Starting phenix.real_space_refine on Wed Mar 4 05:01:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m5r_30090/03_2026/6m5r_30090.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m5r_30090/03_2026/6m5r_30090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6m5r_30090/03_2026/6m5r_30090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m5r_30090/03_2026/6m5r_30090.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6m5r_30090/03_2026/6m5r_30090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m5r_30090/03_2026/6m5r_30090.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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 Zn 2 6.06 5 S 50 5.16 5 C 7008 2.51 5 N 1996 2.21 5 O 1999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11055 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 4924 Classifications: {'peptide': 646} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 30, 'TRANS': 615} Chain breaks: 3 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4, 'HIS:plan': 1, 'ARG:plan': 4, 'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "B" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5296 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 35, 'TRANS': 653} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'HIS:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 833 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5857 SG CYS B 121 29.367 53.359 51.647 1.00 29.72 S ATOM 10821 SG CYS C 101 29.841 52.098 54.795 1.00 44.32 S ATOM 6446 SG CYS B 197 52.080 57.130 48.889 1.00 30.65 S ATOM 6464 SG CYS B 200 54.032 56.988 51.829 1.00 34.04 S Time building chain proxies: 2.52, per 1000 atoms: 0.23 Number of scatterers: 11055 At special positions: 0 Unit cell: (109.2, 107.1, 118.65, 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) Zn 2 29.99 S 50 16.00 O 1999 8.00 N 1996 7.00 C 7008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 669.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 121 " pdb="ZN ZN B 801 " - pdb=" SG CYS C 101 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 124 " pdb=" ZN B 802 " pdb="ZN ZN B 802 " - pdb=" SG CYS B 197 " pdb="ZN ZN B 802 " - pdb=" ND1 HIS B 225 " pdb="ZN ZN B 802 " - pdb=" SG CYS B 200 " 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2704 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 5 sheets defined 54.1% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 38 through 42 removed outlier: 4.233A pdb=" N LEU A 41 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG A 42 " --> pdb=" O ASP A 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 38 through 42' Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 73 through 78 Processing helix chain 'A' and resid 81 through 89 removed outlier: 4.481A pdb=" N SER A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 94 removed outlier: 3.762A pdb=" N LYS A 94 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 119 removed outlier: 4.039A pdb=" N ARG A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 141 Proline residue: A 132 - end of helix removed outlier: 3.863A pdb=" N ASN A 135 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 150 through 169 removed outlier: 3.931A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR A 169 " --> pdb=" O GLN A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 221 removed outlier: 3.963A pdb=" N LEU A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE A 215 " --> pdb=" O HIS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 236 removed outlier: 4.420A pdb=" N LEU A 234 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 263 through 277 removed outlier: 3.888A pdb=" N LEU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 269 " --> pdb=" O THR A 265 " (cutoff:3.500A) Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 290 through 292 No H-bonds generated for 'chain 'A' and resid 290 through 292' Processing helix chain 'A' and resid 293 through 308 removed outlier: 3.977A pdb=" N VAL A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N CYS A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 336 through 340 removed outlier: 4.088A pdb=" N SER A 339 " --> pdb=" O PHE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 374 removed outlier: 3.715A pdb=" N ILE A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A 374 " --> pdb=" O MET A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 398 removed outlier: 3.545A pdb=" N ASN A 398 " --> pdb=" O SER A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 401 No H-bonds generated for 'chain 'A' and resid 399 through 401' Processing helix chain 'A' and resid 418 through 424 removed outlier: 4.536A pdb=" N VAL A 421 " --> pdb=" O MET A 418 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS A 424 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 454 through 458 removed outlier: 3.554A pdb=" N SER A 458 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 489 Processing helix chain 'A' and resid 496 through 500 Processing helix chain 'A' and resid 549 through 569 Processing helix chain 'A' and resid 585 through 601 Processing helix chain 'A' and resid 639 through 653 Processing helix chain 'A' and resid 672 through 682 Processing helix chain 'A' and resid 706 through 721 Processing helix chain 'B' and resid 6 through 33 removed outlier: 4.024A pdb=" N ARG B 12 " --> pdb=" O PRO B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 43 through 58 Processing helix chain 'B' and