Starting phenix.real_space_refine on Sun Aug 24 13:13:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f2j_50147/08_2025/9f2j_50147.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f2j_50147/08_2025/9f2j_50147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f2j_50147/08_2025/9f2j_50147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f2j_50147/08_2025/9f2j_50147.map" model { file = "/net/cci-nas-00/data/ceres_data/9f2j_50147/08_2025/9f2j_50147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f2j_50147/08_2025/9f2j_50147.cif" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6643 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 75 5.16 5 C 9460 2.51 5 N 2380 2.21 5 O 2731 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14646 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 10204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1253, 10204 Classifications: {'peptide': 1253} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 1214} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 4333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4333 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 12, 'TRANS': 534} Chain breaks: 1 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.13, per 1000 atoms: 0.21 Number of scatterers: 14646 At special positions: 0 Unit cell: (89.05, 115.7, 215.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 75 16.00 O 2731 8.00 N 2380 7.00 C 9460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 430 " - pdb=" SG CYS B 454 " distance=2.04 Simple disulfide: pdb=" SG CYS A 141 " - pdb=" SG CYS A 526 " distance=2.03 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 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " BETA1-6 " NAG C 1 " - " FUC C 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG D 1 " - " FUC D 6 " NAG-ASN " NAG A 701 " - " ASN A 441 " " NAG C 1 " - " ASN A 491 " " NAG D 1 " - " ASN A 516 " Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 555.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3384 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 17 sheets defined 44.2% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'B' and resid 80 through 101 removed outlier: 3.832A pdb=" N THR B 101 " --> pdb=" O ARG B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 Processing helix chain 'B' and resid 216 through 233 removed outlier: 3.639A pdb=" N THR B 220 " --> pdb=" O ASP B 216 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR B 233 " --> pdb=" O GLY B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 267 Processing helix chain 'B' and resid 269 through 274 removed outlier: 3.606A pdb=" N ILE B 274 " --> pdb=" O ALA B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 300 Processing helix chain 'B' and resid 309 through 322 removed outlier: 3.512A pdb=" N MET B 313 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 347 Processing helix chain 'B' and resid 350 through 359 Processing helix chain 'B' and resid 409 through 411 No H-bonds generated for 'chain 'B' and resid 409 through 411' Processing helix chain 'B' and resid 467 through 471 removed outlier: 3.736A pdb=" N ASN B 470 " --> pdb=" O SER B 467 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE B 471 " --> pdb=" O GLU B 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 467 through 471' Processing helix chain 'B' and resid 496 through 506 Processing helix chain 'B' and resid 549 through 557 removed outlier: 3.508A pdb=" N GLN B 557 " --> pdb=" O TYR B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 576 Processing helix chain 'B' and resid 587 through 595 Processing helix chain 'B' and resid 602 through 619 Processing helix chain 'B' and resid 636 through 642 Processing helix chain 'B' and resid 643 through 646 removed outlier: 3.906A pdb=" N MET B 646 " --> pdb=" O ILE B 643 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 643 through 646' Processing helix chain 'B' and resid 648 through 660 Processing helix chain 'B' and resid 689 through 721 Processing helix chain 'B' and resid 721 through 753 removed outlier: 3.633A pdb=" N GLN B 753 " --> pdb=" O TYR B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 762 Processing helix chain 'B' and resid 765 through 800 removed outlier: 4.274A pdb=" N LEU B 769 " --> pdb=" O ASN B 765 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN B 783 " --> pdb=" O LYS B 779 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET B 800 " --> pdb=" O LEU B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 824 removed outlier: 3.863A pdb=" N GLY B 804 " --> pdb=" O MET B 800 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG B 807 " --> pdb=" O TYR B 803 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP B 817 " --> pdb=" O ALA B 813 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA B 818 " --> pdb=" O SER B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 847 removed outlier: 4.076A pdb=" N THR B 847 " --> pdb=" O ASN B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 856 removed outlier: 3.559A pdb=" N LYS B 855 " --> pdb=" O GLN B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 872 removed outlier: 3.646A pdb=" N THR B 865 " --> pdb=" O ARG B 861 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 877 Processing helix chain 'B' and resid 954 through 958 Processing helix chain 'B' and resid 1080 through 1092 Processing helix chain 'B' and resid 1266 through 1270 removed outlier: 3.799A pdb=" N GLN B1270 " --> pdb=" O TYR B1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 103 Processing helix chain 'A' and resid 105 through 131 removed outlier: 4.236A pdb=" N ALA A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 152 through 168 removed outlier: 3.806A pdb=" N LEU A 156 " --> pdb=" O MET A 152 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 168 " --> pdb=" O ILE A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 174 through 194 removed outlier: 3.547A pdb=" N PHE A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 213 Processing helix chain 'A' and resid 215 through 225 removed outlier: 3.553A pdb=" N GLU A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 232 through 258 removed outlier: 3.850A pdb=" N ILE A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE A 242 " --> pdb=" O TRP A 238 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 284 through 294 Processing helix chain 'A' and resid 300 through 308 Processing helix chain 'A' and resid 309 through 329 Processing helix chain 'A' and resid 371 through 381 Processing helix chain 'A' and resid 387 through 426 removed outlier: 3.676A pdb=" N TYR A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL A 409 " --> pdb=" O TYR A 405 " (cutoff:3.500A) Proline residue: A 412 - end of helix removed