Starting phenix.real_space_refine on Tue Jul 29 05:28:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m5r_30090/07_2025/6m5r_30090.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m5r_30090/07_2025/6m5r_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6m5r_30090/07_2025/6m5r_30090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m5r_30090/07_2025/6m5r_30090.map" model { file = "/net/cci-nas-00/data/ceres_data/6m5r_30090/07_2025/6m5r_30090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m5r_30090/07_2025/6m5r_30090.cif" } resolution = 3.5 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= 0.011 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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 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: 6.39, per 1000 atoms: 0.58 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: 2.74 Conformation dependent library (CDL) restraints added in 1.4 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: 1.16 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: 3.24 Time building geometry restraints manager: 3.28 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: 1.140 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.960 Find NCS groups from input model: 0.300 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:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.430 ------------------------------------------------------------------------------- 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 : 11.54 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.16605 ( 483) hydrogen bonds : angle 6.07484 ( 1398) metal coordination : bond 0.23982 ( 6) covalent geometry : bond 0.00528 (11288) covalent geometry : angle 0.77425 (15336) *********************** 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 : 1.275 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: 0.2839 time to fit residues: 94.3682 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 : 1.225 ------------------------------------------------------------------------------- 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 119 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 144 HIS B 152 GLN 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 = 0.4022 r_free = 0.4022 target = 0.171613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.132546 restraints weight = 15004.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.133427 restraints weight = 10159.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.134782 restraints weight = 7526.455| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.559 11294 Z= 0.241 Angle : 0.646 8.490 15336 Z= 0.329 Chirality : 0.043 0.286 1758 Planarity : 0.004 0.050 2003 Dihedral : 7.449 59.131 1643 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.21 % Favored : 89.72 % Rotamer: Outliers : 5.82 % Allowed : 19.22 % Favored : 74.96 % Cbeta Deviations : 0.00 % 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: -2.52 (0.22), residues: 1420 helix: -0.65 (0.20), residues: 685 sheet: -1.35 (0.49), residues: 106 loop : -2.95 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 658 HIS 0.007 0.001 HIS A 646 PHE 0.019 0.002 PHE A 633 TYR 0.017 0.001 TYR A 397 ARG 0.004 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.04239 ( 483) hydrogen bonds : angle 4.45471 ( 1398) metal coordination : bond 0.22859 ( 6) covalent geometry : bond 0.00389 (11288) covalent geometry : angle 0.64566 (15336) *********************** 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 215 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 149 time to evaluate : 1.256 Fit side-chains revert: symmetry clash REVERT: A 405 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7404 (pt0) REVERT: A 509 ASP cc_start: 0.6681 (t0) cc_final: 0.6304 (t0) REVERT: A 533 TYR cc_start: 0.7498 (m-80) cc_final: 0.7297 (m-10) REVERT: A 574 ARG cc_start: 0.6950 (mmp80) cc_final: 0.6568 (mmp80) REVERT: A 707 ASP cc_start: 0.5109 (p0) cc_final: 0.4793 (p0) REVERT: B 38 HIS cc_start: 0.7673 (m90) cc_final: 0.7092 (m-70) REVERT: B 389 ASP cc_start: 0.8442 (t0) cc_final: 0.8196 (t0) REVERT: B 644 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8509 (tt) REVERT: B 667 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.7466 (m-80) outliers start: 66 outliers final: 40 residues processed: 208 average time/residue: 0.2563 time to fit residues: 75.8113 Evaluate side-chains 175 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 133 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 228 VAL 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 49 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 92 GLU 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 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 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 52 optimal weight: 20.0000 chunk 109 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 54 optimal weight: 30.0000 chunk 26 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 770 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.169625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.132069 restraints weight = 15290.