Starting phenix.real_space_refine on Tue May 20 14:24:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f2j_50147/05_2025/9f2j_50147.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f2j_50147/05_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_50147/05_2025/9f2j_50147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f2j_50147/05_2025/9f2j_50147.map" model { file = "/net/cci-nas-00/data/ceres_data/9f2j_50147/05_2025/9f2j_50147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f2j_50147/05_2025/9f2j_50147.cif" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 11.37, per 1000 atoms: 0.78 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: 4.28 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.66 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: 5.90 Time building geometry restraints manager: 4.90 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: 18.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.010 Extract box with map and model: 0.740 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 38.450 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.630 ------------------------------------------------------------------------------- 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 : 10.89 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (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 TRP 0.015 0.001 TRP B1266 HIS 0.004 0.001 HIS B 223 PHE 0.062 0.002 PHE A 273 TYR 0.019 0.001 TYR B 751 ARG 0.006 0.000 ARG A 174 Details of bonding type rmsd link_NAG-ASN : bond 0.18501 ( 3) link_NAG-ASN : angle 7.95975 ( 9) 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_ALPHA1-3 : bond 0.04028 ( 1) link_ALPHA1-3 : angle 5.13463 ( 3) hydrogen bonds : bond 0.13603 ( 676) hydrogen bonds : angle 5.69418 ( 1944) link_BETA1-6 : bond 0.02682 ( 2) link_BETA1-6 : angle 3.15546 ( 6) SS BOND : bond 0.00478 ( 2) SS BOND : angle 2.77898 ( 4) covalent geometry : bond 0.00448 (14981) covalent geometry : angle 0.67474 (20269) *********************** 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 : 1.598 Fit side-chains revert: symmetry clash 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: 0.7474 (tt0) REVERT: B 197 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7798 (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: 0.8289 (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: 0.7429 (mtm110) REVERT: B 1041 ILE cc_start: 0.8857 (pt) cc_final: 0.8410 (mt) REVERT: A 122 ASP cc_start: 0.4806 (t70) cc_final: 0.4123 (t0) REVERT: A 291 MET cc_start: 0.3647 (OUTLIER) cc_final: 0.2778 (ttp) REVERT: A 453 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7320 (mppt) REVERT: A 511 ASN cc_start: 0.7874 (m-40) cc_final: 0.7561 (p0) outliers start: 19 outliers final: 3 residues processed: 257 average time/residue: 0.2668 time to fit residues: 102.1052 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 : 1.724 ------------------------------------------------------------------------------- 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 151 optimal weight: 7.9990 chunk 135 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 319 GLN ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 GLN A 507 HIS ** 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 = 0.3663 r_free = 0.3663 target = 0.111455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.084472 restraints weight = 37144.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.082607 restraints weight = 33255.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.083332 restraints weight = 29161.746| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14992 Z= 0.235 Angle : 0.688 12.493 20300 Z= 0.350 Chirality : 0.048 0.523 2251 Planarity : 0.004 0.053 2564 Dihedral : 11.657 123.707 2134 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.32 % Allowed : 25.67 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.20), residues: 1784 helix: 1.61 (0.20), residues: 722 sheet: -0.34 (0.33), residues: 231 loop : -0.98 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 263 HIS 0.005 0.002 HIS B1064 PHE 0.015 0.002 PHE A 188 TYR 0.018 0.002 TYR A 618 ARG 0.005 0.001 ARG A 174 Details of bonding type rmsd link_NAG-ASN : bond 0.00954 ( 3) link_NAG-ASN : angle 5.29328 ( 9) link_ALPHA1-6 : bond 0.00490 ( 1) link_ALPHA1-6 : angle 2.81969 ( 3) link_BETA1-4 : bond 0.01282 ( 2) link_BETA1-4 : angle 1.95036 ( 6) link_ALPHA1-3 : bond 0.01141 ( 1) link_ALPHA1-3 : angle 5.06959 ( 3) hydrogen bonds : bond 0.05217 ( 676) hydrogen bonds : angle 4.57484 ( 1944) link_BETA1-6 : bond 0.01116 ( 2) link_BETA1-6 : angle 3.23718 ( 6) SS BOND : bond 0.00366 ( 2) SS BOND : angle 1.03671 ( 4) covalent geometry : bond 0.00538 (14981) covalent geometry : angle 0.67239 (20269) *********************** 