) cc_final: 0.8208 (t) REVERT: H 586 PHE cc_start: 0.8734 (m-80) cc_final: 0.8459 (m-80) REVERT: H 596 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.6783 (mtpp) REVERT: I 213 LYS cc_start: 0.8589 (ptmm) cc_final: 0.8213 (ptmm) REVERT: I 654 ARG cc_start: 0.6937 (ptp-170) cc_final: 0.6706 (ptp90) REVERT: I 673 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.8052 (mp0) REVERT: J 107 TRP cc_start: 0.7554 (t-100) cc_final: 0.7336 (t-100) outliers start: 52 outliers final: 16 residues processed: 313 average time/residue: 0.7122 time to fit residues: 255.7861 Evaluate side-chains 286 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 261 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 651 LYS Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 604 GLU Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 200 ASN Chi-restraints excluded: chain H residue 204 ILE Chi-restraints excluded: chain H residue 468 LYS Chi-restraints excluded: chain H residue 483 PHE Chi-restraints excluded: chain H residue 596 LYS Chi-restraints excluded: chain I residue 472 SER Chi-restraints excluded: chain I residue 673 GLU Chi-restraints excluded: chain J residue 117 GLU Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 186 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 335 optimal weight: 5.9990 chunk 138 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 140 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 221 optimal weight: 8.9990 chunk 15 optimal weight: 0.5980 chunk 195 optimal weight: 0.7980 chunk 263 optimal weight: 8.9990 chunk 243 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN C 442 HIS H 327 GLN H 542 GLN ** I 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 513 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.130564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.088943 restraints weight = 55585.599| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.67 r_work: 0.3089 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28791 Z= 0.137 Angle : 0.538 8.664 39188 Z= 0.276 Chirality : 0.041 0.193 4390 Planarity : 0.005 0.064 4843 Dihedral : 9.960 88.457 4419 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.06 % Allowed : 13.16 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.33 (0.15), residues: 3331 helix: 1.43 (0.14), residues: 1449 sheet: -0.39 (0.29), residues: 304 loop : -0.80 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG C 750 TYR 0.019 0.001 TYR I 533 PHE 0.020 0.001 PHE C 41 TRP 0.011 0.001 TRP I 330 HIS 0.012 0.001 HIS C 442 Details of bonding type rmsd covalent geometry : bond 0.00321 (28789) covalent geometry : angle 0.53795 (39188) hydrogen bonds : bond 0.03664 ( 1221) hydrogen bonds : angle 4.43966 ( 3412) Misc. bond : bond 0.00026 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 275 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LEU cc_start: 0.8619 (mp) cc_final: 0.8417 (mp) REVERT: A 196 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7892 (mmp80) REVERT: A 307 GLN cc_start: 0.7718 (mp10) cc_final: 0.7341 (mp10) REVERT: A 485 ARG cc_start: 0.8484 (mtp180) cc_final: 0.8117 (ttm-80) REVERT: A 515 GLU cc_start: 0.8540 (tt0) cc_final: 0.8071 (tm-30) REVERT: A 531 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8004 (mm) REVERT: A 538 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7829 (ttm) REVERT: B 169 MET cc_start: 0.9031 (mmp) cc_final: 0.8702 (mmm) REVERT: B 212 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8579 (mp) REVERT: B 363 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.6873 (mtp180) REVERT: B 369 MET cc_start: 0.8698 (mtp) cc_final: 0.8388 (mtt) REVERT: B 621 MET cc_start: 0.9122 (ttt) cc_final: 0.8790 (tpp) REVERT: B 704 ARG cc_start: 0.8195 (ttp-110) cc_final: 0.7993 (ttm-80) REVERT: C 100 ASN cc_start: 0.8066 (t0) cc_final: 0.7763 (t0) REVERT: C 187 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8089 (mtpm) REVERT: C 279 ARG cc_start: 0.8592 (ttp80) cc_final: 0.8230 (tmt170) REVERT: H 229 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7504 (mtm180) REVERT: H 290 VAL cc_start: 0.9006 (OUTLIER) cc_final: 0.8799 (t) REVERT: H 325 GLU cc_start: 0.8470 (tm-30) cc_final: 0.7919 (tm-30) REVERT: H 539 THR cc_start: 0.8541 (p) cc_final: 0.8153 (t) REVERT: H 586 PHE cc_start: 0.8735 (m-80) cc_final: 0.8443 (m-80) REVERT: H 596 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.6826 (mtpp) REVERT: I 210 TYR cc_start: 0.6118 (OUTLIER) cc_final: 0.5092 (p90) REVERT: I 213 LYS cc_start: 0.8530 (ptmm) cc_final: 0.8163 (ptmm) REVERT: J 31 MET cc_start: 0.6133 (ppp) cc_final: 0.5891 (pp-130) outliers start: 62 outliers final: 24 residues processed: 321 average time/residue: 0.7094 time to fit residues: 260.0050 Evaluate side-chains 290 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 