Starting phenix.real_space_refine on Sun Dec 29 17:51:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m5s_30091/12_2024/6m5s_30091.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m5s_30091/12_2024/6m5s_30091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m5s_30091/12_2024/6m5s_30091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m5s_30091/12_2024/6m5s_30091.map" model { file = "/net/cci-nas-00/data/ceres_data/6m5s_30091/12_2024/6m5s_30091.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m5s_30091/12_2024/6m5s_30091.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 101 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 3, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} 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: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} 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 31.952 45.248 52.606 1.00 29.72 S ATOM 10821 SG CYS C 101 32.764 44.141 55.743 1.00 44.32 S ATOM 6446 SG CYS B 197 53.212 53.899 49.307 1.00 30.65 S ATOM 6464 SG CYS B 200 55.214 54.207 52.200 1.00 34.04 S Time building chain proxies: 7.17, per 1000 atoms: 0.65 Number of scatterers: 11055 At special positions: 0 Unit cell: (108.16, 96.72, 118.56, 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: 2.69 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.04 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: 3.761A 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: 3.932A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N THR A 169 " --> pdb=" O GLN A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 221 removed outlier: 3.964A 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: 4.421A 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: 4.032A 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: 3.544A 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: 3.553A 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: 3.607A 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: 3.680A 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: 4.016A 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: 3.605A 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: 3.701A 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: 3.548A 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: 3.546A 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: 4.082A pdb=" N ASP B 419 " --> pdb=" O PRO B 415 " (cutoff:3.500A) removed outlier: 3.650A 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: 3.996A pdb=" N THR B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG B 501 " --> pdb=" O ARG B 497 " (cutoff:3.500A) removed outlier: 3.607A 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: 3.711A 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: 3.574A 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: 3.572A 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: 3.832A pdb=" N ALA B 681 " --> pdb=" O PRO B 677 " (cutoff:3.500A) removed outlier: 3.739A 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: 4.130A 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: 3.941A 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: 6.909A 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: 4.544A 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: 6.600A pdb=" N ALA A 537 " --> pdb=" O GLU A 661 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL A 663 " --> pdb=" O ALA A 537 " (cutoff:3.500A) removed outlier: 5.476A 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: 7.544A 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: 2.98 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2256 1.33 - 1.45: 2669 1.45 - 1.57: 6288 1.57 - 1.69: 4 1.69 - 1.81: 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 1.491 -0.036 9.60e-03 1.09e+04 1.41e+01 bond pdb=" CA VAL A 525 " pdb=" CB VAL A 525 " ideal model delta sigma weight residual 1.537 1.581 -0.043 1.26e-02 6.30e+03 1.18e+01 bond pdb=" C ARG A 490 " pdb=" O ARG A 490 " ideal model delta sigma weight residual 1.244 1.211 0.034 1.00e-02 1.00e+04 1.12e+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 1.07e+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 - 1.71: 14660 1.71 - 3.41: 568 3.41 - 5.12: 87 5.12 - 6.82: 18 6.82 - 8.53: 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 111.62 115.81 -4.19 7.90e-01 1.60e+00 2.81e+01 angle pdb=" N ARG A 420 " pdb=" CA ARG A 420 " pdb=" C ARG A 420 " ideal model delta sigma weight residual 111.82 106.51 5.31 1.16e+00 7.43e-01 2.09e+01 angle pdb=" O PRO A 624 " pdb=" C PRO A 624 " pdb=" N PRO A 625 " ideal model delta sigma weight residual 121.31 123.23 -1.92 4.60e-01 4.73e+00 1.75e+01 angle pdb=" N VAL A 656 " pdb=" CA VAL A 656 " pdb=" C VAL A 656 " ideal model delta sigma weight residual 108.11 113.88 -5.77 1.40e+00 5.10e-01 1.70e+01 angle pdb=" N PHE A 573 " pdb=" CA PHE A 573 " pdb=" C PHE A 573 " ideal model delta sigma weight residual 109.07 115.56 -6.49 1.61e+00 3.86e-01 1.62e+01 ... (remaining 15331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5989 17.97 - 35.93: 592 35.93 - 53.90: 128 53.90 - 71.86: 21 71.86 - 89.83: 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 