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 231 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 162 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 197 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7810 (tm-30) REVERT: B 530 LEU cc_start: 0.9130 (mt) cc_final: 0.8863 (tt) REVERT: B 808 LEU cc_start: 0.9232 (mt) cc_final: 0.9026 (mt) REVERT: B 1041 ILE cc_start: 0.8931 (pt) cc_final: 0.8572 (mt) REVERT: B 1113 MET cc_start: 0.9356 (mmm) cc_final: 0.8979 (mmm) REVERT: A 253 MET cc_start: 0.6463 (tpp) cc_final: 0.6002 (tpp) REVERT: A 257 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7506 (tt) REVERT: A 276 TRP cc_start: 0.6566 (p-90) cc_final: 0.6208 (p-90) REVERT: A 291 MET cc_start: 0.6029 (OUTLIER) cc_final: 0.4335 (ttp) REVERT: A 311 ASP cc_start: 0.2733 (OUTLIER) cc_final: 0.2293 (p0) REVERT: A 370 ILE cc_start: 0.1150 (OUTLIER) cc_final: 0.0708 (pt) REVERT: A 414 MET cc_start: 0.8440 (mmm) cc_final: 0.7939 (mmm) outliers start: 69 outliers final: 25 residues processed: 220 average time/residue: 0.2277 time to fit residues: 78.5808 Evaluate side-chains 162 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 1.623 ------------------------------------------------------------------------------- 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 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 223 PHE 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 31 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.109179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.082963 restraints weight = 37455.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.082270 restraints weight = 32480.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.082729 restraints weight = 28930.938| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 14992 Z= 0.242 Angle : 0.649 12.940 20300 Z= 0.333 Chirality : 0.046 0.491 2251 Planarity : 0.004 0.049 2564 Dihedral : 9.738 113.709 2125 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.38 % Allowed : 25.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.20), residues: 1784 helix: 1.43 (0.19), residues: 726 sheet: -0.46 (0.33), residues: 230 loop : -1.05 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 263 HIS 0.005 0.002 HIS B 269 PHE 0.027 0.002 PHE A 411 TYR 0.015 0.001 TYR B1030 ARG 0.003 0.001 ARG A 174 Details of bonding type rmsd link_NAG-ASN : bond 0.00746 ( 3) link_NAG-ASN : angle 5.11366 ( 9) link_ALPHA1-6 : bond 0.00529 ( 1) link_ALPHA1-6 : angle 2.04526 ( 3) link_BETA1-4 : bond 0.00766 ( 2) link_BETA1-4 : angle 1.39515 ( 6) link_ALPHA1-3 : bond 0.00951 ( 1) link_ALPHA1-3 : angle 3.14766 ( 3) hydrogen bonds : bond 0.05060 ( 676) hydrogen bonds : angle 4.57933 ( 1944) link_BETA1-6 : bond 0.01545 ( 2) link_BETA1-6 : angle 3.30204 ( 6) SS BOND : bond 0.00113 ( 2) SS BOND : angle 1.08513 ( 4) covalent geometry : bond 0.00555 (14981) covalent geometry : angle 0.63558 (20269) *********************** 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 211 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 141 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 197 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: B 330 LYS cc_start: 0.8980 (mmmt) cc_final: 0.8508 (mmmt) REVERT: B 530 LEU cc_start: 0.9137 (mt) cc_final: 0.8884 (tt) REVERT: B 808 LEU cc_start: 0.9246 (mt) cc_final: 0.9036 (mt) REVERT: B 1113 MET cc_start: 0.9331 (mmm) cc_final: 0.9055 (mmm) REVERT: A 124 VAL cc_start: 0.8700 (OUTLIER) cc_final: 0.8477 (p) REVERT: A 153 ILE cc_start: 0.6452 (mm) cc_final: 0.6023 (tp) REVERT: A 253 MET cc_start: 0.6608 (tpp) cc_final: 0.6270 (tpp) REVERT: A 291 MET cc_start: 0.5626 (tpp) cc_final: 0.4181 (tmm) REVERT: A 292 VAL cc_start: 0.6745 (t) cc_final: 0.6495 (t) REVERT: A 307 MET cc_start: 0.2840 (ptm) cc_final: 0.2561 (ptm) REVERT: A 434 HIS cc_start: 0.6795 (OUTLIER) cc_final: 0.6461 (m-70) outliers start: 70 outliers final: 41 residues processed: 198 average time/residue: 0.2184 time to fit residues: 68.3993 Evaluate side-chains 170 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 126 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ILE 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 307 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 714 VAL Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 886 ASN Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 1020 THR 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 1146 THR Chi-restraints excluded: chain B residue 1174 VAL 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 224 SER Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 245 THR 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 535 ASP 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 644 ILE 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 82 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 chunk 61 optimal weight: 0.0060 chunk 171 optimal weight: 7.