resid 60 through 70 removed outlier: 4.143A pdb=" N GLY B 64 " --> pdb=" O ARG B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 101 removed outlier: 3.933A pdb=" N THR B 79 " --> pdb=" O PRO B 75 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU B 92 " --> pdb=" O TRP B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 156 removed outlier: 3.606A pdb=" N GLU B 147 " --> pdb=" O LEU B 143 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN B 152 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 180 removed outlier: 3.919A pdb=" N PHE B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 207 removed outlier: 4.094A pdb=" N LEU B 204 " --> pdb=" O CYS B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 218 Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.604A pdb=" N TYR B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 267 removed outlier: 3.859A pdb=" N LEU B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 314 removed outlier: 3.700A pdb=" N LEU B 311 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLN B 312 " --> pdb=" O SER B 309 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 313 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 355 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 376 through 381 removed outlier: 3.987A pdb=" N ILE B 381 " --> pdb=" O ASP B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 400 removed outlier: 3.549A pdb=" N GLN B 391 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 414 removed outlier: 3.503A pdb=" N VAL B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 432 removed outlier: 3.616A pdb=" N CYS B 418 " --> pdb=" O SER B 414 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP B 419 " --> pdb=" O PRO B 415 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA B 432 " --> pdb=" O ALA B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 507 removed outlier: 3.926A pdb=" N ILE B 488 " --> pdb=" O THR B 484 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG B 501 " --> pdb=" O ARG B 497 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 504 " --> pdb=" O ARG B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 531 removed outlier: 3.543A pdb=" N ARG B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG B 520 " --> pdb=" O GLY B 516 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY B 524 " --> pdb=" O ARG B 520 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET B 529 " --> pdb=" O GLU B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 560 removed outlier: 4.056A pdb=" N ALA B 544 " --> pdb=" O PRO B 540 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY B 549 " --> pdb=" O ALA B 545 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 550 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR B 560 " --> pdb=" O PHE B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 587 removed outlier: 4.549A pdb=" N ALA B 578 " --> pdb=" O GLY B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 594 No H-bonds generated for 'chain 'B' and resid 592 through 594' Processing helix chain 'B' and resid 595 through 608 removed outlier: 3.866A pdb=" N ARG B 602 " --> pdb=" O SER B 598 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN B 608 " --> pdb=" O PHE B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 634 removed outlier: 3.581A pdb=" N SER B 630 " --> pdb=" O ALA B 626 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL B 634 " --> pdb=" O SER B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 640 Processing helix chain 'B' and resid 641 through 646 Processing helix chain 'B' and resid 676 through 700 removed outlier: 3.833A pdb=" N ALA B 681 " --> pdb=" O PRO B 677 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B 682 " --> pdb=" O THR B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 773 removed outlier: 3.786A pdb=" N ILE B 764 " --> pdb=" O ASP B 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 4.019A pdb=" N ALA C 21 " --> pdb=" O ILE C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 35 Processing helix chain 'C' and resid 52 through 57 Processing helix chain 'C' and resid 61 through 81 removed outlier: 3.533A pdb=" N LEU C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR C 81 " --> pdb=" O SER C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 128 removed outlier: 3.640A pdb=" N GLU C 105 " --> pdb=" O CYS C 101 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP C 123 " --> pdb=" O ASN C 119 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS C 125 " --> pdb=" O PHE C 121 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=AA2, first strand: chain 'A' and resid 255 through 257 Processing sheet with id=AA3, first strand: chain 'A' and resid 314 through 316 removed outlier: 3.940A pdb=" N SER A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 616 through 619 removed outlier: 6.194A pdb=" N VAL A 576 " --> pdb=" O LEU A 618 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASP A 503 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ARG A 528 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLY A 527 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE A 535 " --> pdb=" O GLY A 527 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N TYR A 529 " --> pdb=" O TYR A 533 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR A 533 " --> pdb=" O TYR A 529 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N TYR A 533 " --> pdb=" O MET A 657 