256 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 604 GLU Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 200 ASN Chi-restraints excluded: chain H residue 204 ILE Chi-restraints excluded: chain H residue 229 ARG Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 482 SER Chi-restraints excluded: chain H residue 483 PHE Chi-restraints excluded: chain H residue 596 LYS Chi-restraints excluded: chain H residue 620 VAL Chi-restraints excluded: chain I residue 210 TYR Chi-restraints excluded: chain I residue 294 VAL Chi-restraints excluded: chain I residue 472 SER Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 117 GLU Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 186 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 177 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 265 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 202 optimal weight: 0.7980 chunk 171 optimal weight: 0.1980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN C 442 HIS H 327 GLN H 542 GLN ** I 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.131290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.089987 restraints weight = 55460.171| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.65 r_work: 0.3102 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 28791 Z= 0.123 Angle : 0.533 9.315 39188 Z= 0.274 Chirality : 0.040 0.204 4390 Planarity : 0.005 0.067 4843 Dihedral : 9.916 87.864 4419 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.86 % Allowed : 13.59 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.35 (0.15), residues: 3331 helix: 1.47 (0.14), residues: 1449 sheet: -0.47 (0.30), residues: 296 loop : -0.78 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 750 TYR 0.019 0.001 TYR I 533 PHE 0.020 0.001 PHE C 41 TRP 0.017 0.001 TRP J 107 HIS 0.012 0.001 HIS C 442 Details of bonding type rmsd covalent geometry : bond 0.00290 (28789) covalent geometry : angle 0.53350 (39188) hydrogen bonds : bond 0.03515 ( 1221) hydrogen bonds : angle 4.39560 ( 3412) Misc. bond : bond 0.00032 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 265 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8399 (mp) REVERT: A 126 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.7068 (tm-30) REVERT: A 196 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7867 (mmp80) REVERT: A 307 GLN cc_start: 0.7728 (mp10) cc_final: 0.7335 (mp10) REVERT: A 515 GLU cc_start: 0.8535 (tt0) cc_final: 0.8055 (tm-30) REVERT: A 538 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7737 (ttm) REVERT: B 169 MET cc_start: 0.9017 (mmp) cc_final: 0.8681 (mmm) REVERT: B 212 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8582 (mp) REVERT: B 363 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.6836 (mtp180) REVERT: B 369 MET cc_start: 0.8733 (mtp) cc_final: 0.8355 (mtp) REVERT: B 619 GLN cc_start: 0.8339 (mt0) cc_final: 0.8060 (mt0) REVERT: B 621 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8673 (tpp) REVERT: C 100 ASN cc_start: 0.8001 (t0) cc_final: 0.7721 (t0) REVERT: C 187 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8069 (mtpm) REVERT: C 279 ARG cc_start: 0.8584 (ttp80) cc_final: 0.8229 (tmt170) REVERT: H 229 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7486 (mtm180) REVERT: H 325 GLU cc_start: 0.8459 (tm-30) cc_final: 0.7902 (tm-30) REVERT: H 596 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.6826 (mtpp) REVERT: I 210 TYR cc_start: 0.5965 (OUTLIER) cc_final: 0.4954 (p90) REVERT: I 213 LYS cc_start: 0.8540 (ptmm) cc_final: 0.8188 (ptmm) REVERT: I 673 GLU cc_start: 0.8341 (mp0) cc_final: 0.8122 (pm20) REVERT: J 31 MET cc_start: 0.6171 (ppp) cc_final: 0.5948 (pp-130) outliers start: 56 outliers final: 25 residues processed: 303 average time/residue: 0.7283 time to fit residues: 251.6169 Evaluate side-chains 287 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 251 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 621 MET Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 604 GLU Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 200 ASN Chi-restraints excluded: chain H residue 204 ILE Chi-restraints excluded: chain H residue 229 ARG Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 596 LYS Chi-restraints excluded: chain I residue 210 TYR Chi-restraints excluded: chain I residue 214 PHE Chi-restraints excluded: chain I residue 294 VAL Chi-restraints excluded: chain I residue 472 SER Chi-restraints excluded: chain I residue 601 VAL Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 117 GLU Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 186 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 18 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 169 optimal weight: 5.9990 chunk 190 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 