Starting phenix.real_space_refine on Wed Jul 30 16:59:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vgh_31969/07_2025/7vgh_31969.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vgh_31969/07_2025/7vgh_31969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vgh_31969/07_2025/7vgh_31969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vgh_31969/07_2025/7vgh_31969.map" model { file = "/net/cci-nas-00/data/ceres_data/7vgh_31969/07_2025/7vgh_31969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vgh_31969/07_2025/7vgh_31969.cif" } resolution = 3.39 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= 0.000 sd= 0.004 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 12 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: 6 Type Number sf(0) Gaussians P 1 5.49 5 Mg 1 5.21 5 S 57 5.16 5 C 7976 2.51 5 N 2084 2.21 5 O 2285 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12404 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2654 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 30, 'TRANS': 307} Chain: "B" Number of atoms: 9584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1183, 9584 Classifications: {'peptide': 1183} Link IDs: {'PTRANS': 32, 'TRANS': 1150} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 51 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, '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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: "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 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.98, per 1000 atoms: 0.56 Number of scatterers: 12404 At special positions: 0 Unit cell: (99.882, 107.4, 173.988, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 57 16.00 P 1 15.00 Mg 1 11.99 O 2285 8.00 N 2084 7.00 C 7976 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 162 " distance=2.04 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 " MAN C 3 " - " MAN C 4 " " MAN D 3 " - " MAN D 6 " ALPHA1-4 " NAG C 2 " - " MAN C 3 " " NAG D 2 " - " MAN D 3 " ALPHA1-6 " MAN D 3 " - " MAN D 4 " " MAN D 4 " - " MAN D 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A 401 " - " ASN A 286 " " NAG C 1 " - " ASN B 368 " " NAG D 1 " - " ASN A 171 " " NAG E 1 " - " ASN A 75 " Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.6 seconds 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2854 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 10 sheets defined 41.7% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 31 through 57 removed outlier: 4.053A pdb=" N ALA A 35 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Proline residue: A 37 - end of helix removed outlier: 3.833A pdb=" N GLY A 43 " --> pdb=" O PHE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.574A pdb=" N VAL A 78 " --> pdb=" O ASN A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 129 through 135 removed outlier: 3.655A pdb=" N GLY A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 removed outlier: 3.783A pdb=" N GLN A 151 " --> pdb=" O ALA A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 216 through 220 Processing helix chain 'A' and resid 232 through 236 Processing helix chain 'A' and resid 247 through 255 removed outlier: 3.643A pdb=" N ARG A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 342 removed outlier: 3.581A pdb=" N ILE A 319 " --> pdb=" O PRO A 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 76 removed outlier: 3.787A pdb=" N GLN B 76 " --> pdb=" O TYR B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 118 through 131 removed outlier: 3.890A pdb=" N LEU B 122 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 170 removed outlier: 3.885A pdb=" N THR B 155 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP B 163 " --> pdb=" O ASP B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 175 Processing helix chain 'B' and resid 190 through 194 removed outlier: 3.538A pdb=" N GLU B 193 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 248 removed outlier: 3.640A pdb=" N GLN B 248 " --> pdb=" O GLU B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 289 through 293 removed outlier: 3.601A pdb=" N ILE B 293 " --> pdb=" O ALA B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 