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N SER A 659 " --> pdb=" O TYR A 533 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE A 535 " --> pdb=" O SER A 659 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLU A 661 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA A 537 " --> pdb=" O GLU A 661 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL A 663 " --> pdb=" O ALA A 537 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLU A 539 " --> pdb=" O VAL A 663 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 707 through 708 removed outlier: 3.691A pdb=" N VAL B 741 " --> pdb=" O VAL B 754 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL B 754 " --> pdb=" O VAL B 741 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1398 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.43 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2326 1.33 - 1.45: 2610 1.45 - 1.57: 6278 1.57 - 1.69: 3 1.69 - 1.82: 71 Bond restraints: 11288 Sorted by residual: bond pdb=" N ARG A 475 " pdb=" CA ARG A 475 " ideal model delta sigma weight residual 1.455 1.490 -0.036 9.60e-03 1.09e+04 1.39e+01 bond pdb=" CA VAL A 525 " pdb=" CB VAL A 525 " ideal model delta sigma weight residual 1.537 1.581 -0.044 1.26e-02 6.30e+03 1.23e+01 bond pdb=" C ARG A 490 " pdb=" O ARG A 490 " ideal model delta sigma weight residual 1.244 1.211 0.033 1.00e-02 1.00e+04 1.11e+01 bond pdb=" CA LEU A 435 " pdb=" C LEU A 435 " ideal model delta sigma weight residual 1.523 1.567 -0.044 1.34e-02 5.57e+03 1.09e+01 bond pdb=" C GLY A 582 " pdb=" O GLY A 582 " ideal model delta sigma weight residual 1.239 1.216 0.023 7.10e-03 1.98e+04 1.03e+01 ... (remaining 11283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 14674 1.72 - 3.43: 555 3.43 - 5.15: 87 5.15 - 6.86: 17 6.86 - 8.58: 3 Bond angle restraints: 15336 Sorted by residual: angle pdb=" N VAL A 477 " pdb=" CA VAL A 477 " pdb=" C VAL A 477 " ideal model delta sigma weight residual 111.62 115.77 -4.15 7.90e-01 1.60e+00 2.77e+01 angle pdb=" N ARG A 420 " pdb=" CA ARG A 420 " pdb=" C ARG A 420 " ideal model delta sigma weight residual 111.82 106.52 5.30 1.16e+00 7.43e-01 2.08e+01 angle pdb=" O PRO A 624 " pdb=" C PRO A 624 " pdb=" N PRO A 625 " ideal model delta sigma weight residual 121.31 123.27 -1.96 4.60e-01 4.73e+00 1.81e+01 angle pdb=" N VAL A 656 " pdb=" CA VAL A 656 " pdb=" C VAL A 656 " ideal model delta sigma weight residual 108.11 113.87 -5.76 1.40e+00 5.10e-01 1.69e+01 angle pdb=" N PHE A 573 " pdb=" CA PHE A 573 " pdb=" C PHE A 573 " ideal model delta sigma weight residual 109.07 115.58 -6.51 1.61e+00 3.86e-01 1.64e+01 ... (remaining 15331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 5991 18.00 - 36.00: 590 36.00 - 53.99: 128 53.99 - 71.99: 21 71.99 - 89.99: 16 Dihedral angle restraints: 6746 sinusoidal: 2576 harmonic: 4170 Sorted by residual: dihedral pdb=" CA CYS B 223 " pdb=" C CYS B 223 " pdb=" N ASN B 224 " pdb=" CA ASN B 224 " ideal model delta harmonic sigma weight residual 180.00 153.60 26.40 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" C VAL A 558 " pdb=" N VAL A 558 " pdb=" CA VAL A 558 " pdb=" CB VAL A 558 " ideal model delta harmonic sigma weight residual -122.00 -133.86 11.86 0 2.50e+00 1.60e-01 2.25e+01 dihedral pdb=" N VAL A 558 " pdb=" C VAL A 558 " pdb=" CA VAL A 558 " pdb=" CB VAL A 558 " ideal model delta harmonic sigma weight residual 123.40 134.87 -11.47 0 2.50e+00 1.60e-01 2.11e+01 ... (remaining 6743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1552 0.074 - 0.147: 170 0.147 - 0.221: 27 0.221 - 0.294: 7 0.294 - 0.368: 2 Chirality restraints: 1758 Sorted by residual: chirality pdb=" CA VAL A 558 " pdb=" N VAL A 558 " pdb=" C VAL A 558 " pdb=" CB VAL A 558 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CA VAL A 506 " pdb=" N VAL A 506 " pdb=" C VAL A 506 " pdb=" CB VAL A 506 " both_signs ideal model delta sigma weight residual False 2.44 2.12 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA VAL A 663 " pdb=" N VAL A 663 " pdb=" C VAL A 663 " pdb=" CB VAL A 663 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1755 not shown) Planarity restraints: 2003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 719 " -0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C ALA A 719 " 0.065 2.00e-02 2.50e+03 pdb=" O ALA A 719 " -0.025 2.00e-02 2.50e+03 pdb=" N ALA A 720 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 720 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" C ALA A 720 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA A 720 " -0.016 2.00e-02 2.50e+03 pdb=" N GLN A 721 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 724 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO A 725 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 725 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 725 " 0.030 5.00e-02 4.00e+02 ... (remaining 2000 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 112 2.59 - 3.17: 9526 3.17 - 3.75: 16631 3.75 - 4.32: 23010 4.32 - 4.90: 38164 Nonbonded interactions: 87443 Sorted by model distance: nonbonded pdb=" O CYS B 223 " pdb="ZN ZN B 802 " model vdw 2.015 2.230 nonbonded pdb=" OE2 GLU B 30 " pdb=" OG SER B 182 " model vdw 2.208 3.040 nonbonded pdb=" OE1 GLU B 203 " pdb=" NH2 ARG B 221 " model vdw 2.245 3.120 nonbonded pdb=" O GLU B 30 " pdb=" NH1 ARG B 34 " model vdw 2.248 3.120 nonbonded pdb=" CD1 ILE C 17 " pdb=" OE2 GLU C 48 " model vdw 2.256 3.460 ... (remaining 87438 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.710 