325 optimal weight: 6.9990 chunk 297 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** A 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 HIS ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 HIS C 442 HIS H 327 GLN H 542 GLN ** I 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 599 ASN I 672 GLN J 169 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.128330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.086696 restraints weight = 57440.779| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.72 r_work: 0.3015 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 28791 Z= 0.181 Angle : 0.575 9.029 39188 Z= 0.295 Chirality : 0.042 0.219 4390 Planarity : 0.005 0.063 4843 Dihedral : 9.982 86.578 4419 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.09 % Allowed : 13.72 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.25 (0.15), residues: 3331 helix: 1.40 (0.14), residues: 1449 sheet: -0.59 (0.29), residues: 302 loop : -0.82 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 654 TYR 0.021 0.001 TYR I 533 PHE 0.021 0.002 PHE C 41 TRP 0.024 0.001 TRP J 107 HIS 0.012 0.001 HIS C 442 Details of bonding type rmsd covalent geometry : bond 0.00432 (28789) covalent geometry : angle 0.57497 (39188) hydrogen bonds : bond 0.03946 ( 1221) hydrogen bonds : angle 4.46516 ( 3412) Misc. bond : bond 0.00013 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 267 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.7014 (tm-30) REVERT: A 307 GLN cc_start: 0.7744 (mp10) cc_final: 0.7351 (mp10) REVERT: A 431 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8591 (tt) REVERT: A 515 GLU cc_start: 0.8551 (tt0) cc_final: 0.7989 (tm-30) REVERT: A 531 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8067 (mm) REVERT: A 538 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7989 (ttm) REVERT: B 212 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8534 (mp) REVERT: B 351 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8583 (pm20) REVERT: B 363 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.6789 (mtp180) REVERT: B 619 GLN cc_start: 0.8353 (mt0) cc_final: 0.8097 (mt0) REVERT: B 621 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8795 (tpp) REVERT: B 653 GLU cc_start: 0.8078 (tp30) cc_final: 0.7743 (mt-10) REVERT: C 187 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.7985 (mtpm) REVERT: C 279 ARG cc_start: 0.8607 (ttp80) cc_final: 0.8238 (tmt170) REVERT: C 328 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8328 (tpp) REVERT: H 229 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7423 (mtm180) REVERT: H 325 GLU cc_start: 0.8445 (tm-30) cc_final: 0.7860 (tm-30) REVERT: H 596 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.6797 (mtpp) REVERT: I 210 TYR cc_start: 0.6055 (OUTLIER) cc_final: 0.5061 (p90) REVERT: I 213 LYS cc_start: 0.8549 (ptmm) cc_final: 0.8187 (ptmm) REVERT: J 31 MET cc_start: 0.6190 (ppp) cc_final: 0.5978 (pp-130) outliers start: 63 outliers final: 29 residues processed: 310 average time/residue: 0.7250 time to fit residues: 256.7888 Evaluate side-chains 290 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 248 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 621 MET Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 604 GLU Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 200 ASN Chi-restraints excluded: chain H residue 204 ILE Chi-restraints excluded: chain H residue 229 ARG Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 482 SER Chi-restraints excluded: chain H residue 483 PHE Chi-restraints excluded: chain H residue 596 LYS Chi-restraints excluded: chain H residue 620 VAL Chi-restraints excluded: chain I residue 210 TYR Chi-restraints excluded: chain I residue 294 VAL Chi-restraints excluded: chain I residue 472 SER Chi-restraints excluded: chain I residue 601 VAL Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 69 MET Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 186 ARG Chi-restraints excluded: chain J residue 211 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 118 optimal weight: 3.9990 chunk 174 optimal weight: 0.0670 chunk 211 optimal weight: 2.9990 chunk 209 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 296 optimal weight: 4.9990 chunk 235 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** A 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 HIS H 327 GLN H 542 GLN ** I 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 672 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.129107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.087471 restraints weight = 62390.293| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.83 r_work: 0.3027 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 28791 Z= 0.148 Angle : 0.558 8.634 39188 Z= 0.286 Chirality : 0.041 