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.131068 restraints weight = 10993.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.132613 restraints weight = 10506.280| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11294 Z= 0.198 Angle : 0.656 8.029 15336 Z= 0.330 Chirality : 0.044 0.224 1758 Planarity : 0.004 0.043 2003 Dihedral : 6.521 59.501 1609 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.00 % Favored : 89.93 % Rotamer: Outliers : 6.53 % Allowed : 19.14 % Favored : 74.34 % Cbeta Deviations : 0.00 % 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: -2.13 (0.22), residues: 1420 helix: -0.28 (0.20), residues: 685 sheet: -1.27 (0.48), residues: 103 loop : -2.79 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 658 HIS 0.007 0.001 HIS B 535 PHE 0.022 0.002 PHE A 241 TYR 0.008 0.001 TYR C 68 ARG 0.005 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 483) hydrogen bonds : angle 4.24185 ( 1398) metal coordination : bond 0.01437 ( 6) covalent geometry : bond 0.00476 (11288) covalent geometry : angle 0.65646 (15336) *********************** 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 223 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 149 time to evaluate : 2.859 Fit side-chains revert: symmetry clash REVERT: A 274 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8068 (mm) REVERT: A 306 ARG cc_start: 0.8108 (ttm110) cc_final: 0.7824 (ttm110) REVERT: A 405 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7428 (pt0) REVERT: A 509 ASP cc_start: 0.7296 (t0) cc_final: 0.7051 (t0) REVERT: A 707 ASP cc_start: 0.5325 (p0) cc_final: 0.5074 (p0) REVERT: A 710 VAL cc_start: 0.8314 (m) cc_final: 0.6878 (m) REVERT: A 714 MET cc_start: 0.7660 (mpp) cc_final: 0.7407 (mpp) REVERT: B 38 HIS cc_start: 0.7799 (m90) cc_final: 0.7041 (m90) REVERT: B 370 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8295 (mm) REVERT: B 389 ASP cc_start: 0.8484 (t0) cc_final: 0.8238 (t0) REVERT: B 411 ARG cc_start: 0.7536 (ptm160) cc_final: 0.7277 (ptm160) REVERT: B 644 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8575 (tt) REVERT: B 667 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.7368 (m-80) outliers start: 74 outliers final: 52 residues processed: 212 average time/residue: 0.3516 time to fit residues: 105.3687 Evaluate side-chains 188 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 132 time to evaluate : 1.480 ------------------------------------------------------------------------------- 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 246 VAL Chi-restraints excluded: chain A residue 274 LEU 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 447 VAL 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 373 LEU Chi-restraints excluded: chain B residue 374 ASP 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 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 Chi-restraints excluded: chain C residue 118 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 62 optimal weight: 0.4980 chunk 41 optimal weight: 8.9990 chunk 138 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 78 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.171241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.132830 restraints weight = 15110.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.133388 restraints weight = 10784.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.135417 restraints weight = 8136.195| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2217 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= 0.136 Angle : 0.602 8.398 15336 Z= 0.303 Chirality : 0.042 0.210 1758 Planarity : 0.004 0.039 2003 Dihedral : 6.221 58.708 1609 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.72 % Favored : 90.21 % Rotamer: Outliers : 5.29 % Allowed : 20.99 % Favored : 73.72 % Cbeta Deviations : 0.00 % 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: -1.73 (0.23), residues: 1420 helix: 0.09 (0.21), residues: 688 sheet: -1.19 (0.48), residues: 103 loop : -2.62 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 658 HIS 0.005 0.001 HIS B 535 PHE 0.015 0.001 PHE A 633 TYR 0.012 0.001 TYR A 397 ARG 0.006 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.03347 ( 483) hydrogen bonds : angle 4.00647 ( 1398) metal coordination : bond 0.00792 ( 6) covalent geometry : bond 0.00318 (11288) covalent geometry : angle 0.60203 (15336) *********************** 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 : 1.196 Fit side-chains REVERT: A 274 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7900 (mm) REVERT: A 302 ASP cc_start: 0.8296 (m-30) cc_final: 0.7417 (m-30) REVERT: A 316 HIS cc_start: 0.5458 (t-170) cc_final: 0.5187 (t-170) REVERT: A 405 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7361 (pt0) REVERT: A 443 MET cc_start: 0.7660 (mpp) cc_final: 0.4428 (ptt) REVERT: A 707 ASP cc_start: 0.5460 (p0) cc_final: 0.5193 (p0) REVERT: A 710 VAL cc_start: 0.8167 (m) cc_final: 0.6581 (m) REVERT: A 714 MET cc_start: 0.7647 (mpp) cc_final: 0.7290 (mpp) REVERT: B 370 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8217 (mm) REVERT: B 389 ASP cc_start: 0.8445 (t0) cc_final: 0.8144 (t0) REVERT: B 411 ARG cc_start: 0.7478 (ptm160) cc_final: 0.7238 (ptm160) REVERT: B 629 TYR cc_start: 0.9048 (m-10) cc_final: 0.8428 (m-80) REVERT: B 644 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8557 (tt) outliers start: 60 outliers final: 44 residues processed: 202 average time/residue: 0.2253 time to fit residues: 65.8191 Evaluate side-chains 183 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 136 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 169 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 274 LEU 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 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 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 352 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 374 ASP 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 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 16 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 70 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 58 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 129 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 121 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 155 GLN A 367 GLN B 38 HIS B 770 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.171068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.132560 restraints weight = 15028.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.133195 restraints weight = 10548.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.134782 restraints weight = 8358.450| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2359 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= 0.141 Angle : 0.610 7.996 15336 Z= 0.304 Chirality : 0.041 0.175 1758 Planarity : 0.004 0.039 2003 Dihedral : 6.086 58.160 1605 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.00 % Favored : 89.93 % Rotamer: Outliers : 6.17 % Allowed : 21.25 % Favored : 72.57 % 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: -1.57 (0.23), residues: 1420 helix: 0.23 (0.21), residues: 693 sheet: -1.06 (0.52), residues: 93 loop : -2.57 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 658 HIS 0.005 0.001 HIS B 535 PHE 0.018 0.001 PHE A 241 TYR 0.007 0.001 TYR C 68 ARG 0.007 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 483) hydrogen bonds : angle 3.94996 ( 1398) metal coordination : bond 0.00805 ( 6) covalent geometry : bond 0.00335 (11288) covalent geometry : angle 0.61037 (15336) *********************** 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 214 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 144 time to evaluate : 1.278 Fit side-chains revert: symmetry clash REVERT: A 306 ARG cc_start: 0.8099 (ttm110) cc_final: 0.7642 (ttm110) REVERT: A 405 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7347 (pt0) REVERT: A 443 MET cc_start: 0.7669 (mpp) cc_final: 0.4428 (ptt) REVERT: A 707 ASP cc_start: 0.5517 (p0) cc_final: 0.5289 (p0) REVERT: A 710 VAL cc_start: 0.8083 (m) cc_final: 0.6478 (m) REVERT: A 714 MET cc_start: 0.7625 (mpp) cc_final: 0.7239 (mpp) REVERT: B 370 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8241 (mm) REVERT: B 375 MET cc_start: 0.8311 (tpp) cc_final: 0.7738 (tpp) REVERT: B 389 ASP cc_start: 0.8442 (t0) cc_final: 0.8126 (t0) REVERT: B 629 TYR cc_start: 0.9056 (m-10) cc_final: 0.8400 (m-80) REVERT: B 644 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8541 (tt) outliers start: 70 outliers final: 50 residues processed: 205 average time/residue: 0.2356 time to fit residues: 68.7467 Evaluate side-chains 184 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 132 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 169 THR 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 485 ARG 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 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 352 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 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 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 57 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 66 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 103 optimal weight: 0.2980 chunk 41 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN B 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.171034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.132993 restraints weight = 15160.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.133121 restraints weight = 11537.