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- 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** ** B1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN A 235 HIS A 377 ASN ** A 446 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 = 0.3638 r_free = 0.3638 target = 0.110167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.084459 restraints weight = 37144.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.083020 restraints weight = 30003.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.083854 restraints weight = 29252.159| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14992 Z= 0.146 Angle : 0.583 12.402 20300 Z= 0.297 Chirality : 0.044 0.490 2251 Planarity : 0.003 0.044 2564 Dihedral : 9.096 111.023 2122 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.19 % Allowed : 27.11 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.20), residues: 1784 helix: 1.65 (0.19), residues: 719 sheet: -0.49 (0.32), residues: 243 loop : -0.99 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 263 HIS 0.005 0.001 HIS B 223 PHE 0.016 0.001 PHE B 338 TYR 0.014 0.001 TYR B1030 ARG 0.003 0.000 ARG A 174 Details of bonding type rmsd link_NAG-ASN : bond 0.00715 ( 3) link_NAG-ASN : angle 4.95161 ( 9) link_ALPHA1-6 : bond 0.01387 ( 1) link_ALPHA1-6 : angle 2.06955 ( 3) link_BETA1-4 : bond 0.00607 ( 2) link_BETA1-4 : angle 1.16048 ( 6) link_ALPHA1-3 : bond 0.01105 ( 1) link_ALPHA1-3 : angle 2.95854 ( 3) hydrogen bonds : bond 0.04453 ( 676) hydrogen bonds : angle 4.42013 ( 1944) link_BETA1-6 : bond 0.01284 ( 2) link_BETA1-6 : angle 2.79953 ( 6) SS BOND : bond 0.00234 ( 2) SS BOND : angle 0.95320 ( 4) covalent geometry : bond 0.00327 (14981) covalent geometry : angle 0.57003 (20269) *********************** 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 193 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 142 time to evaluate : 1.837 Fit side-chains revert: symmetry clash REVERT: B 197 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7344 (tm-30) REVERT: B 313 MET cc_start: 0.7208 (tpp) cc_final: 0.6809 (tpp) REVERT: B 330 LYS cc_start: 0.8908 (mmmt) cc_final: 0.8629 (mmmt) REVERT: B 530 LEU cc_start: 0.9114 (mt) cc_final: 0.8854 (tt) REVERT: B 758 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8969 (mm-30) REVERT: B 808 LEU cc_start: 0.9188 (mt) cc_final: 0.8983 (mt) REVERT: B 1113 MET cc_start: 0.9319 (mmm) cc_final: 0.9061 (mmm) REVERT: A 124 VAL cc_start: 0.8663 (OUTLIER) cc_final: 0.8431 (p) REVERT: A 291 MET cc_start: 0.5848 (tpp) cc_final: 0.4691 (ttp) REVERT: A 311 ASP cc_start: 0.3105 (OUTLIER) cc_final: 0.2412 (p0) REVERT: A 400 MET cc_start: 0.3848 (OUTLIER) cc_final: 0.3438 (tmm) REVERT: A 410 TRP cc_start: 0.6936 (t60) cc_final: 0.6626 (t-100) REVERT: A 434 HIS cc_start: 0.6752 (OUTLIER) cc_final: 0.5866 (m-70) REVERT: A 436 TYR cc_start: 0.7470 (m-10) cc_final: 0.7016 (m-10) REVERT: A 481 ASP cc_start: 0.8284 (t0) cc_final: 0.7856 (t70) outliers start: 51 outliers final: 32 residues processed: 184 average time/residue: 0.2267 time to fit residues: 66.7048 Evaluate side-chains 166 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 1.748 ------------------------------------------------------------------------------- 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 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 361 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 758 GLU Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 864 SER Chi-restraints excluded: chain B residue 878 ILE 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 1144 MET Chi-restraints excluded: chain B residue 1222 VAL Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 124 VAL 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 554 ILE Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 644 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 16 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 85 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** ** B1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 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 = 0.109890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.083868 restraints weight = 37469.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.083532 restraints weight = 32559.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.084037 restraints weight = 27122.221| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14992 Z= 0.151 Angle : 0.584 12.096 20300 Z= 0.296 Chirality : 0.044 0.473 2251 Planarity : 0.003 0.049 2564 Dihedral : 8.667 107.795 2120 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.69 % Allowed : 27.