Starting phenix.real_space_refine on Mon May 26 08:06:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z9r_39868/05_2025/8z9r_39868.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z9r_39868/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8z9r_39868/05_2025/8z9r_39868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z9r_39868/05_2025/8z9r_39868.map" model { file = "/net/cci-nas-00/data/ceres_data/8z9r_39868/05_2025/8z9r_39868.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z9r_39868/05_2025/8z9r_39868.cif" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 18.84, per 1000 atoms: 0.67 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: 6.90 Conformation dependent library (CDL) restraints added in 4.0 seconds 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: 9.82 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: 10.23 Time building geometry restraints manager: 7.98 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: 3.730 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: 0.030 Extract box with map and model: 1.250 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 70.250 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.160 ------------------------------------------------------------------------------- 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 : 7.99 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (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 TRP 0.021 0.001 TRP I 330 HIS 0.008 0.001 HIS A 573 PHE 0.026 0.001 PHE C 41 TYR 0.016 0.001 TYR H 621 ARG 0.010 0.000 ARG C 755 Details of bonding type rmsd hydrogen bonds : bond 0.16639 ( 1221) hydrogen bonds : angle 6.34153 ( 3412) covalent geometry : bond 0.00250 (28789) covalent geometry : angle 0.52933 (39188) 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 : 3.267 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: 1.8510 time to fit residues: 854.2571 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 : 3.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 0.9980 chunk 254 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 171 optimal weight: 0.4980 chunk 136 optimal weight: 2.9990 chunk 263 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 196 optimal weight: 7.9990 chunk 305 optimal weight: 0.0470 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.133005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.092064 restraints weight = 53351.137| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.62 r_work: 0.3138 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 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 = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 28791 Z= 0.129 Angle : 0.569 7.536 39188 Z= 0.293 Chirality : 0.041 0.181 4390 Planarity : 0.005 0.063 4843 Dihedral : 10.258 86.736 4419 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.33 % Allowed : 9.07 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.15), residues: 3331 helix: 1.32 (0.14), residues: 1441 sheet: -0.23 (0.31), residues: 302 loop : -0.74 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 70 HIS 0.013 0.001 HIS C 442 PHE 0.020 0.001 PHE C 41 TYR 0.018 0.001 TYR I 533 ARG 0.010 0.001 ARG C 754 Details of bonding type rmsd hydrogen bonds : bond 0.04169 ( 1221) hydrogen bonds : angle 4.94286 ( 3412) covalent geometry : bond 0.00293 (28789) covalent geometry : angle 0.56874 (39188) Misc. bond : bond 0.00039 ( 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: 40 poor density : 303 time to evaluate : 3.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7659 (mp10) cc_final: 0.7428 (mp10) REVERT: B 112 LYS cc_start: 0.8605 (mptt) cc_final: 0.8379 (mptt) REVERT: B 169 MET cc_start: 0.9074 (mmp) cc_final: 0.8746 (mmm) REVERT: B 213 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.8989 (tppp) REVERT: B 363 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.6955 (mtp180) REVERT: B 369 MET cc_start: 0.8704 (mtp) cc_final: 0.8405 (mtp) REVERT: B 609 MET cc_start: 0.9322 (OUTLIER) cc_final: 0.8960 (tpp) REVERT: C 145 ARG cc_start: 0.8417 (tpp-160) cc_final: 0.7922 (tpp-160) REVERT: C 187 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8372 (mtpm) REVERT: C 279 ARG cc_start: 0.8569 (ttp80) cc_final: 0.8302 (ttt180) REVERT: C 309 GLU cc_start: 0.7637 (tp30) cc_final: 0.6951 (tm-30) REVERT: H 229 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7589 (mtm180) REVERT: H 582 ARG cc_start: 0.8374 (mmp80) cc_final: 0.8104 (tpp-160) REVERT: I 210 TYR cc_start: 0.5903 (OUTLIER) cc_final: 0.4892 (p90) REVERT: I 213 LYS cc_start: 0.8546 (ptmm) cc_final: 0.8237 (ptmm) REVERT: I 469 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7583 (pp20) REVERT: J 107 TRP cc_start: 0.7243 (t-100) cc_final: 0.6548 (t-100) REVERT: J 142 ARG cc_start: 0.8284 (ttp-170) cc_final: 0.8021 (ttp-170) outliers start: 40 outliers final: 12 residues processed: 330 average time/residue: 1.7185 time to fit residues: 644.2303 Evaluate side-chains 279 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 260 time to evaluate : 3.