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.270 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 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 : 0.008 0.447 11294 Z= 0.359 Angle : 0.774 8.576 15336 Z= 0.485 Chirality : 0.052 0.368 1758 Planarity : 0.005 0.055 2003 Dihedral : 15.649 89.991 4042 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.15 % Favored : 90.70 % Rotamer: Outliers : 5.29 % Allowed : 17.28 % Favored : 77.43 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.65 (0.20), residues: 1420 helix: -1.67 (0.18), residues: 677 sheet: -1.46 (0.49), residues: 106 loop : -3.47 (0.21), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 528 TYR 0.018 0.002 TYR A 507 PHE 0.023 0.002 PHE A 634 TRP 0.018 0.001 TRP B 658 HIS 0.009 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00528 (11288) covalent geometry : angle 0.77425 (15336) hydrogen bonds : bond 0.16605 ( 483) hydrogen bonds : angle 6.07484 ( 1398) metal coordination : bond 0.23982 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 191 time to evaluate : 0.317 Fit side-chains REVERT: B 38 HIS cc_start: 0.7679 (m90) cc_final: 0.7130 (m-70) REVERT: B 190 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9001 (pp) REVERT: B 375 MET cc_start: 0.8623 (mmm) cc_final: 0.8189 (tpp) REVERT: B 389 ASP cc_start: 0.8496 (t0) cc_final: 0.8232 (t0) REVERT: B 644 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8534 (tt) REVERT: B 665 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7994 (mmt180) REVERT: B 667 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.7568 (m-80) outliers start: 60 outliers final: 37 residues processed: 245 average time/residue: 0.1214 time to fit residues: 40.0865 Evaluate side-chains 175 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 665 ARG Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 118 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 0.0270 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 102 HIS A 251 GLN A 343 ASN A 351 ASN A 359 ASN A 367 GLN A 670 GLN B 46 GLN B 53 GLN B 124 HIS B 152 GLN B 195 HIS B 323 GLN B 522 GLN B 579 HIS B 614 HIS B 621 GLN C 103 HIS C 126 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.172090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.133075 restraints weight = 15097.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.134173 restraints weight = 9979.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135890 restraints weight = 7310.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135932 restraints weight = 5604.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.136078 restraints weight = 5411.873| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.548 11294 Z= 0.226 Angle : 0.632 8.605 15336 Z= 0.322 Chirality : 0.043 0.286 1758 Planarity : 0.004 0.048 2003 Dihedral : 7.396 59.081 1643 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.86 % Favored : 90.07 % Rotamer: Outliers : 5.47 % Allowed : 19.05 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.22), residues: 1420 helix: -0.61 (0.20), residues: 686 sheet: -1.35 (0.49), residues: 106 loop : -2.94 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 240 TYR 0.017 0.001 TYR A 397 PHE 0.020 0.001 PHE A 633 TRP 0.018 0.002 TRP B 658 HIS 0.006 0.001 HIS A 646 Details of bonding type rmsd covalent geometry : bond 0.00337 (11288) covalent geometry : angle 0.63214 (15336) hydrogen bonds : bond 0.04128 ( 483) hydrogen bonds : angle 4.41668 ( 1398) metal coordination : bond 0.22389 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 152 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 316 HIS cc_start: 0.5901 (t-170) cc_final: 0.5691 (t-170) REVERT: A 405 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7401 (pt0) REVERT: A 504 LEU cc_start: 0.8157 (mt) cc_final: 0.7935 (mp) REVERT: A 509 ASP cc_start: 0.6637 (t0) cc_final: 0.6252 (t0) REVERT: A 574 ARG cc_start: 0.6890 (mmp80) cc_final: 0.6472 (mmp80) REVERT: A 707 ASP cc_start: 0.5078 (p0) cc_final: 0.4732 (p0) REVERT: B 38 HIS cc_start: 0.7671 (m90) cc_final: 0.7084 (m-70) REVERT: B 389 ASP cc_start: 0.8451 (t0) cc_final: 0.8173 (t0) REVERT: B 411 ARG cc_start: 0.7669 (ptm160) cc_final: 0.7413 (ptm160) REVERT: B 567 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8477 (mt) REVERT: B 644 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8530 (tt) REVERT: B 667 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.7392 (m-80) outliers start: 62 outliers final: 38 residues processed: 207 average time/residue: 0.1050 time to fit residues: 30.6801 Evaluate side-chains 172 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 118 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 96 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 ASN A 102 HIS A 155 GLN A 211 HIS A 340 HIS A 367 GLN B 144 HIS B 770 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.170346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.131800 restraints weight = 15235.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.132830 restraints weight = 10663.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.133933 restraints weight = 8309.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.134212 restraints weight = 6288.