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.20), residues: 1784 helix: 1.68 (0.19), residues: 720 sheet: -0.33 (0.33), residues: 237 loop : -1.01 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 263 HIS 0.005 0.001 HIS B 223 PHE 0.020 0.001 PHE A 226 TYR 0.014 0.001 TYR B 612 ARG 0.004 0.000 ARG A 302 Details of bonding type rmsd link_NAG-ASN : bond 0.00656 ( 3) link_NAG-ASN : angle 4.80191 ( 9) link_ALPHA1-6 : bond 0.01514 ( 1) link_ALPHA1-6 : angle 2.27656 ( 3) link_BETA1-4 : bond 0.00650 ( 2) link_BETA1-4 : angle 1.02946 ( 6) link_ALPHA1-3 : bond 0.01153 ( 1) link_ALPHA1-3 : angle 2.67432 ( 3) hydrogen bonds : bond 0.04330 ( 676) hydrogen bonds : angle 4.40926 ( 1944) link_BETA1-6 : bond 0.01265 ( 2) link_BETA1-6 : angle 2.70958 ( 6) SS BOND : bond 0.00218 ( 2) SS BOND : angle 0.92274 ( 4) covalent geometry : bond 0.00342 (14981) covalent geometry : angle 0.57209 (20269) *********************** 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 192 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 133 time to evaluate : 1.740 Fit side-chains revert: symmetry clash REVERT: B 197 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7335 (tm-30) REVERT: B 313 MET cc_start: 0.7107 (tpp) cc_final: 0.6865 (tpp) REVERT: B 330 LYS cc_start: 0.8917 (mmmt) cc_final: 0.8638 (mmmt) REVERT: B 530 LEU cc_start: 0.9099 (mt) cc_final: 0.8847 (tt) REVERT: B 781 MET cc_start: 0.8433 (mmm) cc_final: 0.8042 (mmm) REVERT: A 124 VAL cc_start: 0.8625 (OUTLIER) cc_final: 0.8412 (p) REVERT: A 267 MET cc_start: 0.5468 (mpp) cc_final: 0.4629 (mpp) REVERT: A 291 MET cc_start: 0.5903 (tpp) cc_final: 0.4928 (ttp) REVERT: A 315 MET cc_start: 0.2457 (tmm) cc_final: -0.0056 (mtt) REVERT: A 400 MET cc_start: 0.4070 (tmm) cc_final: 0.3735 (tmm) REVERT: A 410 TRP cc_start: 0.6865 (t60) cc_final: 0.6629 (t-100) REVERT: A 434 HIS cc_start: 0.6734 (OUTLIER) cc_final: 0.5800 (m-70) REVERT: A 436 TYR cc_start: 0.7460 (m-10) cc_final: 0.7044 (m-10) REVERT: A 481 ASP cc_start: 0.8232 (t0) cc_final: 0.7830 (t70) outliers start: 59 outliers final: 45 residues processed: 181 average time/residue: 0.2190 time to fit residues: 63.7046 Evaluate side-chains 173 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 125 time to evaluate : 1.681 ------------------------------------------------------------------------------- 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 130 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 361 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 815 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 1024 LEU 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 93 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 144 SER 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 283 CYS 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 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 644 ILE Chi-restraints excluded: chain A residue 658 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 163 optimal weight: 4.9990 chunk 115 optimal weight: 0.2980 chunk 73 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 ASN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 ASN A 449 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.107782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.082113 restraints weight = 37867.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.081444 restraints weight = 32871.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.082063 restraints weight = 28828.233| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 14992 Z= 0.240 Angle : 0.656 15.018 20300 Z= 0.331 Chirality : 0.046 0.469 2251 Planarity : 0.004 0.053 2564 Dihedral : 8.536 107.475 2120 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.70 % Allowed : 26.42 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.20), residues: 1784 helix: 1.44 (0.19), residues: 720 sheet: -0.44 (0.35), residues: 223 loop : -1.09 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 263 HIS 0.006 0.001 HIS A 93 PHE 0.025 0.002 PHE A 398 TYR 0.015 0.002 TYR B1030 ARG 0.007 0.001 ARG A 302 Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 3) link_NAG-ASN : angle 4.68636 ( 9) link_ALPHA1-6 : bond 0.01594 ( 1) link_ALPHA1-6 : angle 2.36612 ( 3) link_BETA1-4 : bond 0.00968 ( 2) link_BETA1-4 : angle 0.97573 ( 6) link_ALPHA1-3 : bond 0.01099 ( 1) link_ALPHA1-3 : angle 2.96838 ( 3) hydrogen bonds : bond 0.04881 ( 676) hydrogen bonds : angle 4.67300 ( 1944) link_BETA1-6 : bond 0.01225 ( 2) link_BETA1-6 : angle 2.92919 ( 6) SS BOND : bond 0.00209 ( 2) SS BOND : angle 1.11664 ( 4) covalent geometry : bond 0.00557 (14981) covalent geometry : angle 0.64528 (20269) *********************** 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 