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 31 optimal weight: 3.9990 chunk 283 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 235 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 265 optimal weight: 0.9990 chunk 188 optimal weight: 0.6980 chunk 289 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 60 optimal weight: 0.3980 chunk 12 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 C 154 GLN C 442 HIS ** C 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 691 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.131710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.091196 restraints weight = 46445.066| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.44 r_work: 0.3139 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28791 Z= 0.126 Angle : 0.539 7.454 39188 Z= 0.278 Chirality : 0.041 0.178 4390 Planarity : 0.005 0.063 4843 Dihedral : 10.084 88.757 4419 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.59 % Allowed : 11.10 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.15), residues: 3331 helix: 1.41 (0.14), residues: 1442 sheet: -0.28 (0.30), residues: 302 loop : -0.76 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 330 HIS 0.013 0.001 HIS C 442 PHE 0.020 0.001 PHE C 41 TYR 0.020 0.001 TYR I 533 ARG 0.010 0.000 ARG C 750 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 1221) hydrogen bonds : angle 4.63135 ( 3412) covalent geometry : bond 0.00291 (28789) covalent geometry : angle 0.53930 (39188) Misc. bond : bond 0.00039 ( 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 337 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 289 time to evaluate : 3.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.8313 (ptm-80) cc_final: 0.8048 (ptm-80) REVERT: A 304 ASN cc_start: 0.7643 (m-40) cc_final: 0.7337 (m110) REVERT: A 307 GLN cc_start: 0.7772 (mp10) cc_final: 0.7444 (mp10) REVERT: A 485 ARG cc_start: 0.8425 (mtp180) cc_final: 0.8090 (ttm-80) REVERT: B 144 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8050 (mt-10) REVERT: B 169 MET cc_start: 0.9063 (mmp) cc_final: 0.8790 (mmm) REVERT: B 369 MET cc_start: 0.8663 (mtp) cc_final: 0.8296 (mtp) REVERT: B 609 MET cc_start: 0.9275 (OUTLIER) cc_final: 0.8984 (tpp) REVERT: B 651 LYS cc_start: 0.8544 (ttpp) cc_final: 0.7932 (tttp) REVERT: C 100 ASN cc_start: 0.8060 (t0) cc_final: 0.7779 (t0) REVERT: C 145 ARG cc_start: 0.8434 (tpp-160) cc_final: 0.7860 (tpp-160) REVERT: C 187 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8087 (mtpm) REVERT: C 279 ARG cc_start: 0.8554 (ttp80) cc_final: 0.8291 (ttt180) REVERT: C 309 GLU cc_start: 0.7660 (tp30) cc_final: 0.6948 (tm-30) REVERT: H 229 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7570 (mtm180) REVERT: H 325 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8014 (tm-30) REVERT: H 456 GLU cc_start: 0.8020 (tp30) cc_final: 0.7040 (mp0) REVERT: H 468 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7983 (mmtt) REVERT: H 539 THR cc_start: 0.8507 (p) cc_final: 0.8207 (t) REVERT: H 596 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.6747 (mtpp) REVERT: I 210 TYR cc_start: 0.6035 (OUTLIER) cc_final: 0.4986 (p90) REVERT: I 213 LYS cc_start: 0.8502 (ptmm) cc_final: 0.8236 (ptmm) REVERT: J 107 TRP cc_start: 0.7455 (t-100) cc_final: 0.7227 (t-100) REVERT: J 142 ARG cc_start: 0.8267 (ttp-170) cc_final: 0.8051 (ttp-170) outliers start: 48 outliers final: 14 residues processed: 323 average time/residue: 1.7912 time to fit residues: 671.9544 Evaluate side-chains 282 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 262 time to evaluate : 3.547 ------------------------------------------------------------------------------- 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 212 ILE Chi-restraints excluded: chain B residue 259 ASP 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 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 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 140 optimal weight: 0.7980 chunk 273 optimal weight: 2.9990 chunk 251 optimal weight: 0.0040 chunk 90 optimal weight: 0.9990 chunk 323 optimal weight: 8.9990 chunk 21 optimal weight: 0.0020 chunk 268 optimal weight: 0.9980 chunk 294 optimal weight: 2.9990 chunk 329 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 335 optimal weight: 5.9990 overall best weight: 0.5602 ------------------------------------------------------------------------------- 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 ** C 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 327 GLN H 542 GLN I 227 ASN ** I 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 567 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.132329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.091244 restraints weight = 56020.666| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.67 r_work: 0.3153 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 28791 Z= 0.110 Angle : 0.520 7.427 39188 Z= 0.268 Chirality : 0.040 0.181 4390 Planarity : 0.005 0.063 4843 Dihedral : 9.965 89.740 4419 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.59 % Allowed : 12.43 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 3331 helix: 1.46 (0.14), residues: 1447 sheet: -0.26 (0.30), residues: 299 loop : -0.76 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 330 HIS 0.012 0.001 HIS C 442 PHE 0.020 0.001 PHE C 41 TYR 0.019 0.001 TYR I 533 ARG 0.015 0.000 ARG C 750 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 1221) hydrogen bonds : angle 4.47901 ( 3412) covalent geometry : bond 0.00253 (28789) covalent geometry : angle 0.52006 (39188) Misc. bond : bond 0.00041 ( 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 327 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 279 time to evaluate : 3.