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.134322 restraints weight = 5866.395| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11294 Z= 0.187 Angle : 0.640 7.997 15336 Z= 0.323 Chirality : 0.043 0.212 1758 Planarity : 0.004 0.043 2003 Dihedral : 6.486 59.883 1609 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.79 % Favored : 90.14 % Rotamer: Outliers : 6.44 % Allowed : 19.49 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.22), residues: 1420 helix: -0.28 (0.20), residues: 693 sheet: -1.21 (0.48), residues: 103 loop : -2.83 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 172 TYR 0.017 0.001 TYR A 533 PHE 0.023 0.002 PHE A 360 TRP 0.018 0.002 TRP B 658 HIS 0.007 0.001 HIS B 535 Details of bonding type rmsd covalent geometry : bond 0.00450 (11288) covalent geometry : angle 0.64006 (15336) hydrogen bonds : bond 0.03763 ( 483) hydrogen bonds : angle 4.20765 ( 1398) metal coordination : bond 0.01097 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 145 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 306 ARG cc_start: 0.8114 (ttm110) cc_final: 0.7811 (ttm110) REVERT: A 316 HIS cc_start: 0.5847 (t-170) cc_final: 0.5585 (t-170) REVERT: A 405 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7410 (pt0) REVERT: A 443 MET cc_start: 0.7663 (mpp) cc_final: 0.4343 (ptt) REVERT: A 509 ASP cc_start: 0.7201 (t0) cc_final: 0.6929 (t0) REVERT: A 574 ARG cc_start: 0.6935 (mmp80) cc_final: 0.6595 (mmp80) REVERT: A 707 ASP cc_start: 0.5351 (p0) cc_final: 0.5099 (p0) REVERT: A 710 VAL cc_start: 0.8250 (m) cc_final: 0.6825 (m) REVERT: A 714 MET cc_start: 0.7699 (mpp) cc_final: 0.7366 (mpp) REVERT: B 38 HIS cc_start: 0.7753 (m90) cc_final: 0.7003 (m90) REVERT: B 370 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8241 (mm) REVERT: B 389 ASP cc_start: 0.8435 (t0) cc_final: 0.8207 (t0) REVERT: B 567 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8492 (mt) REVERT: B 644 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8545 (tt) REVERT: B 667 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.7403 (m-80) outliers start: 73 outliers final: 48 residues processed: 207 average time/residue: 0.0968 time to fit residues: 28.6925 Evaluate side-chains 187 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 135 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 128 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 chunk 72 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 86 ASN A 367 GLN B 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.172712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.134577 restraints weight = 15293.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.133740 restraints weight = 10067.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.135057 restraints weight = 8588.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135852 restraints weight = 6536.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.136207 restraints weight = 5736.418| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11294 Z= 0.117 Angle : 0.589 8.939 15336 Z= 0.296 Chirality : 0.041 0.208 1758 Planarity : 0.004 0.039 2003 Dihedral : 6.100 59.560 1606 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 5.29 % Allowed : 20.81 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.23), residues: 1420 helix: 0.13 (0.21), residues: 689 sheet: -1.06 (0.52), residues: 93 loop : -2.55 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 172 TYR 0.017 0.001 TYR A 533 PHE 0.014 0.001 PHE A 633 TRP 0.016 0.002 TRP B 658 HIS 0.005 0.001 HIS B 535 Details of bonding type rmsd covalent geometry : bond 0.00266 (11288) covalent geometry : angle 0.58927 (15336) hydrogen bonds : bond 0.03261 ( 483) hydrogen bonds : angle 3.96532 ( 1398) metal coordination : bond 0.00811 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 152 time to evaluate : 0.402 Fit side-chains REVERT: A 405 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7327 (pt0) REVERT: A 707 ASP cc_start: 0.5545 (p0) cc_final: 0.5264 (p0) REVERT: A 710 VAL cc_start: 0.8089 (m) cc_final: 0.6564 (m) REVERT: A 714 MET cc_start: 0.7523 (mpp) cc_final: 0.7147 (mpp) REVERT: B 38 HIS cc_start: 0.7875 (m90) cc_final: 0.7100 (m90) REVERT: B 370 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8208 (mm) REVERT: B 389 ASP cc_start: 0.8441 (t0) cc_final: 0.8153 (t0) REVERT: B 567 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8426 (mt) REVERT: B 605 GLU cc_start: 0.7728 (tt0) cc_final: 0.7444 (tt0) REVERT: B 629 TYR cc_start: 0.9061 (m-10) cc_final: 0.8389 (m-80) REVERT: B 644 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8573 (tt) outliers start: 60 outliers final: 42 residues processed: 203 average time/residue: 0.1013 time to fit residues: 29.5100 Evaluate side-chains 174 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 129 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 118 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 103 optimal weight: 0.6980 chunk 131 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 75 optimal weight: 0.2980 chunk 73 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 367 GLN B 770 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.173361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.135242 restraints weight = 15017.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.136074 restraints weight = 9607.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.137093 restraints weight = 7650.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.137616 restraints weight = 5834.