outlier: 3.844A pdb=" N LYS A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 535 through 548 removed outlier: 3.773A pdb=" N TYR A 539 " --> pdb=" O ASP A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 558 removed outlier: 4.307A pdb=" N GLY A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 581 Processing helix chain 'A' and resid 582 through 586 Processing helix chain 'A' and resid 588 through 603 Processing helix chain 'A' and resid 604 through 617 removed outlier: 3.682A pdb=" N LEU A 617 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 648 removed outlier: 3.964A pdb=" N ALA A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 671 removed outlier: 3.510A pdb=" N ILE A 657 " --> pdb=" O LYS A 653 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 144 through 148 removed outlier: 3.733A pdb=" N VAL B 137 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN B 136 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYR B 21 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LYS B 34 " --> pdb=" O PRO B 46 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY B 155 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU B 47 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL B 152 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU B 164 " --> pdb=" O ARG B 187 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 126 through 127 Processing sheet with id=AA3, first strand: chain 'B' and resid 213 through 214 removed outlier: 4.491A pdb=" N VAL B 373 " --> pdb=" O LEU B 416 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 455 through 458 removed outlier: 7.943A pdb=" N TYR B 426 " --> pdb=" O LYS B 541 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N TYR B 543 " --> pdb=" O TYR B 426 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU B 428 " --> pdb=" O TYR B 543 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU B 545 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N CYS B 430 " --> pdb=" O LEU B 545 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 479 through 481 Processing sheet with id=AA6, first strand: chain 'B' and resid 567 through 569 removed outlier: 6.335A pdb=" N ALA B 567 " --> pdb=" O VAL B 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 881 through 883 Processing sheet with id=AA8, first strand: chain 'B' and resid 895 through 900 removed outlier: 4.192A pdb=" N ILE B 964 " --> pdb=" O LYS B1056 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ASP B1058 " --> pdb=" O TYR B 962 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TYR B 962 " --> pdb=" O ASP B1058 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL B 976 " --> pdb=" O ILE B 964 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ASN B 966 " --> pdb=" O TRP B 974 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N TRP B 974 " --> pdb=" O ASN B 966 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 904 through 906 removed outlier: 4.304A pdb=" N PHE B1072 " --> pdb=" O SER B 944 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER B 944 " --> pdb=" O PHE B1072 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU B1074 " --> pdb=" O SER B 942 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N SER B 942 " --> pdb=" O LEU B1074 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE B1031 " --> pdb=" O LEU B1035 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LEU B1035 " --> pdb=" O ILE B1031 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1112 through 1115 Processing sheet with id=AB2, first strand: chain 'B' and resid 1122 through 1126 Processing sheet with id=AB3, first strand: chain 'B' and resid 1149 through 1151 removed outlier: 3.630A pdb=" N MET B1144 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 517 " --> pdb=" O MET B1144 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 499 " --> pdb=" O THR A 518 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N PHE A 459 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1160 through 1164 removed outlier: 5.602A pdb=" N ILE B1182 " --> pdb=" O LEU B1193 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1160 through 1164 removed outlier: 3.513A pdb=" N ASP B1178 " --> pdb=" O MET B1223 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N MET B1237 " --> pdb=" O ILE B1250 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 428 through 431 removed outlier: 6.406A pdb=" N LYS A 428 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N GLN A 450 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE A 430 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET A 444 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 465 " --> pdb=" O MET A 444 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A 467 " --> pdb=" O ASN A 446 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE A 448 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE A 469 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLN A 450 " --> pdb=" O PHE A 469 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 428 through 431 removed outlier: 6.406A pdb=" N LYS A 428 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N GLN A 450 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE A 430 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET A 444 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 465 " --> pdb=" O MET A 444 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A 467 " --> pdb=" O ASN A 446 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE A 448 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE A 469 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLN A 450 " --> pdb=" O PHE A 469 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N TYR A 488 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL A 467 " --> pdb=" O TYR A 488 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N LYS A 490 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE A 469 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N PHE A 489 " --> pdb=" O ILE A 510 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 493 through 495 681 hydrogen bonds defined for protein. 