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7847 (mmp80) REVERT: A 307 GLN cc_start: 0.7750 (mp10) cc_final: 0.7382 (mp10) REVERT: A 485 ARG cc_start: 0.8481 (mtp180) cc_final: 0.8118 (ttm-80) REVERT: A 515 GLU cc_start: 0.8500 (tt0) cc_final: 0.8089 (tm-30) REVERT: B 122 ARG cc_start: 0.7947 (mmm160) cc_final: 0.7183 (mmm160) REVERT: B 144 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8059 (mt-10) REVERT: B 169 MET cc_start: 0.8974 (mmp) cc_final: 0.8740 (mmm) REVERT: B 212 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8541 (mp) REVERT: B 369 MET cc_start: 0.8646 (mtp) cc_final: 0.8355 (mtp) REVERT: B 609 MET cc_start: 0.9267 (OUTLIER) cc_final: 0.8950 (tpp) REVERT: B 621 MET cc_start: 0.9092 (ttt) cc_final: 0.8678 (tpp) REVERT: B 651 LYS cc_start: 0.8491 (ttpp) cc_final: 0.7876 (tttp) REVERT: B 652 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8182 (mm-30) REVERT: C 100 ASN cc_start: 0.7945 (t0) cc_final: 0.7681 (t0) REVERT: C 145 ARG cc_start: 0.8431 (tpp-160) cc_final: 0.7864 (tpp-160) REVERT: C 187 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8103 (mtpm) REVERT: C 279 ARG cc_start: 0.8560 (ttp80) cc_final: 0.8310 (ttt180) REVERT: H 325 GLU cc_start: 0.8463 (tm-30) cc_final: 0.7920 (tm-30) REVERT: H 456 GLU cc_start: 0.8008 (tp30) cc_final: 0.7116 (mp0) REVERT: H 468 LYS cc_start: 0.8193 (mmtt) cc_final: 0.7980 (mmtt) REVERT: H 539 THR cc_start: 0.8503 (p) cc_final: 0.8206 (t) REVERT: H 596 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.6745 (mtpp) REVERT: I 213 LYS cc_start: 0.8545 (ptmm) cc_final: 0.8193 (ptmm) REVERT: I 255 LYS cc_start: 0.8507 (tptt) cc_final: 0.8292 (tptp) REVERT: I 673 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.8016 (mp0) outliers start: 48 outliers final: 17 residues processed: 309 average time/residue: 1.6744 time to fit residues: 589.5095 Evaluate side-chains 276 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 253 time to evaluate : 2.981 ------------------------------------------------------------------------------- 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 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 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 197 VAL Chi-restraints excluded: chain H residue 204 ILE Chi-restraints excluded: chain H residue 596 LYS Chi-restraints excluded: chain I residue 214 PHE 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 75 optimal weight: 0.0170 chunk 110 optimal weight: 0.0980 chunk 259 optimal weight: 0.0030 chunk 204 optimal weight: 3.9990 chunk 281 optimal weight: 6.9990 chunk 245 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 273 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 247 optimal weight: 0.4980 chunk 193 optimal weight: 0.8980 overall best weight: 0.3028 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.134525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.093808 restraints weight = 55320.813| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.67 r_work: 0.3176 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 28791 Z= 0.098 Angle : 0.509 9.511 39188 Z= 0.261 Chirality : 0.040 0.185 4390 Planarity : 0.004 0.063 4843 Dihedral : 9.866 89.472 4419 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.79 % Allowed : 13.02 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.15), residues: 3331 helix: 1.54 (0.14), residues: 1448 sheet: -0.24 (0.30), residues: 298 loop : -0.74 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 107 HIS 0.013 0.001 HIS C 442 PHE 0.019 0.001 PHE J 79 TYR 0.019 0.001 TYR J 110 ARG 0.018 0.000 ARG C 750 Details of bonding type rmsd hydrogen bonds : bond 0.03198 ( 1221) hydrogen bonds : angle 4.36266 ( 3412) covalent geometry : bond 0.00218 (28789) covalent geometry : angle 0.50928 (39188) Misc. bond : bond 0.00046 ( 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 331 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 277 time to evaluate : 3.