333 through 364 removed outlier: 3.785A pdb=" N TYR B 339 " --> pdb=" O TYR B 335 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.550A pdb=" N SER B 369 " --> pdb=" O VAL B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 397 removed outlier: 3.866A pdb=" N TRP B 390 " --> pdb=" O PHE B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 420 removed outlier: 3.532A pdb=" N VAL B 410 " --> pdb=" O VAL B 406 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 426 removed outlier: 5.748A pdb=" N GLN B 424 " --> pdb=" O TRP B 421 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR B 426 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 447 removed outlier: 3.717A pdb=" N LEU B 445 " --> pdb=" O ASN B 442 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY B 446 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 519 removed outlier: 3.788A pdb=" N ILE B 513 " --> pdb=" O ASP B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 526 removed outlier: 4.320A pdb=" N ARG B 525 " --> pdb=" O GLU B 521 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN B 526 " --> pdb=" O PRO B 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 521 through 526' Processing helix chain 'B' and resid 526 through 531 removed outlier: 3.587A pdb=" N LEU B 531 " --> pdb=" O PHE B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 564 removed outlier: 3.860A pdb=" N ALA B 557 " --> pdb=" O PRO B 553 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU B 558 " --> pdb=" O ASP B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 626 Processing helix chain 'B' and resid 635 through 649 removed outlier: 3.871A pdb=" N THR B 639 " --> pdb=" O THR B 635 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE B 646 " --> pdb=" O ALA B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 678 removed outlier: 4.360A pdb=" N GLU B 668 " --> pdb=" O LYS B 664 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TRP B 669 " --> pdb=" O GLU B 665 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL B 678 " --> pdb=" O MET B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 692 Processing helix chain 'B' and resid 713 through 724 Processing helix chain 'B' and resid 737 through 746 removed outlier: 3.884A pdb=" N ASN B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE B 742 " --> pdb=" O THR B 738 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLY B 743 " --> pdb=" O ALA B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 771 removed outlier: 3.635A pdb=" N SER B 763 " --> pdb=" O GLU B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 810 Processing helix chain 'B' and resid 841 through 846 removed outlier: 3.689A pdb=" N LYS B 845 " --> pdb=" O ARG B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 857 Processing helix chain 'B' and resid 858 through 860 No H-bonds generated for 'chain 'B' and resid 858 through 860' Processing helix chain 'B' and resid 869 through 883 removed outlier: 3.838A pdb=" N ALA B 874 " --> pdb=" O PRO B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 904 Processing helix chain 'B' and resid 928 through 930 No H-bonds generated for 'chain 'B' and resid 928 through 930' Processing helix chain 'B' and resid 931 through 938 removed outlier: 3.630A pdb=" N LEU B 936 " --> pdb=" O LEU B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 958 removed outlier: 3.728A pdb=" N PHE B 955 " --> pdb=" O LEU B 951 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR B 956 " --> pdb=" O ARG B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 963 Processing helix chain 'B' and resid 963 through 969 removed outlier: 3.869A pdb=" N TRP B 967 " --> pdb=" O LEU B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 972 No H-bonds generated for 'chain 'B' and resid 970 through 972' Processing helix chain 'B' and resid 981 through 986 removed outlier: 3.721A pdb=" N ILE B 985 " --> pdb=" O GLU B 981 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR B 986 " --> pdb=" O ASP B 982 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 981 through 986' Processing helix chain 'B' and resid 994 through 1004 removed outlier: 3.808A pdb=" N LEU B 998 " --> pdb=" O SER B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1018 Processing helix chain 'B' and resid 1019 through 1024 Processing helix chain 'B' and resid 1029 through 1056 removed outlier: 3.597A pdb=" N PHE B1034 " --> pdb=" O TYR B1030 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL B1035 " --> pdb=" O LYS B1031 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE B1050 " --> pdb=" O ILE B1046 " (cutoff:3.500A) Proline residue: B1051 - end of helix Processing helix chain 'B' and resid 1068 through 1079 Processing helix chain 'B' and resid 1082 through 1088 removed outlier: 3.914A pdb=" N ILE B1088 " --> pdb=" O VAL B1084 " (cutoff:3.500A) Processing helix chain 'B' and resid 1096 through 1118 removed outlier: 3.697A pdb=" N ALA B1100 " --> pdb=" O THR B1096 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP B1116 " --> pdb=" O GLY B1112 " (cutoff:3.500A) Processing helix chain 'B' and resid 1135 through 1140 Processing helix chain 'B' and resid 1142 through 1156 removed outlier: 3.606A pdb=" N TRP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B1151 " --> pdb=" O LEU B1147 " (cutoff:3.500A) Processing helix chain 'B' and resid 1157 through 1167 removed outlier: 3.721A pdb=" N VAL B1161 " --> pdb=" O LEU B1157 " (cutoff:3.500A) Processing helix chain 'B' and resid 1173 through 1181 Processing helix chain 'B' and resid 1218 through 1223 removed outlier: 3.733A pdb=" N SER B1222 " --> pdb=" O ALA B1218 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 64 removed outlier: 3.797A pdb=" N HIS A 299 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A 115 " --> pdb=" O HIS A 299 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 108 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N TYR A 112 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N LEU A 265 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU A 114 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ARG A 263 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 100 removed outlier: 4.560A pdb=" N ALA A 282 " --> pdb=" O GLN A 179 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 186 through 189 removed outlier: 4.088A pdb=" N GLU B 179 " --> pdb=" O ARG B 201 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N VAL B 199 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER B 216 " --> pdb=" O HIS B 307 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU B 309 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU B 214 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 238 through 241 removed outlier: 4.037A pdb=" N TYR B 225 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 277 through 279 removed outlier: 4.083A pdb=" N GLY B 277 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 435 through 436 Processing sheet with id=AA7, first strand: chain 'B' and resid 798 through 802 removed outlier: 6.308A pdb=" N LEU B 799 " --> pdb=" O ILE B 864 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N CYS B 866 " --> pdb=" O LEU B 799 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE B 801 " --> pdb=" O CYS B 866 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL B 863 " --> pdb=" O ILE B 728 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE B 451 " --> pdb=" O TRP B 729 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU B 731 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N SER B 453 " --> pdb=" O LEU B 731 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR B 450 " --> pdb=" O LEU B 889 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE B 891 " --> pdb=" O TYR B 450 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE B 452 " --> pdb=" O ILE B 891 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR B 888 " --> pdb=" O ILE B 906 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL B 908 " --> pdb=" O THR B 888 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ALA B 890 " --> pdb=" O VAL B 908 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 475 through 476 removed outlier: 3.935A pdb=" N CYS B 469 " --> pdb=" O TYR B 476 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LEU B 700 " --> pdb=" O TYR B 658 