0.203 4390 Planarity : 0.005 0.064 4843 Dihedral : 9.945 85.936 4419 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.99 % Allowed : 14.42 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.26 (0.15), residues: 3331 helix: 1.42 (0.14), residues: 1449 sheet: -0.58 (0.30), residues: 296 loop : -0.84 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG C 750 TYR 0.018 0.001 TYR I 533 PHE 0.021 0.001 PHE C 41 TRP 0.021 0.001 TRP J 107 HIS 0.013 0.001 HIS C 442 Details of bonding type rmsd covalent geometry : bond 0.00351 (28789) covalent geometry : angle 0.55775 (39188) hydrogen bonds : bond 0.03702 ( 1221) hydrogen bonds : angle 4.40957 ( 3412) Misc. bond : bond 0.00019 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 249 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6851 (tm-30) REVERT: A 307 GLN cc_start: 0.7741 (mp10) cc_final: 0.7305 (mp10) REVERT: A 515 GLU cc_start: 0.8553 (tt0) cc_final: 0.7997 (tm-30) REVERT: A 531 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7896 (mm) REVERT: A 538 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7860 (ttm) REVERT: B 212 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8543 (mp) REVERT: B 351 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8565 (pm20) REVERT: B 363 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.6706 (mtp180) REVERT: B 621 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8770 (tpp) REVERT: B 653 GLU cc_start: 0.8087 (tp30) cc_final: 0.7803 (mt-10) REVERT: C 147 LEU cc_start: 0.8970 (mp) cc_final: 0.8673 (mp) REVERT: C 187 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.7992 (mtpm) REVERT: C 309 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7802 (mm-30) REVERT: H 229 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7411 (mtm180) REVERT: H 325 GLU cc_start: 0.8462 (tm-30) cc_final: 0.7885 (tm-30) REVERT: H 582 ARG cc_start: 0.8452 (mmp80) cc_final: 0.8238 (tpp-160) REVERT: I 210 TYR cc_start: 0.6070 (OUTLIER) cc_final: 0.5099 (p90) REVERT: I 213 LYS cc_start: 0.8544 (ptmm) cc_final: 0.8181 (ptmm) REVERT: I 214 PHE cc_start: 0.7688 (OUTLIER) cc_final: 0.7487 (m-10) REVERT: J 31 MET cc_start: 0.6201 (ppp) cc_final: 0.6001 (pp-130) REVERT: J 48 LYS cc_start: 0.5726 (OUTLIER) cc_final: 0.5485 (mptt) outliers start: 60 outliers final: 33 residues processed: 294 average time/residue: 0.7319 time to fit residues: 244.8374 Evaluate side-chains 291 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 246 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 621 MET Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 604 GLU Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 200 ASN Chi-restraints excluded: chain H residue 204 ILE Chi-restraints excluded: chain H residue 229 ARG Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 482 SER Chi-restraints excluded: chain H residue 483 PHE Chi-restraints excluded: chain H residue 620 VAL Chi-restraints excluded: chain I residue 210 TYR Chi-restraints excluded: chain I residue 214 PHE Chi-restraints excluded: chain I residue 294 VAL Chi-restraints excluded: chain I residue 385 ILE Chi-restraints excluded: chain I residue 472 SER Chi-restraints excluded: chain I residue 601 VAL Chi-restraints excluded: chain I residue 673 GLU Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain J residue 69 MET Chi-restraints excluded: chain J residue 117 GLU Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 186 ARG Chi-restraints excluded: chain J residue 211 SER Chi-restraints excluded: chain J residue 233 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 207 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 258 optimal weight: 0.9990 chunk 298 optimal weight: 5.9990 chunk 290 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** A 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 530 ASN C 442 HIS H 327 GLN H 542 GLN ** I 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.129674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.088591 restraints weight = 53807.096| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.64 r_work: 0.3041 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 28791 Z= 0.131 Angle : 0.551 8.426 39188 Z= 0.282 Chirality : 0.041 0.229 4390 Planarity : 0.005 0.066 4843 Dihedral : 9.906 85.205 4419 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.76 % Allowed : 14.92 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.15), residues: 3331 helix: 1.43 (0.14), residues: 1452 sheet: -0.59 (0.30), residues: 296 loop : -0.82 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG C 750 TYR 0.018 0.001 TYR I 533 PHE 0.020 0.001 PHE C 41 TRP 0.014 0.001 TRP J 107 HIS 0.013 0.001 HIS C 442 Details of bonding type rmsd covalent geometry : bond 0.00309 (28789) covalent geometry : angle 0.55142 (39188) hydrogen bonds : bond 0.03560 ( 1221) hydrogen bonds : angle 4.37660 ( 3412) Misc. bond : bond 0.00029 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 259 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6967 (tm-30) REVERT: A 196 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8238 (mmp80) REVERT: A 307 GLN cc_start: 0.7779 (mp10) cc_final: 0.7338 (mp10) REVERT: A 515 GLU cc_start: 0.8523 (tt0) cc_final: 0.7963 (tm-30) REVERT: A 531 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7946 (mm) REVERT: A 538 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7760 (ttm) REVERT: B 212 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8533 (mp) REVERT: B 351 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8533 (pm20) REVERT: B 363 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.6721 (mtp180) REVERT: B 619 GLN cc_start: 0.8233 (mt0) cc_final: 0.8007 (mt0) REVERT: B 621 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8726 (tpp) REVERT: B 651 LYS cc_start: 0.8346 (tppp) cc_final: 0.8037 (ttmt) REVERT: B 653 GLU cc_start: 0.8034 (tp30) cc_final: 0.7752 (mt-10) REVERT: C 147 LEU cc_start: 0.8945 (mp) cc_final: 0.8640 (mp) REVERT: C 187 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.7979 (mtpm) REVERT: C 279 ARG cc_start: 0.8575 (ttp80) cc_final: 0.8270 (ttt180) REVERT: C 309 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7593 (mm-30) REVERT: C 328 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8300 (tpp) REVERT: H 229 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7419 (mtm180) REVERT: H 325 GLU cc_start: 0.8432 (tm-30) cc_final: 0.7833 (tm-30) REVERT: H 582 ARG cc_start: 0.8357 (mmp80) cc_final: 0.8121 (tpp-160) REVERT: I 210 TYR cc_start: 0.6054 (OUTLIER) cc_final: 0.5067 (p90) REVERT: I 213 LYS cc_start: 0.8538 (ptmm) cc_final: 0.8182 (ptmm) REVERT: I 255 LYS cc_start: 0.8543 (tptt) cc_final: 0.8196 (tptp) REVERT: I 408 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7862 (tp) REVERT: J 48 LYS cc_start: 0.5732 (OUTLIER) cc_final: 0.5499 (mptt) outliers start: 53 outliers final: 32 residues processed: 296 average time/residue: 0.7150 time to fit residues: 242.0475 Evaluate side-chains 294 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 248 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 621 MET Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 604 GLU Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 200 ASN Chi-restraints excluded: chain H residue 204 ILE Chi-restraints excluded: chain H residue 229 ARG Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 483 PHE Chi-restraints excluded: chain H residue 620 VAL Chi-restraints excluded: chain I residue 210 TYR Chi-restraints excluded: chain I residue 294 VAL Chi-restraints excluded: chain I residue 385 ILE Chi-restraints excluded: chain I residue 408 ILE Chi-restraints excluded: chain I residue 472 SER Chi-restraints excluded: chain I residue 601 VAL Chi-restraints excluded: chain I residue 673 GLU Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain J residue 69 MET Chi-restraints excluded: chain J residue 117 GLU Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 186 ARG Chi-restraints excluded: chain J residue 211 SER Chi-restraints excluded: chain J residue 233 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 334 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 297 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 295 optimal weight: 0.9990 chunk 333 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 255 optimal weight: 4.9990 chunk 177 optimal weight: 0.2980 chunk 92 optimal weight: 0.4980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** A 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 HIS H 327 GLN H 542 GLN ** I 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.130119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.088936 restraints weight = 57836.090| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.74 r_work: 0.3057 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.146 28791 Z= 0.124 Angle : 0.550 8.311 39188 Z= 0.281 Chirality : 0.040 0.228 4390 Planarity : 0.005 0.069 4843 Dihedral : 9.873 84.858 4419 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.76 % Allowed : 14.92 % Favored : 83.32 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % 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: 0.30 (0.15), residues: 3331 helix: 1.45 (0.14), residues: 1451 sheet: -0.58 (0.30), residues: 296 loop : -0.81 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG C 750 TYR 0.018 0.001 TYR I 533 PHE 0.020 0.001 PHE C 41 TRP 0.013 0.001 TRP J 107 HIS 0.014 0.001 HIS C 442 Details of bonding type rmsd covalent geometry : bond 0.00297 (28789) covalent geometry : angle 0.54979 (39188) hydrogen bonds : bond 0.03463 ( 1221) hydrogen bonds : angle 4.34231 ( 3412) Misc. bond : bond 0.00035 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 250 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6966 (tm-30) REVERT: A 196 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8270 (mmp80) REVERT: A 307 GLN cc_start: 0.7769 (mp10) cc_final: 0.7334 (mp10) REVERT: A 515 GLU cc_start: 0.8534 (tt0) cc_final: 0.7983 (tm-30) REVERT: A 531 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7910 (mm) REVERT: A 538 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7666 (ttm) REVERT: B 169 MET cc_start: 0.8947 (mmp) cc_final: 0.8608 (mmm) REVERT: B 212 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8530 (mp) REVERT: B 351 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8562 (pm20) REVERT: B 363 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.6756 (mtp180) REVERT: B 619 GLN cc_start: 0.8234 (mt0) cc_final: 0.7995 (mt0) REVERT: B 621 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8726 (tpp) REVERT: B 651 LYS cc_start: 0.8363 (tppp) cc_final: 0.8057 (ttmt) REVERT: B 653 GLU cc_start: 0.8018 (tp30) cc_final: 0.7711 (mt-10) REVERT: C 187 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.7980 (mtpm) REVERT: C 279 ARG cc_start: 0.8590 (ttp80) cc_final: 0.8301 (ttt180) REVERT: C 328 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8322 (tpp) REVERT: H 325 GLU cc_start: 0.8444 (tm-30) cc_final: 0.7840 (tm-30) REVERT: H 582 ARG cc_start: 0.8381 (mmp80) cc_final: 0.8154 (tpp-160) REVERT: I 210 TYR cc_start: 0.6086 (OUTLIER) cc_final: 0.5258 (p90) REVERT: I 213 LYS cc_start: 0.8469 (ptmm) cc_final: 0.8129 (ptmm) REVERT: I 214 PHE cc_start: 0.7657 (m-10) cc_final: 0.7450 (m-10) REVERT: I 255 LYS cc_start: 0.8503 (tptt) cc_final: 0.8148 (tptp) REVERT: I 408 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7874 (tp) REVERT: J 48 LYS cc_start: 0.5721 (OUTLIER) cc_final: 0.5489 (mptt) REVERT: J 127 ASP cc_start: 0.8609 (t0) cc_final: 0.7950 (t0) outliers start: 53 outliers final: 32 residues processed: 289 average time/residue: 0.7258 time to fit residues: 239.4255 Evaluate side-chains 291 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 246 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 621 MET Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 604 GLU Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 200 ASN Chi-restraints excluded: chain H residue 204 ILE Chi-restraints excluded: chain H residue 310 LYS Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 483 PHE Chi-restraints excluded: chain H residue 620 VAL Chi-restraints excluded: chain I residue 210 TYR Chi-restraints excluded: chain I residue 294 VAL Chi-restraints excluded: chain I residue 385 ILE Chi-restraints excluded: chain I residue 408 ILE Chi-restraints excluded: chain I residue 472 SER Chi-restraints excluded: chain I residue 601 VAL Chi-restraints excluded: chain I residue 673 GLU Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain J residue 117 GLU Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 186 ARG Chi-restraints excluded: chain J residue 211 SER Chi-restraints excluded: chain J residue 233 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 135 optimal weight: 0.6980 chunk 136 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 293 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 200 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 302 optimal weight: 5.9990 chunk 229 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 286 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** A 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 HIS H 327 GLN H 542 GLN ** I 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.129882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.088744 restraints weight = 56034.523| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.70 r_work: 0.3052 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.133 28791 Z= 0.132 Angle : 0.554 10.969 39188 Z= 0.282 Chirality : 0.041 0.237 4390 Planarity : 0.005 0.069 4843 Dihedral : 9.866 84.584 4419 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.59 % Allowed : 15.12 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.32 (0.15), residues: 3331 helix: 1.46 (0.14), residues: 1451 sheet: -0.56 (0.30), residues: 297 loop : -0.81 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG C 750 TYR 0.019 0.001 TYR J 110 PHE 0.021 0.001 PHE J 79 TRP 0.012 0.001 TRP J 107 HIS 0.014 0.001 HIS C 442 Details of bonding type rmsd covalent geometry : bond 0.00317 (28789) covalent geometry : angle 0.55440 (39188) hydrogen bonds : bond 0.03508 ( 1221) hydrogen bonds : angle 4.34067 ( 3412) Misc. bond : bond 0.00031 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13215.14 seconds wall clock time: 224 minutes 44.12 seconds (13484.12 seconds total)