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7734 (mmp80) REVERT: A 307 GLN cc_start: 0.7717 (mp10) cc_final: 0.7385 (mp10) REVERT: A 451 MET cc_start: 0.8858 (ttp) cc_final: 0.8186 (ttm) REVERT: A 485 ARG cc_start: 0.8480 (mtp180) cc_final: 0.8111 (ttm-80) REVERT: A 515 GLU cc_start: 0.8476 (tt0) cc_final: 0.8054 (tm-30) REVERT: B 122 ARG cc_start: 0.7936 (mmm160) cc_final: 0.7195 (mmm160) REVERT: B 144 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8046 (mt-10) REVERT: B 169 MET cc_start: 0.8938 (mmp) cc_final: 0.8690 (mmm) REVERT: B 212 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8554 (mp) REVERT: B 369 MET cc_start: 0.8594 (mtp) cc_final: 0.8331 (mtt) REVERT: B 609 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.8883 (tpp) REVERT: B 621 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8494 (tpp) REVERT: B 651 LYS cc_start: 0.8532 (ttpp) cc_final: 0.7922 (tttp) REVERT: C 142 ARG cc_start: 0.7164 (tpm170) cc_final: 0.6170 (tpt-90) REVERT: C 145 ARG cc_start: 0.8411 (tpp-160) cc_final: 0.7464 (tmm-80) REVERT: C 146 MET cc_start: 0.7246 (mtt) cc_final: 0.6808 (mtt) REVERT: C 187 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8072 (mtpm) REVERT: C 279 ARG cc_start: 0.8543 (ttp80) cc_final: 0.8302 (ttt180) REVERT: H 325 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8022 (tm-30) REVERT: H 456 GLU cc_start: 0.7986 (tp30) cc_final: 0.7099 (mp0) REVERT: H 539 THR cc_start: 0.8461 (p) cc_final: 0.8163 (t) REVERT: H 596 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.6737 (mtpp) REVERT: I 210 TYR cc_start: 0.6012 (OUTLIER) cc_final: 0.4934 (p90) REVERT: I 213 LYS cc_start: 0.8498 (ptmm) cc_final: 0.8161 (ptmm) REVERT: I 255 LYS cc_start: 0.8558 (tptt) cc_final: 0.8164 (tptp) REVERT: I 673 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: J 31 MET cc_start: 0.6153 (ppp) cc_final: 0.5927 (pp-130) outliers start: 54 outliers final: 19 residues processed: 314 average time/residue: 1.7191 time to fit residues: 617.4762 Evaluate side-chains 283 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 256 time to evaluate : 3.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LYS 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 261 GLU Chi-restraints excluded: chain A residue 436 VAL 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 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 483 PHE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 327 optimal weight: 0.0060 chunk 195 optimal weight: 0.3980 chunk 178 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 chunk 318 optimal weight: 8.9990 chunk 188 optimal weight: 0.9980 chunk 135 optimal weight: 0.0570 chunk 168 optimal weight: 0.6980 chunk 202 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 329 optimal weight: 0.0770 overall best weight: 0.2472 ------------------------------------------------------------------------------- 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 B 530 ASN C 442 HIS H 327 GLN H 542 GLN I 132 ASN ** I 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 513 ASN I 599 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.134680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.094176 restraints weight = 56277.734| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.72 r_work: 0.3127 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.099 28791 Z= 0.097 Angle : 0.507 8.370 39188 Z= 0.260 Chirality : 0.039 0.192 4390 Planarity : 0.004 0.067 4843 Dihedral : 9.814 88.692 4419 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.50 % Allowed : 13.92 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.15), residues: 3331 helix: 1.65 (0.14), residues: 1439 sheet: -0.26 (0.30), residues: 302 loop : -0.71 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP J 107 HIS 0.012 0.001 HIS C 442 PHE 0.019 0.001 PHE C 41 TYR 0.018 0.001 TYR I 533 ARG 0.017 0.000 ARG C 750 Details of bonding type rmsd hydrogen bonds : bond 0.03087 ( 1221) hydrogen bonds : angle 4.28294 ( 3412) covalent geometry : bond 0.00219 (28789) covalent geometry : angle 0.50663 (39188) Misc. bond : bond 0.00050 ( 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 326 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 281 time to evaluate : 3.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.7769 (mmp80) REVERT: A 307 GLN cc_start: 0.7678 (mp10) cc_final: 0.7339 (mp10) REVERT: A 435 HIS cc_start: 0.7566 (m-70) cc_final: 0.7354 (m170) REVERT: A 451 MET cc_start: 0.8752 (ttp) cc_final: 0.8145 (ttm) REVERT: A 485 ARG cc_start: 0.8377 (mtp180) cc_final: 0.7988 (ttm-80) REVERT: A 515 GLU cc_start: 0.8425 (tt0) cc_final: 0.7972 (tm-30) REVERT: A 582 ARG cc_start: 0.8736 (mmm160) cc_final: 0.8491 (mmm160) REVERT: B 122 ARG cc_start: 0.7849 (mmm160) cc_final: 0.7068 (mmm160) REVERT: B 144 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8044 (mt-10) REVERT: B 169 MET cc_start: 0.8843 (mmp) cc_final: 0.8596 (mmm) REVERT: B 212 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8536 (mt) REVERT: B 213 LYS cc_start: 0.8945 (tppt) cc_final: 0.8667 (tppp) REVERT: B 412 GLU cc_start: 0.8369 (mp0) cc_final: 0.7914 (mp0) REVERT: B 609 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8760 (tpp) REVERT: B 621 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8681 (tpp) REVERT: B 651 LYS cc_start: 0.8375 (ttpp) cc_final: 0.7764 (tttp) REVERT: B 653 GLU cc_start: 0.8030 (tp30) cc_final: 0.7737 (mt-10) REVERT: C 142 ARG cc_start: 0.7152 (tpm170) cc_final: 0.6100 (tpt-90) REVERT: C 145 ARG cc_start: 0.8459 (tpp-160) cc_final: 0.7410 (tmm-80) REVERT: C 146 MET cc_start: 0.7122 (mtt) cc_final: 0.6677 (mtt) REVERT: C 279 ARG cc_start: 0.8558 (ttp80) cc_final: 0.8320 (ttt180) REVERT: H 325 GLU cc_start: 0.8426 (tm-30) cc_final: 0.7937 (tm-30) REVERT: H 539 THR cc_start: 0.8388 (p) cc_final: 0.8091 (t) REVERT: H 596 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.6629 (mtpp) REVERT: I 30 TYR cc_start: 0.8041 (m-80) cc_final: 0.7665 (m-80) REVERT: I 210 TYR cc_start: 0.5961 (OUTLIER) cc_final: 0.4957 (p90) REVERT: I 213 LYS cc_start: 0.8514 (ptmm) cc_final: 0.8168 (ptmm) REVERT: I 255 LYS cc_start: 0.8510 (tptt) cc_final: 0.8118 (tptp) REVERT: I 673 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7997 (mp0) REVERT: J 31 MET cc_start: 0.6057 (ppp) cc_final: 0.5836 (pp-130) outliers start: 45 outliers final: 21 residues processed: 307 average time/residue: 1.5788 time to fit residues: 556.7559 Evaluate side-chains 283 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 255 time to evaluate : 3.194 ------------------------------------------------------------------------------- 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 261 GLU Chi-restraints excluded: chain A residue 478 LEU 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 273 VAL 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 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 483 PHE Chi-restraints excluded: chain H residue 596 LYS Chi-restraints excluded: chain I residue 3 LEU 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 673 GLU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 117 GLU 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 71 optimal weight: 3.9990 chunk 21 optimal weight: 0.0020 chunk 120 optimal weight: 0.8980 chunk 156 optimal weight: 0.7980 chunk 298 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 260 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- 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 B 619 GLN C 442 HIS H 327 GLN H 542 GLN I 132 ASN ** I 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 169 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.132812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.092383 restraints weight = 48746.257| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.54 r_work: 0.3065 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1883 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= 0.116 Angle : 0.524 8.080 39188 Z= 0.268 Chirality : 0.040 0.202 4390 Planarity : 0.004 0.063 4843 Dihedral : 9.799 89.630 4419 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.59 % Allowed : 14.58 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.15), residues: 3331 helix: 1.63 (0.14), residues: 1448 sheet: -0.33 (0.29), residues: 304 loop : -0.72 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 107 HIS 0.013 0.001 HIS C 442 PHE 0.019 0.001 PHE C 41 TYR 0.019 0.001 TYR I 533 ARG 0.012 0.000 ARG C 750 Details of bonding type rmsd hydrogen bonds : bond 0.03296 ( 1221) hydrogen bonds : angle 4.26385 ( 3412) covalent geometry : bond 0.00272 (28789) covalent geometry : angle 0.52361 (39188) Misc. bond : bond 0.00038 ( 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 320 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 272 time to evaluate : 3.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6835 (tm-30) REVERT: A 196 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7804 (mmp80) REVERT: A 307 GLN cc_start: 0.7687 (mp10) cc_final: 0.7328 (mp10) REVERT: A 485 ARG cc_start: 0.8362 (mtp180) cc_final: 0.7977 (ttm-80) REVERT: A 515 GLU cc_start: 0.8419 (tt0) cc_final: 0.7966 (tm-30) REVERT: B 122 ARG cc_start: 0.7843 (mmm160) cc_final: 0.7061 (mmm160) REVERT: B 144 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7973 (mt-10) REVERT: B 169 MET cc_start: 0.8919 (mmp) cc_final: 0.8668 (mmm) REVERT: B 212 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8492 (mp) REVERT: B 213 LYS cc_start: 0.8944 (tppt) cc_final: 0.8721 (tppp) REVERT: B 609 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8715 (tpp) REVERT: B 621 MET cc_start: 0.9042 (ttt) cc_final: 0.8698 (tpp) REVERT: B 653 GLU cc_start: 0.8045 (tp30) cc_final: 0.7811 (mt-10) REVERT: B 686 ARG cc_start: 0.8161 (mtp85) cc_final: 0.7860 (mtt-85) REVERT: C 142 ARG cc_start: 0.7252 (tpm170) cc_final: 0.6305 (tpt-90) REVERT: C 146 MET cc_start: 0.7235 (mtt) cc_final: 0.6905 (mtt) REVERT: C 279 ARG cc_start: 0.8541 (ttp80) cc_final: 0.8300 (ttt180) REVERT: H 325 GLU cc_start: 0.8432 (tm-30) cc_final: 0.7948 (tm-30) REVERT: H 456 GLU cc_start: 0.7936 (tm-30) cc_final: 0.6922 (mp0) REVERT: H 539 THR cc_start: 0.8456 (p) cc_final: 0.8132 (t) REVERT: H 582 ARG cc_start: 0.8395 (tpp-160) cc_final: 0.8158 (mmp80) REVERT: H 596 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.6653 (mtpp) REVERT: I 210 TYR cc_start: 0.6003 (OUTLIER) cc_final: 0.4997 (p90) REVERT: I 213 LYS cc_start: 0.8521 (ptmm) cc_final: 0.8205 (ptmm) REVERT: I 255 LYS cc_start: 0.8529 (tptt) cc_final: 0.8143 (tptp) outliers start: 48 outliers final: 28 residues processed: 305 average time/residue: 1.6383 time to fit residues: 573.6598 Evaluate side-chains 295 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 261 time to evaluate : 3.