209 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 134 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 197 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7462 (tm-30) REVERT: B 330 LYS cc_start: 0.8908 (mmmt) cc_final: 0.8611 (mmmt) REVERT: B 530 LEU cc_start: 0.9157 (mt) cc_final: 0.8789 (tt) REVERT: A 124 VAL cc_start: 0.8587 (OUTLIER) cc_final: 0.8355 (p) REVERT: A 267 MET cc_start: 0.5628 (mpp) cc_final: 0.4843 (mpp) REVERT: A 291 MET cc_start: 0.5969 (tpp) cc_final: 0.5046 (ttp) REVERT: A 400 MET cc_start: 0.4476 (OUTLIER) cc_final: 0.4188 (tmm) REVERT: A 410 TRP cc_start: 0.7003 (t60) cc_final: 0.6732 (t-100) REVERT: A 434 HIS cc_start: 0.6791 (OUTLIER) cc_final: 0.6494 (m-70) REVERT: A 481 ASP cc_start: 0.8223 (t0) cc_final: 0.7889 (t70) outliers start: 75 outliers final: 52 residues processed: 198 average time/residue: 0.2294 time to fit residues: 71.2615 Evaluate side-chains 179 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 123 time to evaluate : 1.730 ------------------------------------------------------------------------------- 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 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 361 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 574 GLU Chi-restraints excluded: chain B residue 714 VAL 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 1121 LYS Chi-restraints excluded: chain B residue 1144 MET Chi-restraints excluded: chain B residue 1146 THR Chi-restraints excluded: chain B residue 1174 VAL Chi-restraints excluded: chain B residue 1222 VAL Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain B residue 1287 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 283 CYS 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 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 644 ILE 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 131 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 174 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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** ** B1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.108096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.083049 restraints weight = 37720.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.081211 restraints weight = 33838.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.081784 restraints weight = 30416.708| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14992 Z= 0.188 Angle : 0.615 12.239 20300 Z= 0.310 Chirality : 0.045 0.483 2251 Planarity : 0.003 0.054 2564 Dihedral : 7.995 104.330 2120 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.01 % Allowed : 27.36 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.20), residues: 1784 helix: 1.52 (0.19), residues: 719 sheet: -0.44 (0.34), residues: 223 loop : -1.06 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 276 HIS 0.005 0.001 HIS B 223 PHE 0.033 0.001 PHE A 411 TYR 0.015 0.001 TYR B1030 ARG 0.009 0.000 ARG B 996 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 3) link_NAG-ASN : angle 4.77062 ( 9) link_ALPHA1-6 : bond 0.01935 ( 1) link_ALPHA1-6 : angle 2.62120 ( 3) link_BETA1-4 : bond 0.00680 ( 2) link_BETA1-4 : angle 0.89868 ( 6) link_ALPHA1-3 : bond 0.01081 ( 1) link_ALPHA1-3 : angle 2.58492 ( 3) hydrogen bonds : bond 0.04527 ( 676) hydrogen bonds : angle 4.56970 ( 1944) link_BETA1-6 : bond 0.01268 ( 2) link_BETA1-6 : angle 2.88313 ( 6) SS BOND : bond 0.00224 ( 2) SS BOND : angle 1.04564 ( 4) covalent geometry : bond 0.00433 (14981) covalent geometry : angle 0.60347 (20269) *********************** 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 199 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 135 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 197 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7361 (tm-30) REVERT: B 330 LYS cc_start: 0.8877 (mmmt) cc_final: 0.8300 (mmmt) REVERT: B 530 LEU cc_start: 0.9184 (mt) cc_final: 0.8809 (tt) REVERT: A 124 VAL cc_start: 0.8436 (OUTLIER) cc_final: 0.8156 (p) REVERT: A 267 MET cc_start: 0.5867 (mpp) cc_final: 0.5180 (mpp) REVERT: A 291 MET cc_start: 0.6286 (tpp) cc_final: 0.5309 (ttp) REVERT: A 315 MET cc_start: 0.2522 (tmm) cc_final: -0.0011 (mtt) REVERT: A 400 MET cc_start: 0.4358 (OUTLIER) cc_final: 0.4003 (tmm) REVERT: A 410 TRP cc_start: 0.6952 (t60) cc_final: 0.6632 (t-100) REVERT: A 434 HIS cc_start: 0.6728 (OUTLIER) cc_final: 0.6420 (m-70) REVERT: A 481 ASP cc_start: 0.8237 (t0) cc_final: 0.7911 (t70) outliers start: 64 outliers final: 46 residues processed: 187 average time/residue: 0.2202 time to fit residues: 64.8347 Evaluate side-chains 175 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 125 time to evaluate : 1.555 ------------------------------------------------------------------------------- 