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.134830 restraints weight = 9343.533| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2496 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= 0.144 Angle : 0.601 8.036 15336 Z= 0.300 Chirality : 0.042 0.249 1758 Planarity : 0.004 0.038 2003 Dihedral : 6.016 57.065 1605 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.93 % Favored : 90.00 % Rotamer: Outliers : 6.08 % Allowed : 21.34 % Favored : 72.57 % 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: -1.42 (0.23), residues: 1420 helix: 0.32 (0.21), residues: 701 sheet: -1.09 (0.50), residues: 103 loop : -2.47 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 658 HIS 0.006 0.001 HIS B 38 PHE 0.015 0.001 PHE A 241 TYR 0.012 0.001 TYR A 397 ARG 0.007 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.03217 ( 483) hydrogen bonds : angle 3.90595 ( 1398) metal coordination : bond 0.00823 ( 6) covalent geometry : bond 0.00344 (11288) covalent geometry : angle 0.60062 (15336) *********************** 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 205 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 136 time to evaluate : 1.263 Fit side-chains REVERT: A 405 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7323 (pt0) REVERT: A 707 ASP cc_start: 0.5346 (p0) cc_final: 0.5145 (p0) REVERT: A 710 VAL cc_start: 0.8085 (m) cc_final: 0.6564 (m) REVERT: A 714 MET cc_start: 0.7547 (mpp) cc_final: 0.7177 (mpp) REVERT: B 370 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8175 (mm) REVERT: B 389 ASP cc_start: 0.8465 (t0) cc_final: 0.8171 (t0) REVERT: B 629 TYR cc_start: 0.9081 (m-10) cc_final: 0.8409 (m-80) REVERT: B 644 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8580 (tt) outliers start: 69 outliers final: 54 residues processed: 196 average time/residue: 0.2285 time to fit residues: 64.5231 Evaluate side-chains 182 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 126 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 50 THR 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 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 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 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 327 ASP 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 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 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 57 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 102 VAL 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 77 optimal weight: 4.9990 chunk 119 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 0.0470 chunk 28 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 770 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.172218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.134522 restraints weight = 15194.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.134793 restraints weight = 11571.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.136562 restraints weight = 9171.808| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2640 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= 0.123 Angle : 0.592 8.138 15336 Z= 0.296 Chirality : 0.041 0.182 1758 Planarity : 0.004 0.037 2003 Dihedral : 5.728 56.614 1601 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.86 % Favored : 90.07 % Rotamer: Outliers : 5.11 % Allowed : 22.66 % 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 (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: -1.28 (0.23), residues: 1420 helix: 0.42 (0.21), residues: 702 sheet: -1.13 (0.50), residues: 103 loop : -2.36 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 658 HIS 0.007 0.001 HIS A 316 PHE 0.013 0.001 PHE A 633 TYR 0.006 0.001 TYR B 721 ARG 0.006 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.03116 ( 483) hydrogen bonds : angle 3.86450 ( 1398) metal coordination : bond 0.00725 ( 6) covalent geometry : bond 0.00291 (11288) covalent geometry : angle 0.59176 (15336) *********************** 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 191 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 133 time to evaluate : 1.129 Fit side-chains REVERT: A 405 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7305 (pt0) REVERT: A 443 MET cc_start: 0.7651 (mpp) cc_final: 0.4242 (ptt) REVERT: A 707 ASP cc_start: 0.5348 (p0) cc_final: 0.5131 (p0) REVERT: A 710 VAL cc_start: 0.8084 (m) cc_final: 0.6844 (m) REVERT: A 714 MET cc_start: 0.7527 (mpp) cc_final: 0.7152 (mpp) REVERT: B 49 LEU cc_start: 0.9250 (tt) cc_final: 0.9014 (tt) REVERT: B 370 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8106 (mm) REVERT: B 389 ASP cc_start: 0.8444 (t0) cc_final: 0.8121 (t0) REVERT: B 629 TYR cc_start: 0.9035 (m-10) cc_final: 0.8354 (m-80) REVERT: B 644 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8575 (tt) outliers start: 58 outliers final: 47 residues processed: 182 average time/residue: 0.2137 time to fit residues: 56.3207 Evaluate side-chains 174 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 125 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 50 THR 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 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 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 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 327 ASP 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 565 THR Chi-restraints excluded: chain B residue 601 HIS 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 761 VAL Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 35 VAL 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 111 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 42 optimal weight: 0.4980 chunk 140 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.171435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.133672 restraints weight = 15226.