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+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 -133.88 11.88 0 2.50e+00 1.60e-01 2.26e+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 123.40 134.89 -11.49 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: 1556 0.074 - 0.147: 166 0.147 - 0.221: 27 0.221 - 0.295: 7 0.295 - 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 2.53e+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 3.76e-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 2.45e-02 6.02e+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 " -0.015 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 5.49e-02 4.82e+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: 16628 3.75 - 4.32: 23015 4.32 - 4.90: 38163 Nonbonded interactions: 87444 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 87439 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: 3.770 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: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 29.070 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 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 : 0.005 0.056 11288 Z= 0.350 Angle : 0.775 8.528 15336 Z= 0.485 Chirality : 0.052 0.368 1758 Planarity : 0.005 0.055 2003 Dihedral : 15.649 89.827 4042 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.23 % Favored : 90.63 % Rotamer: Outliers : 5.29 % Allowed : 17.37 % Favored : 77.34 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.018 0.001 TRP B 658 HIS 0.009 0.001 HIS A 540 PHE 0.023 0.002 PHE A 634 TYR 0.018 0.002 TYR A 507 ARG 0.005 0.000 ARG A 528 *********************** 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 347 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 287 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ASN cc_start: 0.8085 (t0) cc_final: 0.7739 (t0) REVERT: B 115 MET cc_start: 0.7743 (mmm) cc_final: 0.7425 (tpp) REVERT: B 190 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8362 (pp) REVERT: B 329 PHE cc_start: 0.7239 (t80) cc_final: 0.6802 (t80) REVERT: B 387 SER cc_start: 0.8003 (p) cc_final: 0.7636 (t) REVERT: B 667 TYR cc_start: 0.7349 (OUTLIER) cc_final: 0.5681 (m-80) REVERT: C 13 LEU cc_start: 0.6179 (mt) cc_final: 0.5923 (mp) outliers start: 60 outliers final: 10 residues processed: 334 average time/residue: 0.3035 time to fit residues: 134.9532 Evaluate side-chains 159 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 558 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 374 ASP Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 761 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 36 optimal weight: 0.0030 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 67 optimal weight: 0.0370 chunk 82 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.1872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 HIS A 155 GLN A 211 HIS A 343 ASN A 351 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN A 408 ASN ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 ASN B 46 GLN B 53 GLN ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 GLN B 195 HIS ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 HIS B 621 GLN ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 HIS C 126 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11288 Z= 0.220 Angle : 0.703 10.628 15336 Z= 0.355 Chirality : 0.044 0.307 1758 Planarity : 0.005 0.037 2003 Dihedral : 5.969 59.984 1601 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 4.94 % Allowed : 21.87 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.21), residues: 1420 helix: -0.75 (0.19), residues: 691 sheet: -1.29 (0.49), residues: 106 loop : -3.01 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 485 HIS 0.010 0.001 HIS A 540 PHE 0.025 0.002 PHE A 241 TYR 0.010 0.001 TYR A 717 ARG 0.009 0.001 ARG B 665 *********************** 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 208 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 152 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ASN cc_start: 0.7933 (t0) cc_final: 0.7683 (t0) REVERT: A 103 THR cc_start: 0.8308 (OUTLIER) cc_final: 0.8037 (m) REVERT: A 107 GLU cc_start: 0.7466 (pm20) cc_final: 0.7080 (pm20) REVERT: A 272 ILE cc_start: 0.7528 (OUTLIER) cc_final: 0.7282 (mm) REVERT: A 357 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.5878 (pp20) REVERT: B 115 MET cc_start: 0.7682 (mmm) cc_final: 0.7319 (tpp) REVERT: B 190 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8334 (pp) REVERT: B 329 PHE cc_start: 0.7300 (t80) cc_final: 0.6819 (t80) REVERT: B 333 LEU cc_start: 0.8815 (mt) cc_final: 0.8497 (mt) REVERT: B 560 THR cc_start: 0.8501 (p) cc_final: 0.8278 (t) REVERT: B 667 TYR cc_start: 0.7457 (OUTLIER) cc_final: 0.6112 (m-80) REVERT: C 13 LEU cc_start: 0.6199 (mt) cc_final: 0.5848 (mp) REVERT: C 66 LEU cc_start: 0.8849 (tp) cc_final: 0.8635 (tt) outliers start: 56 outliers final: 29 residues processed: 199 average time/residue: 0.2412 time to fit residues: 68.0356 Evaluate side-chains 146 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 682 ASN Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 601 HIS Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 129 optimal weight: 8.9990 chunk 139 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 44 optimal weight: 30.0000 chunk 103 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 359 ASN A 408 ASN ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 GLN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 HIS B 614 HIS B 621 GLN ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 11288 Z= 0.378 Angle : 0.763 10.472 15336 Z= 0.390 Chirality : 0.046 0.232 1758 Planarity : 0.005 0.037 2003 Dihedral : 5.888 57.858 1592 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 5.47 % Allowed : 22.