1944 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.99 Time building geometry restraints manager: 1.58 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: 3307 1.33 - 1.45: 3479 1.45 - 1.58: 8068 1.58 - 1.70: 1 1.70 - 1.82: 126 Bond restraints: 14981 Sorted by residual: bond pdb=" N ILE B 634 " pdb=" CA ILE B 634 " ideal model delta sigma weight residual 1.460 1.489 -0.029 7.30e-03 1.88e+04 1.56e+01 bond pdb=" N GLY A 148 " pdb=" CA GLY A 148 " ideal model delta sigma weight residual 1.445 1.478 -0.033 1.01e-02 9.80e+03 1.09e+01 bond pdb=" N ILE A 153 " pdb=" CA ILE A 153 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.15e+00 bond pdb=" N VAL B 621 " pdb=" CA VAL B 621 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.24e-02 6.50e+03 8.67e+00 bond pdb=" C1 NAG D 1 " pdb=" C2 NAG D 1 " ideal model delta sigma weight residual 1.532 1.589 -0.057 2.00e-02 2.50e+03 8.19e+00 ... (remaining 14976 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 19847 2.10 - 4.21: 372 4.21 - 6.31: 37 6.31 - 8.41: 8 8.41 - 10.51: 5 Bond angle restraints: 20269 Sorted by residual: angle pdb=" CA ILE B 632 " pdb=" C ILE B 632 " pdb=" O ILE B 632 " ideal model delta sigma weight residual 121.70 117.68 4.02 1.06e+00 8.90e-01 1.44e+01 angle pdb=" CA VAL B1180 " pdb=" C VAL B1180 " pdb=" O VAL B1180 " ideal model delta sigma weight residual 121.63 117.88 3.75 9.90e-01 1.02e+00 1.44e+01 angle pdb=" CA ASP B1178 " pdb=" C ASP B1178 " pdb=" O ASP B1178 " ideal model delta sigma weight residual 121.87 117.57 4.30 1.16e+00 7.43e-01 1.37e+01 angle pdb=" N LYS B 626 " pdb=" CA LYS B 626 " pdb=" C LYS B 626 " ideal model delta sigma weight residual 112.87 108.45 4.42 1.20e+00 6.94e-01 1.36e+01 angle pdb=" CA ASP A 529 " pdb=" C ASP A 529 " pdb=" O ASP A 529 " ideal model delta sigma weight residual 122.41 118.10 4.31 1.21e+00 6.83e-01 1.27e+01 ... (remaining 20264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.03: 8052 24.03 - 48.05: 773 48.05 - 72.08: 106 72.08 - 96.11: 12 96.11 - 120.13: 24 Dihedral angle restraints: 8967 sinusoidal: 3698 harmonic: 5269 Sorted by residual: dihedral pdb=" C2 FUC D 6 " pdb=" C1 FUC D 6 " pdb=" O5 FUC D 6 " pdb=" C5 FUC D 6 " ideal model delta sinusoidal sigma weight residual 57.68 -62.45 120.13 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" CA GLN B 7 " pdb=" C GLN B 7 " pdb=" N PHE B 8 " pdb=" CA PHE B 8 " ideal model delta harmonic sigma weight residual -180.00 -160.57 -19.43 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" C2 MAN D 5 " pdb=" C1 MAN D 5 " pdb=" O5 MAN D 5 " pdb=" C5 MAN D 5 " ideal model delta sinusoidal sigma weight residual -57.62 54.83 -112.45 1 3.00e+01 1.11e-03 1.47e+01 ... (remaining 8964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.964: 2249 0.964 - 1.928: 0 1.928 - 2.892: 0 2.892 - 3.856: 1 3.856 - 4.820: 1 Chirality restraints: 2251 Sorted by residual: chirality pdb=" C1 FUC C 2 " pdb=" O6 NAG C 1 " pdb=" C2 FUC C 2 " pdb=" O5 FUC C 2 " both_signs ideal model delta sigma weight residual False -2.40 2.42 -4.82 2.00e-02 2.50e+03 5.81e+04 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 0.69 -3.09 2.00e-02 2.50e+03 2.39e+04 chirality pdb=" C1 MAN D 4 " pdb=" O3 BMA D 3 " pdb=" C2 MAN D 4 " pdb=" O5 MAN D 4 " both_signs ideal model delta sigma weight residual False 2.40 2.17 0.23 2.00e-02 2.50e+03 1.29e+02 ... (remaining 2248 not shown) Planarity restraints: 2567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.184 2.00e-02 2.50e+03 1.52e-01 2.89e+02 pdb=" C7 NAG C 1 " -0.049 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.133 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.247 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 441 " -0.006 2.00e-02 2.50e+03 4.93e-02 3.04e+01 pdb=" CG ASN A 441 " -0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN A 441 " 0.048 2.00e-02 2.50e+03 pdb=" ND2 ASN A 441 " -0.080 2.00e-02 2.50e+03 pdb=" C1 NAG A 701 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B1179 " 0.395 9.50e-02 1.11e+02 1.77e-01 1.92e+01 pdb=" NE ARG B1179 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG B1179 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B1179 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B1179 " 0.014 2.00e-02 2.50e+03 ... (remaining 2564 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 136 2.61 - 3.18: 12967 3.18 - 3.75: 22284 3.75 - 4.33: 30471 4.33 - 4.90: 51066 Nonbonded interactions: 116924 Sorted by model distance: nonbonded pdb=" OH TYR A 222 " pdb=" O PRO A 298 " model vdw 2.035 3.040 nonbonded pdb=" OD1 ASP B 461 " pdb=" NZ LYS B 731 " model vdw 2.172 3.120 nonbonded pdb=" OG SER A 181 " pdb=" O GLY A 211 " model vdw 2.177 3.040 nonbonded pdb=" O LYS B 840 " pdb=" OG1 THR B 844 " model vdw 2.207 3.040 nonbonded pdb=" O SER A 603 " pdb=" OG SER A 603 " model vdw 2.210 3.040 ... (remaining 116919 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: 20.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.700 Find NCS groups from input model: 0.080 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.304 14992 Z= 0.277 Angle : 0.721 16.555 20300 Z= 0.395 Chirality : 0.131 4.820 2251 Planarity : 0.006 0.177 2564 Dihedral : 18.599 120.135 5577 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.19 % Allowed : 26.74 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.20), residues: 1784 helix: 1.69 (0.20), residues: 708 sheet: -0.33 (0.34), residues: 218 loop : -1.21 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 174 TYR 0.019 0.001 TYR B 751 PHE 0.062 0.002 PHE A 273 TRP 0.015 0.001 TRP B1266 HIS 0.004 0.001 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00448 (14981) covalent geometry : angle 0.67474 (20269) SS BOND : bond 0.00478 ( 2) SS BOND : angle 2.77898 ( 4) hydrogen bonds : bond 0.13603 ( 676) hydrogen bonds : angle 5.69418 ( 1944) link_ALPHA1-3 : bond 0.04028 ( 1) link_ALPHA1-3 : angle 5.13463 ( 3) link_ALPHA1-6 : bond 0.03860 ( 1) link_ALPHA1-6 : angle 3.78169 ( 3) link_BETA1-4 : bond 0.02745 ( 2) link_BETA1-4 : angle 9.60575 ( 6) link_BETA1-6 : bond 0.02682 ( 2) link_BETA1-6 : angle 3.15546 ( 6) link_NAG-ASN : bond 0.18501 ( 3) link_NAG-ASN : angle 7.95975 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 246 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 ASP cc_start: 0.8172 (p0) cc_final: 0.7903 (p0) REVERT: B 147 GLU cc_start: 0.7784 (tp30) cc_final: 0.7475 (tt0) REVERT: B 197 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7796 (tm-30) REVERT: B 279 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8634 (mt-10) REVERT: B 352 ASP cc_start: 0.8508 (t0) cc_final: 0.8290 (t0) REVERT: B 474 ASP cc_start: 0.8100 (p0) cc_final: 0.7808 (p0) REVERT: B 530 LEU cc_start: 0.9164 (mt) cc_final: 0.8865 (tt) REVERT: B 1034 ARG cc_start: 0.7787 (ttp-110) cc_final: 0.7428 (mtm110) REVERT: B 1041 ILE cc_start: 0.8857 (pt) cc_final: 0.8441 (mt) REVERT: A 122 ASP cc_start: 0.4806 (t70) cc_final: 0.4125 (t0) REVERT: A 291 MET cc_start: 0.3647 (OUTLIER) cc_final: 0.2785 (ttp) REVERT: A 453 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7319 (mppt) outliers start: 19 outliers final: 3 residues processed: 257 average time/residue: 0.1203 time to fit residues: 46.1084 Evaluate side-chains 155 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 535 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 HIS B 184 GLN B 224 GLN B 288 ASN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN B 533 ASN B 570 ASN B 697 ASN B 739 GLN B 765 ASN B 778 ASN B 913 GLN B 954 ASN B1026 ASN B1064 HIS B1147 ASN B1199 GLN B1216 ASN B1233 ASN B1245 ASN A 272 HIS ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 GLN A 507 HIS ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.111262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.084145 restraints weight = 36967.