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N TYR B 658 " --> pdb=" O LEU B 700 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY B 702 " --> pdb=" O LEU B 656 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU B 654 " --> pdb=" O THR B 704 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE B 661 " --> pdb=" O ILE B 614 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE B 614 " --> pdb=" O ILE B 661 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N SER B 604 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE B 593 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE B 606 " --> pdb=" O LEU B 591 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 538 through 539 Processing sheet with id=AB1, first strand: chain 'B' and resid 568 through 572 removed outlier: 6.117A pdb=" N PHE B 569 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N SER B 580 " --> pdb=" O PHE B 569 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA B 571 " --> pdb=" O THR B 578 " (cutoff:3.500A) 415 hydrogen bonds defined for protein. 1149 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: 4.10 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3944 1.35 - 1.47: 3347 1.47 - 1.60: 5332 1.60 - 1.73: 0 1.73 - 1.85: 86 Bond restraints: 12709 Sorted by residual: bond pdb=" C1 MAN D 6 " pdb=" C2 MAN D 6 " ideal model delta sigma weight residual 1.526 1.580 -0.054 2.00e-02 2.50e+03 7.29e+00 bond pdb=" CA ILE B 661 " pdb=" C ILE B 661 " ideal model delta sigma weight residual 1.522 1.553 -0.031 1.44e-02 4.82e+03 4.68e+00 bond pdb=" C5 MAN D 6 " pdb=" O5 MAN D 6 " ideal model delta sigma weight residual 1.418 1.460 -0.042 2.00e-02 2.50e+03 4.35e+00 bond pdb=" C1 MAN D 5 " pdb=" C2 MAN D 5 " ideal model delta sigma weight residual 1.526 1.567 -0.041 2.00e-02 2.50e+03 4.25e+00 bond pdb=" C5 MAN C 3 " pdb=" O5 MAN C 3 " ideal model delta sigma weight residual 1.418 1.458 -0.040 2.00e-02 2.50e+03 3.99e+00 ... (remaining 12704 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 16812 2.10 - 4.19: 365 4.19 - 6.29: 50 6.29 - 8.38: 10 8.38 - 10.48: 2 Bond angle restraints: 17239 Sorted by residual: angle pdb=" C GLU B 662 " pdb=" CA GLU B 662 " pdb=" CB GLU B 662 " ideal model delta sigma weight residual 117.23 108.75 8.48 1.36e+00 5.41e-01 3.89e+01 angle pdb=" N THR B 465 " pdb=" CA THR B 465 " pdb=" C THR B 465 " ideal model delta sigma weight residual 111.02 116.13 -5.11 1.25e+00 6.40e-01 1.67e+01 angle pdb=" N VAL B 624 " pdb=" CA VAL B 624 " pdb=" C VAL B 624 " ideal model delta sigma weight residual 112.96 108.96 4.00 1.00e+00 1.00e+00 1.60e+01 angle pdb=" CA GLU B 662 " pdb=" C GLU B 662 " pdb=" N GLU B 663 " ideal model delta sigma weight residual 119.98 116.81 3.17 8.50e-01 1.38e+00 1.39e+01 angle pdb=" N ARG B 600 " pdb=" CA ARG B 600 " pdb=" C ARG B 600 " ideal model delta sigma weight residual 112.04 106.72 5.32 1.44e+00 4.82e-01 1.37e+01 ... (remaining 17234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.72: 7158 24.72 - 49.43: 435 49.43 - 74.15: 47 74.15 - 98.87: 34 98.87 - 123.59: 17 Dihedral angle restraints: 7691 sinusoidal: 3244 harmonic: 4447 Sorted by residual: dihedral pdb=" CB CYS A 79 " pdb=" SG CYS A 79 " pdb=" SG CYS A 92 " pdb=" CB CYS A 92 " ideal model delta sinusoidal sigma weight residual 93.00 36.85 56.15 1 1.00e+01 1.00e-02 4.25e+01 dihedral pdb=" CA ARG B 572 " pdb=" C ARG B 572 " pdb=" N THR B 573 " pdb=" CA THR B 573 " ideal model delta harmonic sigma weight residual 180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA ASP B 478 " pdb=" C ASP B 478 " pdb=" N HIS B 479 " pdb=" CA HIS B 479 " ideal model delta harmonic sigma weight residual 180.00 155.72 24.28 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 7688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1739 0.081 - 0.162: 171 0.162 - 0.243: 10 0.243 - 0.324: 0 0.324 - 0.405: 1 Chirality restraints: 1921 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 75 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CB ILE B 136 " pdb=" CA ILE B 136 " pdb=" CG1 ILE B 136 " pdb=" CG2 ILE B 136 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CG LEU B1037 " pdb=" CB LEU B1037 " pdb=" CD1 LEU B1037 " pdb=" CD2 