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 361 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 554 LEU 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 1020 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 144 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 283 CYS 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 644 ILE Chi-restraints excluded: chain A residue 658 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 177 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 116 optimal weight: 0.0980 chunk 37 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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** ** B1199 GLN ** 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 = 0.3604 r_free = 0.3604 target = 0.108167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.083446 restraints weight = 37335.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.082028 restraints weight = 30599.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.082342 restraints weight = 27990.908| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4016 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= 0.178 Angle : 0.614 11.961 20300 Z= 0.310 Chirality : 0.045 0.466 2251 Planarity : 0.003 0.053 2564 Dihedral : 7.446 101.934 2120 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.13 % Allowed : 27.61 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.20), residues: 1784 helix: 1.50 (0.19), residues: 723 sheet: -0.44 (0.34), residues: 223 loop : -1.01 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 276 HIS 0.005 0.001 HIS B 223 PHE 0.017 0.001 PHE A 398 TYR 0.015 0.001 TYR B1030 ARG 0.006 0.000 ARG B 996 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 3) link_NAG-ASN : angle 4.64045 ( 9) link_ALPHA1-6 : bond 0.02110 ( 1) link_ALPHA1-6 : angle 2.66941 ( 3) link_BETA1-4 : bond 0.00662 ( 2) link_BETA1-4 : angle 0.87404 ( 6) link_ALPHA1-3 : bond 0.01097 ( 1) link_ALPHA1-3 : angle 2.47195 ( 3) hydrogen bonds : bond 0.04462 ( 676) hydrogen bonds : angle 4.56720 ( 1944) link_BETA1-6 : bond 0.01499 ( 2) link_BETA1-6 : angle 2.68634 ( 6) SS BOND : bond 0.00243 ( 2) SS BOND : angle 1.04210 ( 4) covalent geometry : bond 0.00408 (14981) covalent geometry : angle 0.60245 (20269) *********************** 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 198 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 132 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 LYS cc_start: 0.8886 (mmmt) cc_final: 0.8289 (mmmt) REVERT: B 530 LEU cc_start: 0.9188 (mt) cc_final: 0.8822 (tt) REVERT: A 124 VAL cc_start: 0.8373 (OUTLIER) cc_final: 0.8128 (p) REVERT: A 155 TYR cc_start: 0.6249 (OUTLIER) cc_final: 0.5117 (t80) REVERT: A 253 MET cc_start: 0.6429 (tpp) cc_final: 0.6110 (tpp) REVERT: A 267 MET cc_start: 0.5926 (mpp) cc_final: 0.5242 (mpp) REVERT: A 291 MET cc_start: 0.6249 (tpp) cc_final: 0.5330 (ttp) REVERT: A 315 MET cc_start: 0.2447 (tmm) cc_final: -0.0033 (mtt) REVERT: A 400 MET cc_start: 0.4325 (OUTLIER) cc_final: 0.3964 (tmm) REVERT: A 410 TRP cc_start: 0.6941 (t60) cc_final: 0.6643 (t-100) REVERT: A 416 ARG cc_start: 0.6737 (mmm160) cc_final: 0.6510 (mmm160) REVERT: A 434 HIS cc_start: 0.6747 (OUTLIER) cc_final: 0.6429 (m-70) REVERT: A 460 THR cc_start: 0.8999 (m) cc_final: 0.8632 (p) REVERT: A 481 ASP cc_start: 0.8225 (t0) cc_final: 0.7910 (t70) outliers start: 66 outliers final: 52 residues processed: 186 average time/residue: 0.2619 time to fit residues: 76.3162 Evaluate side-chains 180 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 124 time to evaluate : 1.623 ------------------------------------------------------------------------------- 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 100 SER 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 208 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 276 SER 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 361 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 554 LEU Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 864 SER Chi-restraints excluded: chain B residue 886 ASN 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 1020 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 144 SER 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 283 CYS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 316 ILE 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 644 ILE Chi-restraints excluded: chain A residue 658 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 169 optimal weight: 5.9990 chunk 89 optimal weight: 0.4980 chunk 98 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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** ** B1199 GLN ** 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 = 0.3596 r_free = 0.3596 target = 0.107770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.083292 restraints weight = 37444.