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.082795 restraints weight = 32878.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.083373 restraints weight = 28125.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.083888 restraints weight = 24263.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.083832 restraints weight = 22119.704| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 14992 Z= 0.248 Angle : 0.692 12.795 20300 Z= 0.353 Chirality : 0.048 0.519 2251 Planarity : 0.004 0.053 2564 Dihedral : 11.867 123.341 2134 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.13 % Allowed : 25.67 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.20), residues: 1784 helix: 1.60 (0.20), residues: 723 sheet: -0.35 (0.33), residues: 231 loop : -0.99 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 174 TYR 0.018 0.002 TYR A 618 PHE 0.016 0.002 PHE A 163 TRP 0.028 0.002 TRP A 263 HIS 0.006 0.002 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00567 (14981) covalent geometry : angle 0.67471 (20269) SS BOND : bond 0.00207 ( 2) SS BOND : angle 1.00887 ( 4) hydrogen bonds : bond 0.05307 ( 676) hydrogen bonds : angle 4.60271 ( 1944) link_ALPHA1-3 : bond 0.01751 ( 1) link_ALPHA1-3 : angle 5.17389 ( 3) link_ALPHA1-6 : bond 0.00109 ( 1) link_ALPHA1-6 : angle 3.22212 ( 3) link_BETA1-4 : bond 0.01899 ( 2) link_BETA1-4 : angle 2.13126 ( 6) link_BETA1-6 : bond 0.01661 ( 2) link_BETA1-6 : angle 3.87059 ( 6) link_NAG-ASN : bond 0.01050 ( 3) link_NAG-ASN : angle 5.25060 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 162 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 197 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7660 (tm-30) REVERT: B 530 LEU cc_start: 0.9099 (mt) cc_final: 0.8849 (tt) REVERT: B 808 LEU cc_start: 0.9241 (mt) cc_final: 0.9035 (mt) REVERT: B 1041 ILE cc_start: 0.8894 (pt) cc_final: 0.8551 (mt) REVERT: B 1113 MET cc_start: 0.9351 (mmm) cc_final: 0.8978 (mmm) REVERT: A 253 MET cc_start: 0.6514 (tpp) cc_final: 0.5985 (tpp) REVERT: A 257 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7485 (tt) REVERT: A 291 MET cc_start: 0.5912 (OUTLIER) cc_final: 0.4229 (ttp) REVERT: A 311 ASP cc_start: 0.2696 (OUTLIER) cc_final: 0.2287 (p0) REVERT: A 370 ILE cc_start: 0.1207 (OUTLIER) cc_final: 0.0782 (pt) REVERT: A 411 PHE cc_start: 0.6412 (m-10) cc_final: 0.5996 (m-10) REVERT: A 414 MET cc_start: 0.8624 (mmm) cc_final: 0.8090 (mmm) outliers start: 66 outliers final: 25 residues processed: 216 average time/residue: 0.1030 time to fit residues: 35.0259 Evaluate side-chains 164 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1121 LYS Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 678 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 175 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 57 optimal weight: 0.2980 chunk 102 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 69 optimal weight: 0.8980 chunk 158 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 GLN B 205 ASN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 GLN A 319 GLN ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 HIS ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 HIS A 553 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.112662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.086050 restraints weight = 37420.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.085426 restraints weight = 33476.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.085743 restraints weight = 27350.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.086267 restraints weight = 23824.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.086755 restraints weight = 21831.909| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14992 Z= 0.129 Angle : 0.583 13.030 20300 Z= 0.297 Chirality : 0.044 0.496 2251 Planarity : 0.003 0.045 2564 Dihedral : 9.783 115.307 2125 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.32 % Allowed : 25.61 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.20), residues: 1784 helix: 1.69 (0.20), residues: 730 sheet: -0.30 (0.33), residues: 237 loop : -0.87 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 174 TYR 0.014 0.001 TYR B1030 PHE 0.021 0.001 PHE A 398 TRP 0.032 0.002 TRP A 263 HIS 0.005 0.001 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00276 (14981) covalent geometry : angle 0.56837 (20269) SS BOND : bond 0.00274 ( 2) SS BOND : angle 0.81607 ( 4) hydrogen bonds : bond 0.04531 ( 676) hydrogen bonds : angle 4.29789 ( 1944) link_ALPHA1-3 : bond 0.01369 ( 1) link_ALPHA1-3 : angle 2.68370 ( 3) link_ALPHA1-6 : bond 0.00831 ( 1) link_ALPHA1-6 : angle 2.56461 ( 3) link_BETA1-4 : bond 0.00653 ( 2) link_BETA1-4 : angle 1.52146 ( 6) link_BETA1-6 : bond 0.01434 ( 2) link_BETA1-6 : angle 3.23405 ( 6) link_NAG-ASN : bond 0.00854 ( 3) link_NAG-ASN : angle 5.19617 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 144 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 197 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7384 (tm-30) REVERT: B 330 LYS cc_start: 0.8962 (mmmt) cc_final: 0.8514 (mmmt) REVERT: B 530 LEU cc_start: 0.9036 (mt) cc_final: 0.8767 (tt) REVERT: B 800 MET cc_start: 0.8838 (mtp) cc_final: 0.8509 (mtt) REVERT: B 1041 ILE cc_start: 0.8869 (pt) cc_final: 0.8430 (mt) REVERT: B 1113 MET cc_start: 0.9313 (mmm) cc_final: 0.9049 (mmm) REVERT: B 1243 ASN cc_start: 0.8026 (p0) cc_final: 0.7583 (p0) REVERT: A 124 VAL cc_start: 0.8704 (OUTLIER) cc_final: 0.8489 (p) REVERT: A 153 ILE cc_start: 0.6440 (mm) cc_final: 0.6037 (tp) REVERT: A 253 MET cc_start: 0.6561 (tpp) cc_final: 0.6058 (tpp) REVERT: A 257 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7524 (tt) REVERT: A 291 MET cc_start: 0.5587 (tpp) cc_final: 0.4120 (tmm) REVERT: A 292 VAL cc_start: 0.6636 (t) cc_final: 0.6368 (t) REVERT: A 297 MET cc_start: 0.6303 (tpt) cc_final: 0.4925 (ttp) REVERT: A 309 LYS cc_start: 0.0894 (OUTLIER) cc_final: 0.0014 (tppt) REVERT: A 311 ASP cc_start: 0.2552 (OUTLIER) cc_final: 0.2350 (p0) REVERT: A 315 MET cc_start: 0.2791 (tmm) cc_final: -0.0047 (mtt) REVERT: A 414 MET cc_start: 0.8748 (mmm) cc_final: 0.8491 (mmm) REVERT: A 434 HIS cc_start: 0.6732 (OUTLIER) cc_final: 0.6496 (m-70) REVERT: A 466 HIS cc_start: 0.7465 (OUTLIER) cc_final: 0.7017 (m90) outliers start: 53 outliers final: 20 residues processed: 188 average time/residue: 0.1003 time to fit residues: 30.3585 Evaluate side-chains 158 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1144 MET Chi-restraints excluded: chain B residue 1222 VAL Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 658 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 176 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 111 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN ** A 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 HIS ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.111315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.085241 restraints weight = 37619.