LEU B1037 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1918 not shown) Planarity restraints: 2188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 959 " 0.019 2.00e-02 2.50e+03 2.11e-02 7.81e+00 pdb=" CG PHE B 959 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE B 959 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE B 959 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 959 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE B 959 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE B 959 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 160 " -0.044 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO A 161 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1191 " -0.021 2.00e-02 2.50e+03 1.46e-02 5.36e+00 pdb=" CG TRP B1191 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP B1191 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP B1191 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B1191 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B1191 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B1191 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1191 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1191 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B1191 " -0.001 2.00e-02 2.50e+03 ... (remaining 2185 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 103 2.57 - 3.15: 10345 3.15 - 3.74: 17831 3.74 - 4.32: 25245 4.32 - 4.90: 41897 Nonbonded interactions: 95421 Sorted by model distance: nonbonded pdb=" OD2 PHD B 454 " pdb="MG MG B1401 " model vdw 1.989 2.170 nonbonded pdb=" O THR B 456 " pdb="MG MG B1401 " model vdw 2.094 2.170 nonbonded pdb=" NH1 ARG B 946 " pdb=" O ASP B1004 " model vdw 2.217 3.120 nonbonded pdb=" O PRO A 279 " pdb=" OH TYR A 283 " model vdw 2.231 3.040 nonbonded pdb=" O PHE A 220 " pdb=" OG1 THR A 223 " model vdw 2.238 3.040 ... (remaining 95416 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 individual isotropic 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.540 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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 0.054 12725 Z= 0.222 Angle : 0.765 10.477 17284 Z= 0.410 Chirality : 0.048 0.405 1921 Planarity : 0.004 0.067 2184 Dihedral : 17.585 123.585 4828 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.37 % Favored : 87.63 % Rotamer: Outliers : 0.23 % Allowed : 0.53 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.21), residues: 1512 helix: -0.52 (0.22), residues: 549 sheet: -0.74 (0.40), residues: 173 loop : -3.16 (0.19), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B1191 HIS 0.007 0.001 HIS B1213 PHE 0.047 0.002 PHE B 959 TYR 0.037 0.002 TYR A 65 ARG 0.007 0.001 ARG B 835 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 4) link_NAG-ASN : angle 3.66980 ( 12) link_ALPHA1-4 : bond 0.01047 ( 2) link_ALPHA1-4 : angle 3.53770 ( 6) link_ALPHA1-6 : bond 0.00338 ( 2) link_ALPHA1-6 : angle 1.64858 ( 6) link_BETA1-4 : bond 0.00754 ( 3) link_BETA1-4 : angle 2.42030 ( 9) link_ALPHA1-3 : bond 0.01415 ( 2) link_ALPHA1-3 : angle 3.38383 ( 6) hydrogen bonds : bond 0.18167 ( 415) hydrogen bonds : angle 6.52313 ( 1149) SS BOND : bond 0.00385 ( 3) SS BOND : angle 2.69247 ( 6) covalent geometry : bond 0.00494 (12709) covalent geometry : angle 0.75015 (17239) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 117 time to evaluate : 1.306 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 120 average time/residue: 0.3138 time to fit residues: 52.8803 Evaluate side-chains 97 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 662 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN B 115 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 GLN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 633 ASN B 872 GLN B 913 GLN B1196 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.115121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.078970 restraints weight = 22185.479| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.51 r_work: 0.2740 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12725 Z= 0.181 Angle : 0.704 11.683 17284 Z= 0.354 Chirality : 0.046 0.270 1921 Planarity : 0.004 0.057 2184 Dihedral : 