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.137658 restraints weight = 5236.242| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11294 Z= 0.118 Angle : 0.587 8.170 15336 Z= 0.292 Chirality : 0.041 0.178 1758 Planarity : 0.004 0.038 2003 Dihedral : 5.968 59.779 1605 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.58 % Favored : 90.35 % Rotamer: Outliers : 5.73 % Allowed : 21.43 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.23), residues: 1420 helix: 0.31 (0.21), residues: 700 sheet: -1.01 (0.53), residues: 93 loop : -2.47 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 240 TYR 0.012 0.001 TYR A 533 PHE 0.017 0.001 PHE A 241 TRP 0.014 0.001 TRP B 658 HIS 0.004 0.001 HIS A 646 Details of bonding type rmsd covalent geometry : bond 0.00275 (11288) covalent geometry : angle 0.58664 (15336) hydrogen bonds : bond 0.03135 ( 483) hydrogen bonds : angle 3.87164 ( 1398) metal coordination : bond 0.00721 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 142 time to evaluate : 0.371 Fit side-chains REVERT: A 302 ASP cc_start: 0.8276 (m-30) cc_final: 0.7792 (m-30) REVERT: A 405 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7293 (pt0) REVERT: A 443 MET cc_start: 0.7695 (mpp) cc_final: 0.4298 (ptt) REVERT: A 707 ASP cc_start: 0.5634 (p0) cc_final: 0.5393 (p0) REVERT: A 710 VAL cc_start: 0.7960 (m) cc_final: 0.6718 (m) REVERT: A 714 MET cc_start: 0.7478 (mpp) cc_final: 0.7068 (mpp) REVERT: B 370 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8160 (mm) REVERT: B 389 ASP cc_start: 0.8422 (t0) cc_final: 0.8111 (t0) REVERT: B 411 ARG cc_start: 0.7434 (ptm160) cc_final: 0.7201 (ptm160) REVERT: B 567 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8481 (mt) REVERT: B 629 TYR cc_start: 0.9039 (m-10) cc_final: 0.8357 (m-80) REVERT: B 644 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8551 (tt) outliers start: 65 outliers final: 46 residues processed: 201 average time/residue: 0.1000 time to fit residues: 28.9125 Evaluate side-chains 178 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 129 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 601 HIS Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 118 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 33 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 140 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 HIS B 770 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.174376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.136499 restraints weight = 14999.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.136443 restraints weight = 9812.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.137616 restraints weight = 8108.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.138254 restraints weight = 6296.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.138536 restraints weight = 5569.856| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11294 Z= 0.116 Angle : 0.587 8.359 15336 Z= 0.292 Chirality : 0.041 0.246 1758 Planarity : 0.004 0.036 2003 Dihedral : 5.661 59.645 1600 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 4.94 % Allowed : 22.05 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.23), residues: 1420 helix: 0.49 (0.21), residues: 701 sheet: -0.98 (0.54), residues: 93 loop : -2.35 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 172 TYR 0.011 0.001 TYR A 397 PHE 0.014 0.001 PHE A 241 TRP 0.014 0.001 TRP B 658 HIS 0.010 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00270 (11288) covalent geometry : angle 0.58657 (15336) hydrogen bonds : bond 0.03044 ( 483) hydrogen bonds : angle 3.77944 ( 1398) metal coordination : bond 0.00749 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 141 time to evaluate : 0.402 Fit side-chains REVERT: A 405 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7243 (pt0) REVERT: A 443 MET cc_start: 0.7622 (mpp) cc_final: 0.4258 (ptt) REVERT: A 707 ASP cc_start: 0.5589 (p0) cc_final: 0.5326 (p0) REVERT: A 714 MET cc_start: 0.7416 (mpp) cc_final: 0.6996 (mpp) REVERT: B 370 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8062 (mm) REVERT: B 375 MET cc_start: 0.8210 (tpp) cc_final: 0.7625 (tpp) REVERT: B 389 ASP cc_start: 0.8397 (t0) cc_final: 0.8089 (t0) REVERT: B 567 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8491 (mt) REVERT: B 629 TYR cc_start: 0.9010 (m-10) cc_final: 0.8402 (m-80) REVERT: B 644 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8539 (tt) outliers start: 56 outliers final: 46 residues processed: 192 average time/residue: 0.0919 time to fit residues: 26.0801 Evaluate side-chains 172 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 123 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 601 HIS Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 118 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 42 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 139 optimal weight: 0.0670 chunk 118 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 64 optimal weight: 0.0980 chunk 117 optimal weight: 0.0970 chunk 57 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 770 GLN C 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.175963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.138527 restraints weight = 14828.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.138240 restraints weight = 9933.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.139650 restraints weight = 7758.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.140068 restraints weight = 6250.