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.084920 restraints weight = 32631.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.085231 restraints weight = 27744.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.085648 restraints weight = 23894.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.085752 restraints weight = 21450.810| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14992 Z= 0.149 Angle : 0.581 12.135 20300 Z= 0.294 Chirality : 0.044 0.480 2251 Planarity : 0.003 0.041 2564 Dihedral : 8.991 111.667 2122 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.57 % Allowed : 25.05 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.20), residues: 1784 helix: 1.73 (0.20), residues: 725 sheet: -0.55 (0.31), residues: 264 loop : -0.87 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 174 TYR 0.014 0.001 TYR B1030 PHE 0.016 0.001 PHE A 411 TRP 0.036 0.002 TRP A 263 HIS 0.005 0.001 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00337 (14981) covalent geometry : angle 0.56800 (20269) SS BOND : bond 0.00227 ( 2) SS BOND : angle 0.92543 ( 4) hydrogen bonds : bond 0.04315 ( 676) hydrogen bonds : angle 4.30460 ( 1944) link_ALPHA1-3 : bond 0.01198 ( 1) link_ALPHA1-3 : angle 3.04955 ( 3) link_ALPHA1-6 : bond 0.01309 ( 1) link_ALPHA1-6 : angle 2.05118 ( 3) link_BETA1-4 : bond 0.00616 ( 2) link_BETA1-4 : angle 1.23955 ( 6) link_BETA1-6 : bond 0.01274 ( 2) link_BETA1-6 : angle 2.73036 ( 6) link_NAG-ASN : bond 0.00679 ( 3) link_NAG-ASN : angle 4.88779 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 139 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 124 ASP cc_start: 0.7998 (p0) cc_final: 0.7789 (p0) REVERT: B 197 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7394 (tm-30) REVERT: B 330 LYS cc_start: 0.8922 (mmmt) cc_final: 0.8455 (mmmt) REVERT: B 530 LEU cc_start: 0.9043 (mt) cc_final: 0.8782 (tt) REVERT: B 808 LEU cc_start: 0.9178 (mt) cc_final: 0.8960 (mt) REVERT: B 1041 ILE cc_start: 0.8867 (pt) cc_final: 0.8491 (mt) REVERT: B 1113 MET cc_start: 0.9291 (mmm) cc_final: 0.8982 (mmm) REVERT: A 124 VAL cc_start: 0.8724 (OUTLIER) cc_final: 0.8475 (p) REVERT: A 253 MET cc_start: 0.6518 (tpp) cc_final: 0.6194 (tpp) REVERT: A 291 MET cc_start: 0.5739 (tpp) cc_final: 0.4389 (tmm) REVERT: A 292 VAL cc_start: 0.6649 (t) cc_final: 0.6391 (t) REVERT: A 297 MET cc_start: 0.6238 (tpt) cc_final: 0.4874 (ttp) REVERT: A 311 ASP cc_start: 0.2702 (OUTLIER) cc_final: 0.2424 (p0) REVERT: A 315 MET cc_start: 0.2952 (tmm) cc_final: 0.0047 (mtt) REVERT: A 400 MET cc_start: 0.3800 (OUTLIER) cc_final: 0.3300 (tmm) REVERT: A 414 MET cc_start: 0.8795 (mmm) cc_final: 0.8423 (mmm) REVERT: A 434 HIS cc_start: 0.6684 (OUTLIER) cc_final: 0.6382 (m-70) REVERT: A 481 ASP cc_start: 0.8210 (t0) cc_final: 0.7798 (t70) REVERT: A 528 MET cc_start: 0.7426 (ptm) cc_final: 0.7082 (ttp) outliers start: 57 outliers final: 29 residues processed: 186 average time/residue: 0.1130 time to fit residues: 33.0237 Evaluate side-chains 163 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1121 LYS Chi-restraints excluded: chain B residue 1144 MET Chi-restraints excluded: chain B residue 1222 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 658 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 HIS A 446 ASN A 511 ASN ** A 553 ASN ** 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 = 0.3644 r_free = 0.3644 target = 0.110488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.085158 restraints weight = 37528.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.084204 restraints weight = 29968.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.084871 restraints weight = 29708.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.085183 restraints weight = 23431.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.085231 restraints weight = 21473.869| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14992 Z= 0.154 Angle : 0.570 12.042 20300 Z= 0.289 Chirality : 0.044 0.459 2251 Planarity : 0.003 0.045 2564 Dihedral : 8.595 108.200 2120 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.19 % Allowed : 26.36 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.20), residues: 1784 helix: 1.76 (0.20), residues: 718 sheet: -0.46 (0.32), residues: 254 loop : -0.89 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 302 TYR 0.014 0.001 TYR B1030 PHE 0.023 0.001 PHE A 226 TRP 0.019 0.001 TRP A 263 HIS 0.005 0.001 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00351 (14981) covalent geometry : angle 0.55788 (20269) SS BOND : bond 0.00216 ( 2) SS BOND : angle 0.88746 ( 4) hydrogen bonds : bond 0.04258 ( 676) hydrogen bonds : angle 4.31317 ( 1944) link_ALPHA1-3 : bond 0.01090 ( 1) link_ALPHA1-3 : angle 2.55899 ( 3) link_ALPHA1-6 : bond 0.01496 ( 1) link_ALPHA1-6 : angle 2.37256 ( 3) link_BETA1-4 : bond 0.00663 ( 2) link_BETA1-4 : angle 1.05444 ( 6) link_BETA1-6 : bond 0.01361 ( 2) link_BETA1-6 : angle 2.80089 ( 6) link_NAG-ASN : bond 0.00539 ( 3) link_NAG-ASN : angle 4.76796 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 137 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: B 124 ASP cc_start: 0.7993 (p0) cc_final: 0.7790 (p0) REVERT: B 197 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7399 (tm-30) REVERT: B 330 LYS cc_start: 0.8906 (mmmt) cc_final: 0.8630 (mmmt) REVERT: B 530 LEU cc_start: 0.9068 (mt) cc_final: 0.8794 (tt) REVERT: B 781 MET cc_start: 0.8383 (mmm) cc_final: 0.7992 (mmm) REVERT: B 808 LEU cc_start: 0.9178 (mt) cc_final: 0.8953 (mt) REVERT: B 1113 MET cc_start: 0.9289 (mmm) cc_final: 0.8347 (mmt) REVERT: A 124 VAL cc_start: 0.8636 (OUTLIER) cc_final: 0.8381 (p) REVERT: A 155 TYR cc_start: 0.6483 (OUTLIER) cc_final: 0.5855 (t80) REVERT: A 267 MET cc_start: 0.5450 (mpp) cc_final: 0.4542 (mpp) REVERT: A 291 MET cc_start: 0.5706 (tpp) cc_final: 0.4681 (ttp) REVERT: A 297 MET cc_start: 0.6261 (tpt) cc_final: 0.4989 (ttp) REVERT: A 311 ASP cc_start: 0.2823 (OUTLIER) cc_final: 0.2388 (p0) REVERT: A 315 MET cc_start: 0.2988 (tmm) cc_final: 0.0083 (mtt) REVERT: A 400 MET cc_start: 0.3991 (tmm) cc_final: 0.3772 (tmm) REVERT: A 414 MET cc_start: 0.8806 (mmm) cc_final: 0.8388 (mmm) REVERT: A 434 HIS cc_start: 0.6762 (OUTLIER) cc_final: 