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 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 261 GLU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 523 VAL 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 273 VAL 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 B residue 705 ILE Chi-restraints excluded: chain C residue 156 CYS 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 343 LEU Chi-restraints excluded: chain H residue 483 PHE Chi-restraints excluded: chain H residue 596 LYS Chi-restraints excluded: chain I residue 133 LEU 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 186 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 104 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 252 optimal weight: 2.9990 chunk 255 optimal weight: 0.0670 chunk 130 optimal weight: 7.9990 chunk 170 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 110 optimal weight: 0.0870 chunk 36 optimal weight: 0.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 327 GLN ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 531 HIS C 442 HIS H 327 GLN H 542 GLN I 132 ASN ** I 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.133522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.093715 restraints weight = 57994.603| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.91 r_work: 0.3087 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 28791 Z= 0.103 Angle : 0.517 7.858 39188 Z= 0.264 Chirality : 0.040 0.201 4390 Planarity : 0.004 0.066 4843 Dihedral : 9.758 89.521 4419 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.53 % Allowed : 14.78 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.15), residues: 3331 helix: 1.67 (0.14), residues: 1442 sheet: -0.28 (0.30), residues: 304 loop : -0.73 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 107 HIS 0.013 0.001 HIS C 442 PHE 0.019 0.001 PHE C 41 TYR 0.017 0.001 TYR I 533 ARG 0.019 0.000 ARG C 750 Details of bonding type rmsd hydrogen bonds : bond 0.03158 ( 1221) hydrogen bonds : angle 4.22985 ( 3412) covalent geometry : bond 0.00237 (28789) covalent geometry : angle 0.51698 (39188) Misc. bond : bond 0.00038 ( 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 310 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 264 time to evaluate : 3.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6849 (tm-30) REVERT: A 196 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7698 (mmp80) REVERT: A 307 GLN cc_start: 0.7677 (mp10) cc_final: 0.7313 (mp10) REVERT: A 485 ARG cc_start: 0.8185 (mtp180) cc_final: 0.7776 (ttm-80) REVERT: A 515 GLU cc_start: 0.8330 (tt0) cc_final: 0.7823 (tm-30) REVERT: B 122 ARG cc_start: 0.7627 (mmm160) cc_final: 0.6905 (mmm160) REVERT: B 144 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7826 (mt-10) REVERT: B 169 MET cc_start: 0.8889 (mmp) cc_final: 0.8652 (mmm) REVERT: B 212 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8503 (mp) REVERT: B 213 LYS cc_start: 0.8898 (tppt) cc_final: 0.8624 (tppp) REVERT: B 225 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8524 (m) REVERT: B 412 GLU cc_start: 0.8305 (mp0) cc_final: 0.8074 (mp0) REVERT: B 609 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8645 (tpp) REVERT: B 621 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8643 (tpp) REVERT: B 651 LYS cc_start: 0.8332 (ttpp) cc_final: 0.7688 (tttp) REVERT: B 686 ARG cc_start: 0.8024 (mtp85) cc_final: 0.7721 (mtt-85) REVERT: C 279 ARG cc_start: 0.8446 (ttp80) cc_final: 0.8146 (tmt170) REVERT: H 325 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7828 (tm-30) REVERT: H 456 GLU cc_start: 0.7982 (tm-30) cc_final: 0.6979 (mp0) REVERT: H 582 ARG cc_start: 0.8355 (tpp-160) cc_final: 0.8094 (mmp80) REVERT: H 596 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.6640 (mtpp) REVERT: I 210 TYR cc_start: 0.6059 (OUTLIER) cc_final: 0.5081 (p90) REVERT: I 213 LYS cc_start: 0.8512 (ptmm) cc_final: 0.8193 (ptmm) REVERT: I 255 LYS cc_start: 0.8474 (tptt) cc_final: 0.8095 (tptp) REVERT: I 408 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7845 (tp) REVERT: I 673 GLU cc_start: 0.8341 (mp0) cc_final: 0.8135 (pm20) outliers start: 46 outliers final: 28 residues processed: 291 average time/residue: 1.7017 time to fit residues: 564.2072 Evaluate side-chains 293 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 256 time to evaluate : 3.192 ------------------------------------------------------------------------------- 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 261 GLU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 273 VAL 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 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 343 LEU Chi-restraints excluded: chain H residue 483 PHE Chi-restraints excluded: chain H residue 596 LYS Chi-restraints excluded: chain I residue 133 LEU 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 408 ILE 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 146 MET Chi-restraints excluded: chain J residue 186 