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.140341 restraints weight = 5597.868| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11294 Z= 0.107 Angle : 0.580 7.893 15336 Z= 0.287 Chirality : 0.040 0.187 1758 Planarity : 0.004 0.036 2003 Dihedral : 5.528 59.864 1600 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 4.67 % Allowed : 22.57 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.23), residues: 1420 helix: 0.63 (0.21), residues: 701 sheet: -0.99 (0.54), residues: 93 loop : -2.27 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 574 TYR 0.010 0.001 TYR A 397 PHE 0.012 0.001 PHE B 313 TRP 0.013 0.001 TRP A 308 HIS 0.004 0.001 HIS A 646 Details of bonding type rmsd covalent geometry : bond 0.00242 (11288) covalent geometry : angle 0.58011 (15336) hydrogen bonds : bond 0.02901 ( 483) hydrogen bonds : angle 3.69430 ( 1398) metal coordination : bond 0.00715 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 136 time to evaluate : 0.317 Fit side-chains REVERT: A 443 MET cc_start: 0.7507 (mpp) cc_final: 0.4172 (ptt) REVERT: A 707 ASP cc_start: 0.5292 (p0) cc_final: 0.5051 (p0) REVERT: A 714 MET cc_start: 0.7464 (mpp) cc_final: 0.7046 (mpp) REVERT: B 49 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.9006 (tt) REVERT: B 240 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8117 (ttm-80) REVERT: B 375 MET cc_start: 0.8196 (tpp) cc_final: 0.7564 (tpp) REVERT: B 389 ASP cc_start: 0.8420 (t0) cc_final: 0.8114 (t0) REVERT: B 430 MET cc_start: 0.6668 (ttt) cc_final: 0.6449 (ttt) REVERT: B 629 TYR cc_start: 0.8968 (m-10) cc_final: 0.8474 (m-10) REVERT: B 644 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8576 (tt) outliers start: 53 outliers final: 44 residues processed: 185 average time/residue: 0.0918 time to fit residues: 24.7161 Evaluate side-chains 169 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 122 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 240 ARG Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 601 HIS Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 118 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 36 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 67 optimal weight: 0.0670 chunk 94 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN B 770 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.171251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.133439 restraints weight = 15226.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.132924 restraints weight = 10934.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.134540 restraints weight = 9502.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.135007 restraints weight = 6889.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.135096 restraints weight = 6559.622| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11294 Z= 0.178 Angle : 0.632 9.333 15336 Z= 0.313 Chirality : 0.043 0.233 1758 Planarity : 0.004 0.037 2003 Dihedral : 5.689 59.414 1600 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 5.47 % Allowed : 22.05 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.23), residues: 1420 helix: 0.56 (0.21), residues: 702 sheet: -1.13 (0.52), residues: 96 loop : -2.24 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 172 TYR 0.013 0.001 TYR A 397 PHE 0.016 0.002 PHE A 633 TRP 0.017 0.002 TRP A 308 HIS 0.004 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00433 (11288) covalent geometry : angle 0.63229 (15336) hydrogen bonds : bond 0.03203 ( 483) hydrogen bonds : angle 3.82036 ( 1398) metal coordination : bond 0.01022 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 123 time to evaluate : 0.364 Fit side-chains REVERT: A 443 MET cc_start: 0.7598 (mpp) cc_final: 0.4283 (ptt) REVERT: A 714 MET cc_start: 0.7510 (mpp) cc_final: 0.7235 (mpp) REVERT: B 240 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7898 (ttt-90) REVERT: B 375 MET cc_start: 0.8243 (tpp) cc_final: 0.7588 (tpp) REVERT: B 389 ASP cc_start: 0.8449 (t0) cc_final: 0.8142 (t0) REVERT: B 582 MET cc_start: 0.9187 (tpp) cc_final: 0.8955 (tpt) REVERT: B 629 TYR cc_start: 0.9053 (m-10) cc_final: 0.8372 (m-80) REVERT: B 644 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8635 (tt) outliers start: 62 outliers final: 50 residues processed: 178 average time/residue: 0.0991 time to fit residues: 25.7032 Evaluate side-chains 170 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 118 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 240 ARG Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 118 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 140 optimal weight: 2.9990 chunk 87 optimal weight: 0.0060 chunk 102 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 2 optimal weight: 0.4980 overall best weight: 1.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 HIS B 770 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.173172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.134959 restraints weight = 14921.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.135130 restraints weight = 9657.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.136689 restraints weight = 7334.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.136870 restraints weight = 6057.