0.5845 (m-70) REVERT: A 436 TYR cc_start: 0.7426 (m-10) cc_final: 0.6967 (m-10) REVERT: A 481 ASP cc_start: 0.8177 (t0) cc_final: 0.7777 (t70) REVERT: A 528 MET cc_start: 0.7546 (ptm) cc_final: 0.7244 (ttp) outliers start: 51 outliers final: 32 residues processed: 178 average time/residue: 0.1006 time to fit residues: 28.4877 Evaluate side-chains 164 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 864 SER Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1054 MET Chi-restraints excluded: chain B residue 1121 LYS Chi-restraints excluded: chain B residue 1144 MET Chi-restraints excluded: chain B residue 1222 VAL Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 634 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 129 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 175 optimal weight: 20.0000 chunk 169 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 176 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 148 optimal weight: 0.4980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.109353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.083730 restraints weight = 37338.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.083046 restraints weight = 32027.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.083310 restraints weight = 28170.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.083833 restraints weight = 24988.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.084128 restraints weight = 22541.932| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14992 Z= 0.185 Angle : 0.594 11.739 20300 Z= 0.301 Chirality : 0.045 0.461 2251 Planarity : 0.003 0.044 2564 Dihedral : 8.297 106.124 2120 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.38 % Allowed : 26.68 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.20), residues: 1784 helix: 1.66 (0.19), residues: 720 sheet: -0.23 (0.34), residues: 231 loop : -0.96 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 416 TYR 0.015 0.001 TYR B1030 PHE 0.026 0.002 PHE A 398 TRP 0.020 0.001 TRP A 276 HIS 0.005 0.001 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00425 (14981) covalent geometry : angle 0.58188 (20269) SS BOND : bond 0.00220 ( 2) SS BOND : angle 0.96881 ( 4) hydrogen bonds : bond 0.04407 ( 676) hydrogen bonds : angle 4.39477 ( 1944) link_ALPHA1-3 : bond 0.01083 ( 1) link_ALPHA1-3 : angle 2.77144 ( 3) link_ALPHA1-6 : bond 0.01622 ( 1) link_ALPHA1-6 : angle 2.37380 ( 3) link_BETA1-4 : bond 0.00684 ( 2) link_BETA1-4 : angle 0.93938 ( 6) link_BETA1-6 : bond 0.01176 ( 2) link_BETA1-6 : angle 2.81683 ( 6) link_NAG-ASN : bond 0.00560 ( 3) link_NAG-ASN : angle 4.65082 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 133 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: B 197 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7421 (tm-30) REVERT: B 330 LYS cc_start: 0.8927 (mmmt) cc_final: 0.8628 (mmmt) REVERT: B 530 LEU cc_start: 0.9099 (mt) cc_final: 0.8825 (tt) REVERT: B 1113 MET cc_start: 0.9287 (mmm) cc_final: 0.8991 (mmm) REVERT: A 99 MET cc_start: 0.4655 (tpp) cc_final: 0.4404 (tpp) REVERT: A 124 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8323 (p) REVERT: A 155 TYR cc_start: 0.6623 (OUTLIER) cc_final: 0.5894 (t80) REVERT: A 267 MET cc_start: 0.5583 (mpp) cc_final: 0.4781 (mpp) REVERT: A 291 MET cc_start: 0.5801 (tpp) cc_final: 0.4887 (ttp) REVERT: A 297 MET cc_start: 0.6348 (tpt) cc_final: 0.5023 (ttp) REVERT: A 315 MET cc_start: 0.3128 (tmm) cc_final: 0.0176 (mtt) REVERT: A 400 MET cc_start: 0.4142 (OUTLIER) cc_final: 0.3807 (tmm) REVERT: A 414 MET cc_start: 0.8722 (mmm) cc_final: 0.8302 (mmm) REVERT: A 434 HIS cc_start: 0.6793 (OUTLIER) cc_final: 0.5844 (m-70) REVERT: A 436 TYR cc_start: 0.7477 (m-10) cc_final: 0.6981 (m-10) REVERT: A 481 ASP cc_start: 0.8181 (t0) cc_final: 0.7776 (t70) outliers start: 54 outliers final: 41 residues processed: 176 average time/residue: 0.0970 time to fit residues: 27.6317 Evaluate side-chains 170 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 124 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 864 SER Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1121 LYS Chi-restraints excluded: chain B residue 1144 MET Chi-restraints excluded: chain B residue 1222 VAL Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 658 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 18 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 152 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 160 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.109256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.084344 restraints weight = 37270.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.082977 restraints weight = 29947.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.083490 restraints weight = 29402.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.083881 restraints weight = 24619.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.084024 restraints weight = 22270.166| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14992 Z= 0.171 Angle : 0.600 12.665 20300 Z= 0.299 Chirality : 0.044 0.459 2251 Planarity : 0.003 0.045 2564 Dihedral : 7.923 103.823 2120 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.51 % Allowed : 26.86 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.20), residues: 1784 helix: 1.68 (0.19), residues: 720 sheet: -0.26 (0.33), residues: 237 loop : -0.95 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 416 TYR 0.015 0.001 TYR B 612 PHE 0.020 0.001 PHE A 226 TRP 0.033 0.001 TRP A 276 HIS 0.005 0.001 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00391 (14981) covalent geometry : angle 0.58822 (20269) SS BOND : bond 0.00217 ( 2) SS BOND : angle 0.95314 ( 4) hydrogen bonds : bond 0.04330 ( 676) hydrogen bonds : angle 4.39295 ( 1944) link_ALPHA1-3 : bond 0.01091 ( 1) link_ALPHA1-3 : angle 2.53354 ( 3) link_ALPHA1-6 : bond 0.01852 ( 1) link_ALPHA1-6 : angle 2.60823 ( 3) link_BETA1-4 : bond 0.00727 ( 2) link_BETA1-4 : angle 0.92408 ( 6) link_BETA1-6 : bond 0.01335 ( 2) link_BETA1-6 : angle 2.78923 ( 6) link_NAG-ASN : bond 0.00567 ( 3) link_NAG-ASN : angle 4.66358 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 137 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 197 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7408 (tm-30) REVERT: B 330 LYS cc_start: 0.8895 (mmmt) cc_final: 0.8348 (mmmt) REVERT: B 530 LEU cc_start: 0.9125 (mt) cc_final: 0.8851 (tt) REVERT: B 1113 MET cc_start: 0.9286 (mmm) cc_final: 0.9009 (mmm) REVERT: A 99 MET cc_start: 0.4547 (tpp) cc_final: 0.4333 (tpp) REVERT: A 155 TYR cc_start: 0.6647 (OUTLIER) cc_final: 0.5975 (t80) REVERT: A 253 MET cc_start: 0.6751 (tpp) cc_final: 0.6500 (tpp) REVERT: A 267 MET cc_start: 0.5641 (mpp) cc_final: 0.4896 (mpp) REVERT: A 291 MET cc_start: 