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.22), residues: 1420 helix: -0.41 (0.20), residues: 704 sheet: -1.27 (0.50), residues: 114 loop : -2.70 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 485 HIS 0.007 0.002 HIS A 102 PHE 0.031 0.003 PHE A 241 TYR 0.012 0.002 TYR B 757 ARG 0.015 0.001 ARG B 646 *********************** 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 181 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 119 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7719 (p90) REVERT: A 102 HIS cc_start: 0.6883 (OUTLIER) cc_final: 0.6214 (p90) REVERT: A 210 MET cc_start: 0.8283 (mmm) cc_final: 0.7653 (tpp) REVERT: A 241 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.8287 (m-80) REVERT: B 92 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7213 (mt-10) REVERT: B 158 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8393 (pp) REVERT: B 190 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8359 (pp) REVERT: B 329 PHE cc_start: 0.7306 (t80) cc_final: 0.6825 (t80) REVERT: B 667 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.7663 (t80) REVERT: C 13 LEU cc_start: 0.6334 (mt) cc_final: 0.6017 (mp) outliers start: 62 outliers final: 42 residues processed: 170 average time/residue: 0.1910 time to fit residues: 50.2371 Evaluate side-chains 148 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 99 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 327 ASP 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 530 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 575 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 705 LEU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 102 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 36 optimal weight: 0.0670 chunk 114 optimal weight: 0.9980 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 102 HIS A 408 ASN ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 HIS B 125 GLN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11288 Z= 0.194 Angle : 0.644 12.197 15336 Z= 0.323 Chirality : 0.042 0.161 1758 Planarity : 0.004 0.035 2003 Dihedral : 5.558 57.311 1592 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 5.20 % Allowed : 23.19 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.23), residues: 1420 helix: 0.09 (0.20), residues: 703 sheet: -1.16 (0.54), residues: 94 loop : -2.48 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 485 HIS 0.004 0.001 HIS A 597 PHE 0.026 0.002 PHE A 309 TYR 0.011 0.001 TYR A 214 ARG 0.005 0.000 ARG B 602 *********************** 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 186 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 127 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.8072 (m-80) REVERT: B 158 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8306 (pp) REVERT: B 329 PHE cc_start: 0.7282 (t80) cc_final: 0.6795 (t80) REVERT: B 395 LEU cc_start: 0.7719 (tt) cc_final: 0.7322 (tp) REVERT: B 667 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.7627 (t80) REVERT: C 13 LEU cc_start: 0.6375 (mt) cc_final: 0.6031 (mp) outliers start: 59 outliers final: 30 residues processed: 175 average time/residue: 0.1978 time to fit residues: 52.7441 Evaluate side-chains 142 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 251 ASP 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 530 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 51 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 359 ASN ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11288 Z= 0.359 Angle : 0.729 11.194 15336 Z= 0.370 Chirality : 0.045 0.266 1758 Planarity : 0.005 0.038 2003 Dihedral : 5.531 55.633 1589 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 6.17 % Allowed : 22.31 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.23), residues: 1420 helix: 0.15 (0.20), residues: 701 sheet: -0.95 (0.56), residues: 99 loop : -2.44 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 658 HIS 0.015 0.001 HIS A 102 PHE 0.027 0.002 PHE A 241 TYR 0.015 0.002 TYR B 757 ARG 0.014 0.001 ARG B 646 *********************** 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 183 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 113 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8271 (tpp) cc_final: 0.8057 (tpp) REVERT: A 241 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.8360 (m-80) REVERT: B 92 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6922 (mt-10) REVERT: B 158 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8470 (pp) REVERT: B 329 PHE