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 284 optimal weight: 0.9990 chunk 202 optimal weight: 0.8980 chunk 126 optimal weight: 0.4980 chunk 17 optimal weight: 4.9990 chunk 77 optimal weight: 0.2980 chunk 247 optimal weight: 6.9990 chunk 315 optimal weight: 0.9980 chunk 219 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 5 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 435 HIS ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN C 442 HIS ** C 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 327 GLN H 542 GLN I 132 ASN ** I 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 672 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.133094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.092700 restraints weight = 46680.527| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.50 r_work: 0.3112 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28791 Z= 0.110 Angle : 0.527 8.902 39188 Z= 0.268 Chirality : 0.040 0.206 4390 Planarity : 0.004 0.071 4843 Dihedral : 9.752 89.188 4419 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.56 % Allowed : 14.98 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.15), residues: 3331 helix: 1.68 (0.14), residues: 1443 sheet: -0.33 (0.29), residues: 306 loop : -0.73 (0.15), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.013 0.001 HIS C 442 PHE 0.019 0.001 PHE C 41 TYR 0.017 0.001 TYR I 533 ARG 0.020 0.000 ARG C 750 Details of bonding type rmsd hydrogen bonds : bond 0.03225 ( 1221) hydrogen bonds : angle 4.23227 ( 3412) covalent geometry : bond 0.00257 (28789) covalent geometry : angle 0.52655 (39188) Misc. bond : bond 0.00040 ( 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 318 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 271 time to evaluate : 3.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7746 (mmp80) REVERT: A 307 GLN cc_start: 0.7704 (mp10) cc_final: 0.7327 (mp10) REVERT: A 485 ARG cc_start: 0.8319 (mtp180) cc_final: 0.7929 (ttm-80) REVERT: A 515 GLU cc_start: 0.8381 (tt0) cc_final: 0.7860 (tm-30) REVERT: B 122 ARG cc_start: 0.7760 (mmm160) cc_final: 0.7020 (mmm160) REVERT: B 144 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8005 (mt-10) REVERT: B 169 MET cc_start: 0.8928 (mmp) cc_final: 0.8698 (mmm) REVERT: B 212 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8513 (mt) REVERT: B 213 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8666 (tppp) REVERT: B 225 THR cc_start: 0.8846 (OUTLIER) cc_final: 0.8595 (m) REVERT: B 412 GLU cc_start: 0.8356 (mp0) cc_final: 0.8103 (mp0) REVERT: B 609 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8682 (tpp) REVERT: B 621 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8694 (tpp) REVERT: B 651 LYS cc_start: 0.8341 (ttpp) cc_final: 0.7689 (tttp) REVERT: B 686 ARG cc_start: 0.8104 (mtp85) cc_final: 0.7820 (mtt-85) REVERT: C 279 ARG cc_start: 0.8515 (ttp80) cc_final: 0.8115 (ptt90) REVERT: H 325 GLU cc_start: 0.8406 (tm-30) cc_final: 0.7916 (tm-30) REVERT: H 456 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7011 (mp0) REVERT: H 582 ARG cc_start: 0.8419 (tpp-160) cc_final: 0.8165 (mmp80) REVERT: H 596 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.6684 (mtpp) REVERT: I 210 TYR cc_start: 0.6004 (OUTLIER) cc_final: 0.5150 (p90) REVERT: I 213 LYS cc_start: 0.8512 (ptmm) cc_final: 0.8192 (ptmm) REVERT: I 408 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7897 (tp) REVERT: I 673 GLU cc_start: 0.8304 (mp0) cc_final: 0.8092 (pm20) REVERT: J 31 MET cc_start: 0.6060 (ppp) cc_final: 0.5813 (pp-130) outliers start: 47 outliers final: 28 residues processed: 300 average time/residue: 1.6467 time to fit residues: 567.8283 Evaluate side-chains 294 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 257 time to evaluate : 3.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 478 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 323 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 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 343 LEU 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 133 LEU 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 408 ILE Chi-restraints excluded: chain I residue 472 SER Chi-restraints excluded: chain I residue 601 VAL Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 186 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 121 optimal weight: 0.7980 chunk 96 optimal weight: 0.0570 chunk 111 optimal weight: 0.9980 chunk 202 optimal weight: 0.8980 chunk 326 optimal weight: 0.4980 chunk 132 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 319 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 294 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 435 HIS ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN C 442 HIS ** C 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 327 GLN H 542 GLN I 132 ASN ** I 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.133005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.092230 restraints weight = 63412.802| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.03 r_work: 0.3089 