14.031 124.759 1946 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.63 % Favored : 87.37 % Rotamer: Outliers : 0.69 % Allowed : 9.08 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.21), residues: 1512 helix: -0.22 (0.22), residues: 568 sheet: -0.79 (0.39), residues: 171 loop : -3.26 (0.19), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B1191 HIS 0.005 0.001 HIS B 359 PHE 0.029 0.002 PHE B 959 TYR 0.020 0.001 TYR B1019 ARG 0.006 0.000 ARG A 280 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 4) link_NAG-ASN : angle 3.18196 ( 12) link_ALPHA1-4 : bond 0.01185 ( 2) link_ALPHA1-4 : angle 3.03776 ( 6) link_ALPHA1-6 : bond 0.00585 ( 2) link_ALPHA1-6 : angle 2.30864 ( 6) link_BETA1-4 : bond 0.00524 ( 3) link_BETA1-4 : angle 1.76043 ( 9) link_ALPHA1-3 : bond 0.01155 ( 2) link_ALPHA1-3 : angle 5.22610 ( 6) hydrogen bonds : bond 0.05640 ( 415) hydrogen bonds : angle 5.05046 ( 1149) SS BOND : bond 0.00588 ( 3) SS BOND : angle 2.76705 ( 6) covalent geometry : bond 0.00426 (12709) covalent geometry : angle 0.68666 (17239) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 1.530 Fit side-chains REVERT: B 769 MET cc_start: 0.7503 (tmm) cc_final: 0.6884 (tmm) REVERT: B 1057 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8161 (mm-40) outliers start: 9 outliers final: 6 residues processed: 108 average time/residue: 0.3544 time to fit residues: 55.0477 Evaluate side-chains 97 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain B residue 837 GLN Chi-restraints excluded: chain B residue 885 LYS Chi-restraints excluded: chain B residue 1223 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 40 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 23 optimal weight: 0.0870 chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 3 optimal weight: 0.0980 chunk 140 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 overall best weight: 1.4364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 ASN B1196 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.116830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.084662 restraints weight = 22098.724| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.55 r_work: 0.2765 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12725 Z= 0.130 Angle : 0.637 10.203 17284 Z= 0.317 Chirality : 0.044 0.276 1921 Planarity : 0.004 0.045 2184 Dihedral : 12.295 126.733 1943 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 1.15 % Allowed : 13.74 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.21), residues: 1512 helix: 0.20 (0.23), residues: 562 sheet: -0.64 (0.39), residues: 171 loop : -3.15 (0.19), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 96 HIS 0.006 0.001 HIS B 359 PHE 0.015 0.001 PHE B 345 TYR 0.015 0.001 TYR B1019 ARG 0.004 0.000 ARG A 280 Details of bonding type rmsd link_NAG-ASN : bond 0.00502 ( 4) link_NAG-ASN : angle 2.87922 ( 12) link_ALPHA1-4 : bond 0.01321 ( 2) link_ALPHA1-4 : angle 2.82812 ( 6) link_ALPHA1-6 : bond 0.01019 ( 2) link_ALPHA1-6 : angle 2.61588 ( 6) link_BETA1-4 : bond 0.00461 ( 3) link_BETA1-4 : angle 1.46898 ( 9) link_ALPHA1-3 : bond 0.01170 ( 2) link_ALPHA1-3 : angle 5.07052 ( 6) hydrogen bonds : bond 0.04759 ( 415) hydrogen bonds : angle 4.70981 ( 1149) SS BOND : bond 0.01278 ( 3) SS BOND : angle 2.30247 ( 6) covalent geometry : bond 0.00289 (12709) covalent geometry : angle 0.61919 (17239) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 1.419 Fit side-chains REVERT: A 280 ARG cc_start: 0.8499 (ptt90) cc_final: 0.7583 (ttp80) REVERT: B 105 PHE cc_start: 0.8742 (p90) cc_final: 0.8440 (p90) REVERT: B 709 LYS cc_start: 0.8108 (mmmt) cc_final: 0.7595 (tptm) REVERT: B 769 MET cc_start: 0.7428 (tmm) cc_final: 0.7198 (tmm) REVERT: B 1196 GLN cc_start: 0.6587 (OUTLIER) cc_final: 0.6209 (pp30) outliers start: 15 outliers final: 11 residues processed: 120 average time/residue: 0.3803 time to fit residues: 67.7861 Evaluate side-chains 107 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 564 ASN Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain B residue 837 GLN Chi-restraints excluded: chain B residue 885 LYS Chi-restraints excluded: chain B residue 1196 GLN Chi-restraints excluded: chain