cc_start: 0.7333 (t80) cc_final: 0.6929 (t80) REVERT: B 395 LEU cc_start: 0.7811 (tt) cc_final: 0.7351 (tp) REVERT: B 667 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.7796 (t80) outliers start: 70 outliers final: 46 residues processed: 169 average time/residue: 0.2216 time to fit residues: 55.2266 Evaluate side-chains 156 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 106 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 485 TRP Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 61 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 0.2980 chunk 11 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 408 ASN A 595 HIS ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11288 Z= 0.191 Angle : 0.640 11.712 15336 Z= 0.320 Chirality : 0.042 0.213 1758 Planarity : 0.004 0.036 2003 Dihedral : 5.311 57.271 1589 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 4.41 % Allowed : 23.99 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.23), residues: 1420 helix: 0.46 (0.20), residues: 704 sheet: -0.88 (0.56), residues: 99 loop : -2.34 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 658 HIS 0.016 0.001 HIS A 102 PHE 0.026 0.002 PHE A 241 TYR 0.012 0.001 TYR B 731 ARG 0.008 0.000 ARG A 42 *********************** 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 169 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 119 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8346 (m-80) REVERT: A 490 ARG cc_start: 0.4627 (OUTLIER) cc_final: 0.4415 (mtm110) REVERT: B 92 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6876 (mt-10) REVERT: B 158 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8462 (pp) REVERT: B 329 PHE cc_start: 0.7278 (t80) cc_final: 0.6965 (t80) REVERT: B 395 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7415 (tp) REVERT: B 633 ASN cc_start: 0.8082 (m-40) cc_final: 0.7779 (m-40) outliers start: 50 outliers final: 32 residues processed: 161 average time/residue: 0.2090 time to fit residues: 50.7959 Evaluate side-chains 146 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 376 VAL 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 530 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain C residue 22 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 100 optimal weight: 0.0670 chunk 77 optimal weight: 9.9990 chunk 115 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 63 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 ASN ** A 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11288 Z= 0.179 Angle : 0.635 10.211 15336 Z= 0.317 Chirality : 0.042 0.255 1758 Planarity : 0.004 0.035 2003 Dihedral : 4.934 53.541 1587 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 3.88 % Allowed : 25.40 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.23), residues: 1420 helix: 0.57 (0.20), residues: 703 sheet: -0.97 (0.56), residues: 101 loop : -2.32 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 485 HIS 0.006 0.001 HIS A 595 PHE 0.025 0.002 PHE A 241 TYR 0.018 0.001 TYR B 667 ARG 0.006 0.000 ARG A 42 *********************** 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 164 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 120 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8269 (tpp) cc_final: 0.8054 (mmt) REVERT: A 241 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.8358 (m-80) REVERT: B 92 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6953 (mt-10) REVERT: B 329 PHE cc_start: 0.7244 (t80) cc_final: 0.6965 (t80) REVERT: B 395 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7554 (tp) REVERT: B 633 ASN cc_start: 0.8015 (m-40) cc_final: 0.7752 (m-40) outliers start: 44 outliers final: 32 residues processed: 157 average time/residue: 0.2051 time to fit residues: 48.5833 Evaluate side-chains 147 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 376 VAL 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 530 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 763 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 30.0000 chunk 81 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 ASN ** A 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11288 Z= 0.206 Angle : 0.650 10.849 15336 Z= 0.321 Chirality : 0.042 0.216 1758 Planarity : 0.004 0.036 2003 Dihedral : 4.892 55.965 1587 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 3.88 % Allowed : 25.49 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.23), residues: 1420 helix: 0.65 (0.20), residues: 704 sheet: -1.01 (0.55), residues: 101 loop : -2.26 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 658 HIS 0.006 0.001 HIS A 595 PHE 0.030 0.002 PHE A 256 TYR 0.011 0.001 TYR B 667 ARG 0.005 0.000 ARG A 42 *********************** 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 162 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 118 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8430 (m-80) REVERT: A 370 MET cc_start: 0.6677 (mmm) cc_final: 0.6350 (ptm) REVERT: A 448 ARG cc_start: 0.5950 (mmt90) cc_final: 0.5588 (tpt170) REVERT: B 115 MET cc_start: 0.5810 (mtt) cc_final: 0.5243 (mtt) REVERT: B 329 PHE cc_start: 0.7267 (t80) cc_final: 0.6964 (t80) REVERT: B 395 