0.5884 (tpp) cc_final: 0.4947 (ttp) REVERT: A 297 MET cc_start: 0.6387 (tpt) cc_final: 0.4961 (ttp) REVERT: A 315 MET cc_start: 0.3092 (tmm) cc_final: 0.0161 (mtt) REVERT: A 400 MET cc_start: 0.4305 (OUTLIER) cc_final: 0.4059 (tmm) REVERT: A 410 TRP cc_start: 0.6827 (t60) cc_final: 0.6457 (t60) REVERT: A 414 MET cc_start: 0.8720 (mmm) cc_final: 0.8278 (mmm) REVERT: A 434 HIS cc_start: 0.6777 (OUTLIER) cc_final: 0.6465 (m-70) REVERT: A 481 ASP cc_start: 0.8152 (t0) cc_final: 0.7781 (t70) REVERT: A 490 LYS cc_start: 0.8637 (mmmm) cc_final: 0.7886 (mmtm) outliers start: 56 outliers final: 42 residues processed: 184 average time/residue: 0.1092 time to fit residues: 31.5587 Evaluate side-chains 170 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 124 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 864 SER Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1054 MET Chi-restraints excluded: chain B residue 1121 LYS Chi-restraints excluded: chain B residue 1144 MET Chi-restraints excluded: chain B residue 1222 VAL Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 596 GLN Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 634 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 76 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 177 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 108 optimal weight: 0.2980 chunk 167 optimal weight: 3.9990 chunk 138 optimal weight: 0.0470 chunk 122 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 overall best weight: 0.5882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 ASN A 235 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.110152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.085635 restraints weight = 37456.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.085057 restraints weight = 29022.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.085497 restraints weight = 27015.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.086043 restraints weight = 22260.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.086102 restraints weight = 19556.488| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14992 Z= 0.123 Angle : 0.582 11.578 20300 Z= 0.289 Chirality : 0.043 0.455 2251 Planarity : 0.003 0.044 2564 Dihedral : 7.309 100.154 2120 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.63 % Allowed : 27.86 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.20), residues: 1784 helix: 1.82 (0.19), residues: 719 sheet: -0.23 (0.33), residues: 241 loop : -0.89 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 416 TYR 0.014 0.001 TYR B1030 PHE 0.019 0.001 PHE A 226 TRP 0.035 0.001 TRP A 276 HIS 0.005 0.001 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00272 (14981) covalent geometry : angle 0.57037 (20269) SS BOND : bond 0.00270 ( 2) SS BOND : angle 0.91005 ( 4) hydrogen bonds : bond 0.04000 ( 676) hydrogen bonds : angle 4.29190 ( 1944) link_ALPHA1-3 : bond 0.01035 ( 1) link_ALPHA1-3 : angle 2.17939 ( 3) link_ALPHA1-6 : bond 0.02049 ( 1) link_ALPHA1-6 : angle 2.75164 ( 3) link_BETA1-4 : bond 0.00709 ( 2) link_BETA1-4 : angle 0.90798 ( 6) link_BETA1-6 : bond 0.01526 ( 2) link_BETA1-6 : angle 2.49419 ( 6) link_NAG-ASN : bond 0.00663 ( 3) link_NAG-ASN : angle 4.61760 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 131 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 330 LYS cc_start: 0.8825 (mmmt) cc_final: 0.8323 (mmmt) REVERT: B 530 LEU cc_start: 0.9102 (mt) cc_final: 0.8820 (tt) REVERT: B 1113 MET cc_start: 0.9250 (mmm) cc_final: 0.8302 (mmt) REVERT: A 124 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8251 (p) REVERT: A 155 TYR cc_start: 0.6590 (OUTLIER) cc_final: 0.6034 (t80) REVERT: A 267 MET cc_start: 0.5539 (mpp) cc_final: 0.4839 (mpp) REVERT: A 291 MET cc_start: 0.5799 (tpp) cc_final: 0.4967 (ttp) REVERT: A 297 MET cc_start: 0.6308 (tpt) cc_final: 0.4976 (ttp) REVERT: A 311 ASP cc_start: 0.3114 (OUTLIER) cc_final: 0.2388 (p0) REVERT: A 315 MET cc_start: 0.3154 (tmm) cc_final: 0.0236 (mtt) REVERT: A 400 MET cc_start: 0.4357 (OUTLIER) cc_final: 0.4021 (tmm) REVERT: A 410 TRP cc_start: 0.6652 (t60) cc_final: 0.6393 (t60) REVERT: A 414 MET cc_start: 0.8730 (mmm) cc_final: 0.8387 (mmm) REVERT: A 416 ARG cc_start: 0.6977 (mmm160) cc_final: 0.6259 (tmm-80) REVERT: A 434 HIS cc_start: 0.6755 (OUTLIER) cc_final: 0.5844 (m-70) REVERT: A 436 TYR cc_start: 0.7416 (m-10) cc_final: 0.6974 (m-10) REVERT: A 481 ASP cc_start: 0.8045 (t0) cc_final: 0.7669 (t70) outliers start: 42 outliers final: 32 residues processed: 167 average time/residue: 0.0982 time to fit residues: 26.2960 Evaluate side-chains 165 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 864 SER Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1121 LYS Chi-restraints excluded: chain B residue 1222 VAL Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 596 GLN Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 634 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 26 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 chunk 54 optimal weight: 0.0030 chunk 46 optimal weight: 0.8980 chunk 96 optimal weight: 0.4980 chunk 89 optimal weight: 0.6980 chunk 156 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.110570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.085795 restraints weight = 37310.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.085104 restraints weight = 30640.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.085672 restraints weight = 25932.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.085847 restraints weight = 22026.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.087471 restraints weight = 20092.410| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14992 Z= 0.121 Angle : 0.576 11.401 20300 Z= 0.287 Chirality : 0.043 0.444 2251 Planarity : 0.003 0.043 2564 Dihedral : 6.743 96.167 2117 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.25 % Allowed : 28.30 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.20), residues: 1784 helix: 1.82 (0.20), residues: 723 sheet: -0.18 (0.33), residues: 242 loop : -0.86 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 416 TYR 0.018 0.001 TYR B 612 PHE 0.017 0.001 PHE A 226 TRP 0.040 0.001 TRP A 276 HIS 0.005 0.001 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00266 (14981) covalent geometry : angle 0.56540 (20269) SS BOND : bond 0.00264 ( 2) SS BOND : angle 0.81917 ( 4) hydrogen bonds : bond 0.03892 ( 676) hydrogen bonds : angle 4.27679 ( 1944) link_ALPHA1-3 : bond 0.01044 ( 1) link_ALPHA1-3 : angle 2.10269 ( 3) link_ALPHA1-6 : bond 0.02348 ( 1) link_ALPHA1-6 : angle 2.82734 ( 3) link_BETA1-4 : bond 0.00720 ( 2) link_BETA1-4 : angle 0.88289 ( 6) link_BETA1-6 : bond 0.01663 ( 2) link_BETA1-6 : angle 2.35627 ( 6) link_NAG-ASN : bond 0.00677 ( 