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28791 Z= 0.111 Angle : 0.532 8.490 39188 Z= 0.271 Chirality : 0.040 0.215 4390 Planarity : 0.005 0.070 4843 Dihedral : 9.747 89.047 4419 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.40 % Allowed : 15.22 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.15), residues: 3331 helix: 1.65 (0.14), residues: 1450 sheet: -0.32 (0.29), residues: 306 loop : -0.74 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 70 HIS 0.014 0.001 HIS C 442 PHE 0.022 0.001 PHE J 149 TYR 0.017 0.001 TYR I 533 ARG 0.020 0.000 ARG C 750 Details of bonding type rmsd hydrogen bonds : bond 0.03210 ( 1221) hydrogen bonds : angle 4.23906 ( 3412) covalent geometry : bond 0.00257 (28789) covalent geometry : angle 0.53235 (39188) Misc. bond : bond 0.00038 ( 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 300 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 258 time to evaluate : 3.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7987 (mmp80) REVERT: A 307 GLN cc_start: 0.7744 (mp10) cc_final: 0.7378 (mp10) REVERT: A 485 ARG cc_start: 0.8234 (mtp180) cc_final: 0.7837 (ttm-80) REVERT: A 515 GLU cc_start: 0.8363 (tt0) cc_final: 0.7853 (tm-30) REVERT: B 122 ARG cc_start: 0.7691 (mmm160) cc_final: 0.6997 (mmm160) REVERT: B 144 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7859 (mt-10) REVERT: B 169 MET cc_start: 0.8960 (mmp) cc_final: 0.8733 (mmm) REVERT: B 212 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8570 (mt) REVERT: B 213 LYS cc_start: 0.8915 (tppt) cc_final: 0.8652 (tppp) REVERT: B 412 GLU cc_start: 0.8343 (mp0) cc_final: 0.7938 (mp0) REVERT: B 609 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8716 (tpp) REVERT: B 621 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8669 (tpp) REVERT: B 651 LYS cc_start: 0.8386 (ttpp) cc_final: 0.7737 (tttp) REVERT: B 653 GLU cc_start: 0.7934 (tp30) cc_final: 0.7674 (mt-10) REVERT: B 686 ARG cc_start: 0.7981 (mtp85) cc_final: 0.7679 (mtt-85) REVERT: C 279 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8076 (ptt90) REVERT: H 325 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7816 (tm-30) REVERT: H 582 ARG cc_start: 0.8384 (tpp-160) cc_final: 0.8138 (mmp80) REVERT: H 596 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.6741 (mtpp) REVERT: I 210 TYR cc_start: 0.6002 (OUTLIER) cc_final: 0.5172 (p90) REVERT: I 213 LYS cc_start: 0.8506 (ptmm) cc_final: 0.8191 (ptmm) REVERT: I 255 LYS cc_start: 0.8512 (tptt) cc_final: 0.8128 (tptp) REVERT: I 408 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7867 (tp) REVERT: J 31 MET cc_start: 0.5892 (ppp) cc_final: 0.5658 (pp-130) outliers start: 42 outliers final: 28 residues processed: 285 average time/residue: 1.6516 time to fit residues: 537.2074 Evaluate side-chains 287 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 252 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 478 LEU Chi-restraints excluded: chain A residue 523 VAL 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 273 VAL Chi-restraints excluded: chain B residue 323 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 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 343 LEU 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 133 LEU 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 408 ILE Chi-restraints excluded: chain I residue 472 SER Chi-restraints excluded: chain I residue 601 VAL Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 186 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 32 optimal weight: 0.4980 chunk 49 optimal weight: 0.1980 chunk 94 optimal weight: 0.8980 chunk 119 optimal weight: 0.0370 chunk 16 optimal weight: 6.9990 chunk 130 optimal weight: 0.1980 chunk 75 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 247 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 435 HIS ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN C 442 HIS H 327 GLN H 500 GLN H 542 GLN I 132 ASN ** I 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.134017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.093083 restraints weight = 60504.068| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.82 r_work: 0.3060 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.147 28791 Z= 0.103 Angle : 0.531 10.734 39188 Z= 0.271 Chirality : 0.040 0.213 4390 Planarity : 0.004 0.071 4843 Dihedral : 9.722 89.949 4419 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.40 % Allowed : 15.45 % Favored : 83.16 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 3331 helix: 1.65 (0.14), residues: 1449 sheet: -0.33 (0.29), residues: 317 loop : -0.73 (0.15), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 70 HIS 0.014 0.001 HIS C 442 PHE 0.020 0.001 PHE J 79 TYR 0.019 0.001 TYR J 110 ARG 0.020 0.000 ARG C 750 Details of bonding type rmsd hydrogen bonds : bond 0.03093 ( 1221) hydrogen bonds : angle 4.23791 ( 3412) covalent geometry : bond 0.00244 (28789) covalent geometry : angle 0.53132 (39188) Misc. bond : bond 0.00044 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27498.61 seconds wall clock time: 473 minutes 53.94 seconds (28433.94 seconds total)