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.136965 restraints weight = 5566.058| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11294 Z= 0.138 Angle : 0.614 8.478 15336 Z= 0.303 Chirality : 0.042 0.230 1758 Planarity : 0.004 0.042 2003 Dihedral : 5.647 59.239 1600 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 4.76 % Allowed : 23.02 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.23), residues: 1420 helix: 0.61 (0.21), residues: 702 sheet: -1.06 (0.50), residues: 103 loop : -2.27 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 424 TYR 0.013 0.001 TYR A 397 PHE 0.020 0.001 PHE A 241 TRP 0.014 0.001 TRP B 658 HIS 0.004 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00333 (11288) covalent geometry : angle 0.61373 (15336) hydrogen bonds : bond 0.03047 ( 483) hydrogen bonds : angle 3.78761 ( 1398) metal coordination : bond 0.00864 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 126 time to evaluate : 0.368 Fit side-chains REVERT: A 443 MET cc_start: 0.7530 (mpp) cc_final: 0.4245 (ptt) REVERT: A 714 MET cc_start: 0.7572 (mpp) cc_final: 0.7192 (mpp) REVERT: B 240 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7914 (ttt-90) REVERT: B 375 MET cc_start: 0.8211 (tpp) cc_final: 0.7591 (tpp) REVERT: B 389 ASP cc_start: 0.8439 (t0) cc_final: 0.8146 (t0) REVERT: B 582 MET cc_start: 0.9180 (tpp) cc_final: 0.8959 (tpt) REVERT: B 629 TYR cc_start: 0.9038 (m-10) cc_final: 0.8405 (m-80) REVERT: B 644 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8612 (tt) outliers start: 54 outliers final: 51 residues processed: 175 average time/residue: 0.1015 time to fit residues: 25.4779 Evaluate side-chains 172 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 119 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 240 ARG Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 118 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 131 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 137 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 55 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.173512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.135245 restraints weight = 14889.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.135199 restraints weight = 9873.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.136576 restraints weight = 7641.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.137050 restraints weight = 6261.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.137167 restraints weight = 5554.207| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11294 Z= 0.131 Angle : 0.618 8.300 15336 Z= 0.305 Chirality : 0.042 0.229 1758 Planarity : 0.004 0.037 2003 Dihedral : 5.612 59.215 1600 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 4.85 % Allowed : 22.93 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.24), residues: 1420 helix: 0.68 (0.21), residues: 702 sheet: -1.24 (0.50), residues: 106 loop : -2.22 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 172 TYR 0.011 0.001 TYR A 397 PHE 0.020 0.001 PHE A 241 TRP 0.014 0.001 TRP A 308 HIS 0.004 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00315 (11288) covalent geometry : angle 0.61783 (15336) hydrogen bonds : bond 0.02994 ( 483) hydrogen bonds : angle 3.75033 ( 1398) metal coordination : bond 0.00823 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 129 time to evaluate : 0.413 Fit side-chains REVERT: A 714 MET cc_start: 0.7531 (mpp) cc_final: 0.7128 (mpp) REVERT: B 49 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8996 (tt) REVERT: B 240 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8119 (ttm-80) REVERT: B 375 MET cc_start: 0.8216 (tpp) cc_final: 0.7594 (tpp) REVERT: B 389 ASP cc_start: 0.8438 (t0) cc_final: 0.8138 (t0) REVERT: B 582 MET cc_start: 0.9185 (tpp) cc_final: 0.8892 (tpt) REVERT: B 629 TYR cc_start: 0.9038 (m-10) cc_final: 0.8430 (m-80) REVERT: B 644 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8588 (tt) outliers start: 55 outliers final: 51 residues processed: 178 average time/residue: 0.0975 time to fit residues: 25.4067 Evaluate side-chains 175 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 121 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 240 ARG Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 118 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 126 optimal weight: 0.2980 chunk 95 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.174837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.136860 restraints weight = 14900.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136994 restraints weight = 9984.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.138272 restraints weight = 7527.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.138665 restraints weight = 6413.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.138863 restraints weight = 5705.899| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11294 Z= 0.120 Angle : 0.617 9.555 15336 Z= 0.303 Chirality : 0.042 0.229 1758 Planarity : 0.003 0.037 2003 Dihedral : 5.556 59.697 1600 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 4.76 % Allowed : 23.19 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.24), residues: 1420 helix: 0.71 (0.21), residues: 703 sheet: -1.19 (0.51), residues: 106 loop : -2.20 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 172 TYR 0.012 0.001 TYR A 397 PHE 0.026 0.001 PHE A 241 TRP 0.013 0.001 TRP B 658 HIS 0.004 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00284 (11288) covalent geometry : angle 0.61738 (15336) hydrogen bonds : bond 0.02909 ( 483) hydrogen bonds : angle 3.73015 ( 1398) metal coordination : bond 0.00780 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1664.79 seconds wall clock time: 29 minutes 30.89 seconds (1770.89 seconds total)