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.133637 restraints weight = 10622.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.135368 restraints weight = 8775.491| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11294 Z= 0.147 Angle : 0.609 9.114 15336 Z= 0.302 Chirality : 0.042 0.240 1758 Planarity : 0.004 0.037 2003 Dihedral : 5.701 55.927 1600 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.00 % Favored : 89.93 % Rotamer: Outliers : 5.20 % Allowed : 22.57 % 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 (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: -1.23 (0.23), residues: 1420 helix: 0.46 (0.21), residues: 701 sheet: -1.11 (0.50), residues: 103 loop : -2.33 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 658 HIS 0.004 0.001 HIS A 316 PHE 0.015 0.001 PHE A 633 TYR 0.007 0.001 TYR C 68 ARG 0.008 0.000 ARG B 497 Details of bonding type rmsd hydrogen bonds : bond 0.03151 ( 483) hydrogen bonds : angle 3.86293 ( 1398) metal coordination : bond 0.00851 ( 6) covalent geometry : bond 0.00354 (11288) covalent geometry : angle 0.60889 (15336) *********************** 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 191 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 132 time to evaluate : 1.174 Fit side-chains REVERT: A 405 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7319 (pt0) REVERT: A 443 MET cc_start: 0.7663 (mpp) cc_final: 0.4358 (ptt) REVERT: A 714 MET cc_start: 0.7555 (mpp) cc_final: 0.7124 (mpp) REVERT: B 370 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8159 (mm) REVERT: B 375 MET cc_start: 0.8136 (tpp) cc_final: 0.7774 (tpt) REVERT: B 389 ASP cc_start: 0.8452 (t0) cc_final: 0.8148 (t0) REVERT: B 582 MET cc_start: 0.9207 (tpp) cc_final: 0.8983 (tpt) REVERT: B 629 TYR cc_start: 0.9045 (m-10) cc_final: 0.8340 (m-80) REVERT: B 644 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8622 (tt) outliers start: 59 outliers final: 50 residues processed: 183 average time/residue: 0.2286 time to fit residues: 60.0358 Evaluate side-chains 177 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 125 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 50 THR 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 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 447 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 479 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 138 MET 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 327 ASP 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 512 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 565 THR 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 35 VAL 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 132 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 110 optimal weight: 0.6980 chunk 130 optimal weight: 0.1980 chunk 44 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 87 optimal weight: 0.0570 chunk 115 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4052 r_free = 0.4052 target = 0.174980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.137206 restraints weight = 15026.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.137280 restraints weight = 10096.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.138377 restraints weight = 8021.635| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11294 Z= 0.112 Angle : 0.607 8.627 15336 Z= 0.301 Chirality : 0.041 0.209 1758 Planarity : 0.004 0.036 2003 Dihedral : 5.575 55.999 1600 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 4.32 % Allowed : 23.72 % Favored : 71.96 % 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: -1.06 (0.24), residues: 1420 helix: 0.61 (0.21), residues: 702 sheet: -1.11 (0.50), residues: 103 loop : -2.25 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 308 HIS 0.004 0.001 HIS A 646 PHE 0.018 0.001 PHE A 241 TYR 0.008 0.001 TYR B 721 ARG 0.008 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.02955 ( 483) hydrogen bonds : angle 3.79341 ( 1398) metal coordination : bond 0.00711 ( 6) covalent geometry : bond 0.00257 (11288) covalent geometry : angle 0.60658 (15336) *********************** 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 186 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 137 time to evaluate : 1.108 Fit side-chains REVERT: A 166 LEU cc_start: 0.8550 (tt) cc_final: 0.8294 (tt) REVERT: A 443 MET cc_start: 0.7543 (mpp) cc_final: 0.4141 (ptt) REVERT: A 574 ARG cc_start: 0.7045 (mmp80) cc_final: 0.6781 (mmp80) REVERT: A 714 MET cc_start: 0.7574 (mpp) cc_final: 0.7178 (mpp) REVERT: B 389 ASP cc_start: 0.8390 (t0) cc_final: 0.8081 (t0) REVERT: B 582 MET cc_start: 0.9159 (tpp) cc_final: 0.8850 (tpt) REVERT: B 629 TYR cc_start: 0.8997 (m-10) cc_final: 0.8407 (m-80) REVERT: B 644 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8536 (tt) outliers start: 49 outliers final: 43 residues processed: 178 average time/residue: 0.2167 time to fit residues: 56.2349 Evaluate side-chains 165 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 121 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 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 428 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 452 ASP 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 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 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 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 35 VAL 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 52 optimal weight: 0.0270 chunk 113 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 56 optimal weight: 0.0370 chunk 97 optimal weight: 6.9990 chunk 115 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 9 optimal weight: 0.0570 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 HIS B 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.176837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.138815 restraints weight = 14931.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.137708 restraints weight = 10635.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.139769 restraints weight = 8190.593| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 11294 Z= 0.109 Angle : 0.608 8.712 15336 Z= 0.298 Chirality : 0.041 0.189 1758 Planarity : 0.004 0.036 2003 Dihedral : 5.468 56.466 1600 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 3.70 % Allowed : 25.04 % Favored : 71.25 % 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 (0.24), residues: 1420 helix: 0.71 (0.21), residues: 703 sheet: -1.16 (0.50), residues: 103 loop : -2.23 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 308 HIS 0.004 0.001 HIS A 646 PHE 0.016 0.001 PHE A 241 TYR 0.016 0.001 TYR A 676 ARG 0.009 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.02866 ( 483) hydrogen bonds : angle 3.73134 ( 1398) metal coordination : bond 0.00678 ( 6) covalent geometry : bond 0.00245 (11288) covalent geometry : angle 0.60839 (15336) ********************** 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 172 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 1.272 Fit side-chains REVERT: A 336 PHE cc_start: 0.6384 (m-80) cc_final: 0.6184 (m-80) REVERT: A 443 MET cc_start: 0.7497 (mpp) cc_final: 0.4212 (ptt) REVERT: A 714 MET cc_start: 0.7490 (mpp) cc_final: 0.7047 (mpp) REVERT: B 49 LEU cc_start: 0.9131 (tt) cc_final: 0.8900 (tt) REVERT: B 375 MET cc_start: 0.8155 (tpp) cc_final: 0.7394 (tpp) REVERT: B 389 ASP cc_start: 0.8381 (t0) cc_final: 0.8068 (t0) REVERT: B 582 MET cc_start: 0.9163 (tpp) cc_final: 0.8875 (tpt) REVERT: B 629 TYR cc_start: 0.8961 (m-10) cc_final: 0.8518 (m-10) REVERT: B 644 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8581 (tt) REVERT: C 54 GLU cc_start: 0.7754 (mp0) cc_final: 0.7535 (mp0) outliers start: 42 outliers final: 37 residues processed: 167 average time/residue: 0.2311 time to fit residues: 56.5145 Evaluate side-chains 160 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 1.254 ------------------------------------------------------------------------------- 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 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 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 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 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 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 112 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 82 optimal weight: 0.1980 chunk 131 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.173743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.136549 restraints weight = 14912.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.136552 restraints weight = 9877.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.137919 restraints weight = 7777.166| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11294 Z= 0.146 Angle : 0.631 9.238 15336 Z= 0.311 Chirality : 0.042 0.183 1758 Planarity : 0.004 0.037 2003 Dihedral : 5.532 56.129 1600 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 3.79 % Allowed : 25.22 % Favored : 70.99 % 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: -0.98 (0.24), residues: 1420 helix: 0.68 (0.21), residues: 703 sheet: -1.15 (0.50), residues: 103 loop : -2.20 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 308 HIS 0.004 0.001 HIS C 125 PHE 0.027 0.001 PHE A 241 TYR 0.013 0.001 TYR A 676 ARG 0.008 0.000 ARG B 424 Details of bonding type rmsd hydrogen bonds : bond 0.03033 ( 483) hydrogen bonds : angle 3.76261 ( 1398) metal coordination : bond 0.00892 ( 6) covalent geometry : bond 0.00350 (11288) covalent geometry : angle 0.63118 (15336) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3554.88 seconds wall clock time: 63 minutes 52.84 seconds (3832.84 seconds total)