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.081823 restraints weight = 32029.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.082303 restraints weight = 29370.329| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14992 Z= 0.189 Angle : 0.631 11.980 20300 Z= 0.318 Chirality : 0.045 0.466 2251 Planarity : 0.003 0.053 2564 Dihedral : 7.042 100.260 2117 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.94 % Allowed : 27.61 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.20), residues: 1784 helix: 1.47 (0.19), residues: 726 sheet: -0.51 (0.34), residues: 229 loop : -1.03 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 276 HIS 0.005 0.001 HIS B 223 PHE 0.019 0.001 PHE A 188 TYR 0.017 0.001 TYR B 612 ARG 0.007 0.000 ARG A 174 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 3) link_NAG-ASN : angle 4.62730 ( 9) link_ALPHA1-6 : bond 0.02443 ( 1) link_ALPHA1-6 : angle 2.71696 ( 3) link_BETA1-4 : bond 0.00669 ( 2) link_BETA1-4 : angle 0.85460 ( 6) link_ALPHA1-3 : bond 0.01047 ( 1) link_ALPHA1-3 : angle 2.46352 ( 3) hydrogen bonds : bond 0.04486 ( 676) hydrogen bonds : angle 4.60383 ( 1944) link_BETA1-6 : bond 0.01451 ( 2) link_BETA1-6 : angle 2.48166 ( 6) SS BOND : bond 0.00228 ( 2) SS BOND : angle 1.03331 ( 4) covalent geometry : bond 0.00434 (14981) covalent geometry : angle 0.62025 (20269) *********************** 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 188 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 125 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 LYS cc_start: 0.8892 (mmmt) cc_final: 0.8293 (mmmt) REVERT: B 530 LEU cc_start: 0.9180 (mt) cc_final: 0.8815 (tt) REVERT: A 152 MET cc_start: 0.6404 (tpt) cc_final: 0.6061 (mmt) REVERT: A 155 TYR cc_start: 0.6169 (OUTLIER) cc_final: 0.5224 (t80) REVERT: A 267 MET cc_start: 0.5893 (mpp) cc_final: 0.5234 (mpp) REVERT: A 291 MET cc_start: 0.6243 (tpp) cc_final: 0.5342 (ttp) REVERT: A 296 PHE cc_start: 0.4560 (OUTLIER) cc_final: 0.2022 (t80) REVERT: A 400 MET cc_start: 0.4410 (OUTLIER) cc_final: 0.4124 (tmm) REVERT: A 410 TRP cc_start: 0.6927 (t60) cc_final: 0.6671 (t-100) REVERT: A 416 ARG cc_start: 0.6755 (mmm160) cc_final: 0.6459 (mmm160) REVERT: A 434 HIS cc_start: 0.6705 (OUTLIER) cc_final: 0.6387 (m-70) REVERT: A 481 ASP cc_start: 0.8195 (t0) cc_final: 0.7893 (t70) outliers start: 63 outliers final: 55 residues processed: 178 average time/residue: 0.2472 time to fit residues: 69.5594 Evaluate side-chains 184 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 125 time to evaluate : 1.845 ------------------------------------------------------------------------------- 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 100 SER 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 208 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 276 SER 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 361 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 554 LEU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 864 SER Chi-restraints excluded: chain B residue 886 ASN 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 1020 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 144 SER 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 245 THR Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 316 ILE 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 644 ILE Chi-restraints excluded: chain A residue 658 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 23 optimal weight: 0.7980 chunk 45 optimal weight: 0.1980 chunk 49 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 54 optimal weight: 0.0980 chunk 10 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 176 optimal weight: 20.0000 chunk 143 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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** ** B1199 GLN ** 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 = 0.3629 r_free = 0.3629 target = 0.109676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.084555 restraints weight = 37280.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.084287 restraints weight = 34437.