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7604 (tp) REVERT: B 633 ASN cc_start: 0.7989 (m-40) cc_final: 0.7695 (m-40) REVERT: B 667 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.7380 (t80) outliers start: 44 outliers final: 35 residues processed: 156 average time/residue: 0.2192 time to fit residues: 51.6691 Evaluate side-chains 147 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 376 VAL 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 530 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 763 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 100 optimal weight: 0.0070 chunk 39 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 134 optimal weight: 20.0000 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11288 Z= 0.203 Angle : 0.649 9.914 15336 Z= 0.320 Chirality : 0.042 0.187 1758 Planarity : 0.004 0.035 2003 Dihedral : 4.861 55.524 1587 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 3.70 % Allowed : 25.57 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.23), residues: 1420 helix: 0.75 (0.20), residues: 698 sheet: -1.18 (0.54), residues: 101 loop : -2.28 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 658 HIS 0.006 0.001 HIS A 595 PHE 0.024 0.002 PHE A 241 TYR 0.011 0.001 TYR B 667 ARG 0.005 0.000 ARG A 42 *********************** 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 160 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 118 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.8386 (m-80) REVERT: A 328 ASP cc_start: 0.6035 (p0) cc_final: 0.5529 (t0) REVERT: A 370 MET cc_start: 0.6752 (mmm) cc_final: 0.6379 (ptm) REVERT: A 448 ARG cc_start: 0.5961 (mmt90) cc_final: 0.5554 (tpt170) REVERT: B 329 PHE cc_start: 0.7266 (t80) cc_final: 0.6969 (t80) REVERT: B 395 LEU cc_start: 0.8053 (tt) cc_final: 0.7651 (tp) REVERT: B 633 ASN cc_start: 0.7956 (m-40) cc_final: 0.7569 (m-40) REVERT: B 667 TYR cc_start: 0.8201 (OUTLIER) cc_final: 0.7205 (t80) outliers start: 42 outliers final: 33 residues processed: 155 average time/residue: 0.2214 time to fit residues: 53.4978 Evaluate side-chains 146 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 763 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 112 optimal weight: 0.3980 chunk 11 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 69 optimal weight: 0.3980 chunk 89 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 ASN ** A 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.5513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11288 Z= 0.196 Angle : 0.666 11.666 15336 Z= 0.327 Chirality : 0.044 0.372 1758 Planarity : 0.004 0.038 2003 Dihedral : 4.854 57.675 1587 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 3.26 % Allowed : 25.84 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.23), residues: 1420 helix: 0.74 (0.20), residues: 698 sheet: -1.16 (0.54), residues: 101 loop : -2.24 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP B 88 HIS 0.013 0.001 HIS A 102 PHE 0.031 0.002 PHE A 256 TYR 0.010 0.001 TYR B 757 ARG 0.006 0.000 ARG B 424 ********************** 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 154 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8421 (m-80) REVERT: A 448 ARG cc_start: 0.6061 (mmt90) cc_final: 0.5597 (tpt170) REVERT: B 329 PHE cc_start: 0.7265 (t80) cc_final: 0.7002 (t80) REVERT: B 395 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7675 (tp) REVERT: B 633 ASN cc_start: 0.7952 (m-40) cc_final: 0.7692 (m-40) REVERT: B 667 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.7178 (t80) REVERT: C 13 LEU cc_start: 0.6877 (mt) cc_final: 0.6349 (mp) outliers start: 37 outliers final: 32 residues processed: 149 average time/residue: 0.2141 time to fit residues: 47.9803 Evaluate side-chains 146 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 763 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 0.0570 chunk 103 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 112 optimal weight: 0.0050 chunk 47 optimal weight: 7.9990 chunk 115 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 6 optimal weight: 20.0000 overall best weight: 1.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.115231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.089842 restraints weight = 31358.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.091800 restraints weight = 19453.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.093057 restraints weight = 14152.734| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 11288 Z= 0.252 Angle : 0.913 59.158 15336 Z= 0.513 Chirality : 0.047 0.774 1758 Planarity : 0.004 0.047 2003 Dihedral : 4.932 57.670 1587 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 3.35 % Allowed : 26.37 % Favored : 70.28 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.23), residues: 1420 helix: 0.74 (0.20), residues: 698 sheet: -1.01 (0.54), residues: 101 loop : -2.24 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B 88 HIS 0.010 0.001 HIS A 102 PHE 0.026 0.002 PHE A 256 TYR 0.010 0.001 TYR B 757 ARG 0.005 0.000 ARG B 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2257.77 seconds wall clock time: 42 minutes 52.95 seconds (2572.95 seconds total)