3) link_NAG-ASN : angle 4.52052 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 LYS cc_start: 0.8790 (mmmt) cc_final: 0.8327 (mmmt) REVERT: B 530 LEU cc_start: 0.9078 (mt) cc_final: 0.8799 (tt) REVERT: B 1113 MET cc_start: 0.9248 (mmm) cc_final: 0.8374 (mmt) REVERT: B 1239 LEU cc_start: 0.9088 (tp) cc_final: 0.8756 (tp) REVERT: A 155 TYR cc_start: 0.6624 (OUTLIER) cc_final: 0.5996 (t80) REVERT: A 267 MET cc_start: 0.5586 (mpp) cc_final: 0.4914 (mpp) REVERT: A 291 MET cc_start: 0.5847 (tpp) cc_final: 0.5035 (ttp) REVERT: A 297 MET cc_start: 0.6346 (tpt) cc_final: 0.5012 (ttp) REVERT: A 311 ASP cc_start: 0.3136 (OUTLIER) cc_final: 0.2452 (p0) REVERT: A 315 MET cc_start: 0.2968 (tmm) cc_final: 0.0216 (mtt) REVERT: A 400 MET cc_start: 0.4342 (OUTLIER) cc_final: 0.3976 (tmm) REVERT: A 410 TRP cc_start: 0.6591 (t60) cc_final: 0.6358 (t60) REVERT: A 414 MET cc_start: 0.8694 (mmm) cc_final: 0.8286 (mmm) REVERT: A 434 HIS cc_start: 0.6798 (OUTLIER) cc_final: 0.6483 (m-70) REVERT: A 481 ASP cc_start: 0.7942 (t0) cc_final: 0.7580 (t70) REVERT: A 658 LEU cc_start: 0.3786 (pp) cc_final: 0.2943 (mt) outliers start: 36 outliers final: 27 residues processed: 165 average time/residue: 0.0982 time to fit residues: 26.2925 Evaluate side-chains 161 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 864 SER Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1121 LYS Chi-restraints excluded: chain B residue 1222 VAL Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 596 GLN Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 634 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 129 optimal weight: 8.9990 chunk 68 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 177 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.109374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.084729 restraints weight = 37320.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.083877 restraints weight = 29564.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.084653 restraints weight = 26601.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.085091 restraints weight = 22132.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.085066 restraints weight = 20056.443| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14992 Z= 0.159 Angle : 0.601 11.764 20300 Z= 0.301 Chirality : 0.044 0.442 2251 Planarity : 0.003 0.042 2564 Dihedral : 6.570 96.649 2117 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.44 % Allowed : 28.24 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.20), residues: 1784 helix: 1.72 (0.20), residues: 724 sheet: -0.24 (0.34), residues: 232 loop : -0.88 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 416 TYR 0.014 0.001 TYR B1030 PHE 0.030 0.001 PHE A 398 TRP 0.047 0.002 TRP A 276 HIS 0.005 0.001 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00365 (14981) covalent geometry : angle 0.59086 (20269) SS BOND : bond 0.00222 ( 2) SS BOND : angle 0.89582 ( 4) hydrogen bonds : bond 0.04096 ( 676) hydrogen bonds : angle 4.37019 ( 1944) link_ALPHA1-3 : bond 0.00975 ( 1) link_ALPHA1-3 : angle 2.29371 ( 3) link_ALPHA1-6 : bond 0.02466 ( 1) link_ALPHA1-6 : angle 2.80941 ( 3) link_BETA1-4 : bond 0.00707 ( 2) link_BETA1-4 : angle 0.79753 ( 6) link_BETA1-6 : bond 0.01426 ( 2) link_BETA1-6 : angle 2.28774 ( 6) link_NAG-ASN : bond 0.00562 ( 3) link_NAG-ASN : angle 4.48506 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 LYS cc_start: 0.8832 (mmmt) cc_final: 0.8343 (mmmt) REVERT: B 530 LEU cc_start: 0.9130 (mt) cc_final: 0.8714 (tt) REVERT: B 1113 MET cc_start: 0.9249 (mmm) cc_final: 0.9004 (mmm) REVERT: A 155 TYR cc_start: 0.6666 (OUTLIER) cc_final: 0.6153 (t80) REVERT: A 253 MET cc_start: 0.6691 (tpp) cc_final: 0.6460 (tpp) REVERT: A 267 MET cc_start: 0.5643 (mpp) cc_final: 0.4990 (mpp) REVERT: A 291 MET cc_start: 0.5946 (tpp) cc_final: 0.5047 (ttp) REVERT: A 297 MET cc_start: 0.6344 (tpt) cc_final: 0.5028 (ttp) REVERT: A 315 MET cc_start: 0.3042 (tmm) cc_final: 0.0166 (mtt) REVERT: A 400 MET cc_start: 0.4511 (OUTLIER) cc_final: 0.4150 (tmm) REVERT: A 414 MET cc_start: 0.8714 (mmm) cc_final: 0.8165 (mmp) REVERT: A 416 ARG cc_start: 0.7086 (mmm160) cc_final: 0.6291 (tmm-80) REVERT: A 434 HIS cc_start: 0.6788 (OUTLIER) cc_final: 0.6477 (m-70) REVERT: A 481 ASP cc_start: 0.8054 (t0) cc_final: 0.7750 (t70) REVERT: A 658 LEU cc_start: 0.3770 (pp) cc_final: 0.2910 (mt) outliers start: 39 outliers final: 34 residues processed: 162 average time/residue: 0.0964 time to fit residues: 25.1631 Evaluate side-chains 162 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 864 SER Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1054 MET Chi-restraints excluded: chain B residue 1121 LYS Chi-restraints excluded: chain B residue 1222 VAL Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 596 GLN Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 634 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 67 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 97 optimal weight: 0.0020 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.109666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.085634 restraints weight = 37118.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.083685 restraints weight = 32373.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.084188 restraints weight = 28639.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.085212 restraints weight = 23986.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.085139 restraints weight = 20235.030| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14992 Z= 0.143 Angle : 0.594 11.336 20300 Z= 0.297 Chirality : 0.044 0.441 2251 Planarity : 0.003 0.043 2564 Dihedral : 6.433 96.179 2117 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.44 % Allowed : 28.55 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.20), residues: 1784 helix: 1.77 (0.20), residues: 725 sheet: -0.26 (0.33), residues: 244 loop : -0.83 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 416 TYR 0.020 0.001 TYR B 612 PHE 0.020 0.001 PHE A 226 TRP 0.049 0.002 TRP A 276 HIS 0.005 0.001 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00325 (14981) covalent geometry : angle 0.58333 (20269) SS BOND : bond 0.00232 ( 2) SS BOND : angle 0.89883 ( 4) hydrogen bonds : bond 0.04055 ( 676) hydrogen bonds : angle 4.33635 ( 1944) link_ALPHA1-3 : bond 0.00984 ( 1) link_ALPHA1-3 : angle 2.20041 ( 3) link_ALPHA1-6 : bond 0.02592 ( 1) link_ALPHA1-6 : angle 2.95648 ( 3) link_BETA1-4 : bond 0.00590 ( 2) link_BETA1-4 : angle 0.78697 ( 6) link_BETA1-6 : bond 0.01336 ( 2) link_BETA1-6 : angle 2.23760 ( 6) link_NAG-ASN : bond 0.00609 ( 3) link_NAG-ASN : angle 4.47384 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2576.39 seconds wall clock time: 45 minutes 30.92 seconds (2730.92 seconds total)