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.085081 restraints weight = 27377.009| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14992 Z= 0.121 Angle : 0.603 11.526 20300 Z= 0.301 Chirality : 0.045 0.452 2251 Planarity : 0.003 0.055 2564 Dihedral : 6.559 95.134 2117 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.88 % Allowed : 28.62 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.20), residues: 1784 helix: 1.69 (0.20), residues: 727 sheet: -0.44 (0.32), residues: 246 loop : -0.88 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 276 HIS 0.005 0.001 HIS B 223 PHE 0.020 0.001 PHE A 398 TYR 0.015 0.001 TYR B1030 ARG 0.006 0.000 ARG B 996 Details of bonding type rmsd link_NAG-ASN : bond 0.00684 ( 3) link_NAG-ASN : angle 4.50229 ( 9) link_ALPHA1-6 : bond 0.02709 ( 1) link_ALPHA1-6 : angle 3.08572 ( 3) link_BETA1-4 : bond 0.00671 ( 2) link_BETA1-4 : angle 0.86830 ( 6) link_ALPHA1-3 : bond 0.01082 ( 1) link_ALPHA1-3 : angle 2.10609 ( 3) hydrogen bonds : bond 0.04054 ( 676) hydrogen bonds : angle 4.40482 ( 1944) link_BETA1-6 : bond 0.01423 ( 2) link_BETA1-6 : angle 2.16435 ( 6) SS BOND : bond 0.00299 ( 2) SS BOND : angle 0.89584 ( 4) covalent geometry : bond 0.00260 (14981) covalent geometry : angle 0.59224 (20269) ********************** 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 184 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 138 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 LYS cc_start: 0.8807 (mmmt) cc_final: 0.8268 (mmmt) REVERT: B 530 LEU cc_start: 0.9134 (mt) cc_final: 0.8759 (tt) REVERT: A 124 VAL cc_start: 0.8414 (OUTLIER) cc_final: 0.8210 (p) REVERT: A 155 TYR cc_start: 0.5963 (OUTLIER) cc_final: 0.4947 (t80) REVERT: A 159 MET cc_start: 0.4493 (mmt) cc_final: 0.4122 (mmm) REVERT: A 253 MET cc_start: 0.6482 (tpp) cc_final: 0.6219 (tpp) REVERT: A 267 MET cc_start: 0.5628 (mpp) cc_final: 0.4948 (mpp) REVERT: A 291 MET cc_start: 0.6001 (tpp) cc_final: 0.5292 (ttp) REVERT: A 315 MET cc_start: 0.2659 (tmm) cc_final: 0.0058 (mtt) REVERT: A 400 MET cc_start: 0.4685 (OUTLIER) cc_final: 0.4319 (tmm) REVERT: A 416 ARG cc_start: 0.6626 (mmm160) cc_final: 0.6409 (mmm160) REVERT: A 434 HIS cc_start: 0.6717 (OUTLIER) cc_final: 0.6417 (m-70) REVERT: A 481 ASP cc_start: 0.8058 (t0) cc_final: 0.7841 (t70) outliers start: 46 outliers final: 38 residues processed: 174 average time/residue: 0.2414 time to fit residues: 65.7113 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 : 1.663 ------------------------------------------------------------------------------- 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 208 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 361 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 572 VAL Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 864 SER Chi-restraints excluded: chain B residue 886 ASN Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1020 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 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 245 THR Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 316 ILE 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 537 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 644 ILE Chi-restraints excluded: chain A residue 658 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 118 optimal weight: 0.9980 chunk 54 optimal weight: 0.0870 chunk 84 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 173 optimal weight: 9.9990 chunk 167 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- 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** ** B1199 GLN ** 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 = 0.3622 r_free = 0.3622 target = 0.109235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.084662 restraints weight = 37451.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.083520 restraints weight = 30818.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.084096 restraints weight = 27752.305| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4191 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= 0.139 Angle : 0.617 11.334 20300 Z= 0.307 Chirality : 0.045 0.442 2251 Planarity : 0.003 0.054 2564 Dihedral : 6.430 92.585 2117 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.01 % Allowed : 28.43 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.20), residues: 1784 helix: 1.66 (0.20), residues: 728 sheet: -0.41 (0.33), residues: 241 loop : -0.91 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP A 410 HIS 0.005 0.001 HIS B 223 PHE 0.025 0.001 PHE B 866 TYR 0.021 0.001 TYR B1111 ARG 0.008 0.000 ARG A 174 Details of bonding type rmsd link_NAG-ASN : bond 0.00608 ( 3) link_NAG-ASN : angle 4.39443 ( 9) link_ALPHA1-6 : bond 0.02586 ( 1) link_ALPHA1-6 : angle 2.99060 ( 3) link_BETA1-4 : bond 0.00647 ( 2) link_BETA1-4 : angle 0.83944 ( 6) link_ALPHA1-3 : bond 0.01080 ( 1) link_ALPHA1-3 : angle 2.24986 ( 3) hydrogen bonds : bond 0.04092 ( 676) hydrogen bonds : angle 4.45844 ( 1944) link_BETA1-6 : bond 0.01366 ( 2) link_BETA1-6 : angle 2.22950 ( 6) SS BOND : bond 0.00267 ( 2) SS BOND : angle 0.91069 ( 4) covalent geometry : bond 0.00312 (14981) covalent geometry : angle 0.60712 (20269) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4906.70 seconds wall clock time: 87 minutes 57.36 seconds (5277.36 seconds total)