B residue 1223 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 147 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 146 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.113896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.077637 restraints weight = 22205.981| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.50 r_work: 0.2714 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12725 Z= 0.237 Angle : 0.705 11.543 17284 Z= 0.355 Chirality : 0.047 0.301 1921 Planarity : 0.005 0.058 2184 Dihedral : 11.524 124.628 1943 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.43 % Favored : 87.57 % Rotamer: Outliers : 1.60 % Allowed : 16.49 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.21), residues: 1512 helix: 0.14 (0.23), residues: 561 sheet: -0.66 (0.39), residues: 169 loop : -3.21 (0.19), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B1191 HIS 0.005 0.001 HIS B 965 PHE 0.028 0.002 PHE B 959 TYR 0.021 0.002 TYR B 123 ARG 0.007 0.000 ARG B 631 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 4) link_NAG-ASN : angle 3.17804 ( 12) link_ALPHA1-4 : bond 0.01253 ( 2) link_ALPHA1-4 : angle 3.07999 ( 6) link_ALPHA1-6 : bond 0.01151 ( 2) link_ALPHA1-6 : angle 2.95283 ( 6) link_BETA1-4 : bond 0.00431 ( 3) link_BETA1-4 : angle 1.66543 ( 9) link_ALPHA1-3 : bond 0.00658 ( 2) link_ALPHA1-3 : angle 5.07435 ( 6) hydrogen bonds : bond 0.05860 ( 415) hydrogen bonds : angle 4.79385 ( 1149) SS BOND : bond 0.00266 ( 3) SS BOND : angle 2.82765 ( 6) covalent geometry : bond 0.00569 (12709) covalent geometry : angle 0.68658 (17239) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 1.425 Fit side-chains REVERT: B 94 ASN cc_start: 0.7866 (t0) cc_final: 0.7323 (p0) REVERT: B 709 LYS cc_start: 0.8212 (mmmt) cc_final: 0.7684 (tptm) REVERT: B 834 MET cc_start: 0.3740 (mmm) cc_final: 0.3147 (mmm) outliers start: 21 outliers final: 17 residues processed: 109 average time/residue: 0.2670 time to fit residues: 42.3143 Evaluate side-chains 107 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 564 ASN Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain B residue 837 GLN Chi-restraints excluded: chain B residue 885 LYS Chi-restraints excluded: chain B residue 1084 VAL Chi-restraints excluded: chain B residue 1223 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 131 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 91 optimal weight: 0.5980 chunk 119 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 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 = 0.3443 r_free = 0.3443 target = 0.114209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.078038 restraints weight = 22077.505| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.51 r_work: 0.2722 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12725 Z= 0.200 Angle : 0.674 10.928 17284 Z= 0.339 Chirality : 0.045 0.308 1921 Planarity : 0.004 0.061 2184 Dihedral : 10.742 119.523 1943 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.04 % Favored : 87.96 % Rotamer: Outliers : 1.83 % Allowed : 17.40 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.21), residues: 1512 helix: 0.17 (0.23), residues: 565 sheet: -0.65 (0.39), residues: 171 loop : -3.19 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B1191 HIS 0.004 0.001 HIS B 417 PHE 0.021 0.002 PHE B 959 TYR 0.022 0.001 TYR A 65 ARG 0.007 0.000 ARG B 631 Details of bonding type rmsd link_NAG-ASN : bond 0.00401 ( 4) link_NAG-ASN : angle 3.06973 ( 12) link_ALPHA1-4 : bond 0.01464 ( 2) link_ALPHA1-4 : angle 3.02663 ( 6) link_ALPHA1-6 : bond 0.01296 ( 2) link_ALPHA1-6 : angle 2.91505 ( 6) link_BETA1-4 : bond 0.00492 ( 3) link_BETA1-4 : angle 1.65092 ( 9) link_ALPHA1-3 : bond 0.00577 ( 2) link_ALPHA1-3 : angle 3.68403 ( 6) hydrogen bonds : bond 0.05529 ( 415) hydrogen bonds : angle 4.66682 ( 1149) SS BOND : bond 0.00576 ( 3) SS BOND : angle 2.78575 ( 6) covalent geometry : bond 0.00476 (12709) covalent geometry : angle 0.65905 (17239) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 1.345 Fit side-chains REVERT: A 104 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.5247 (m-80) REVERT: B 94 ASN cc_start: 0.7942 (t0) cc_final: 0.7376 (p0) REVERT: B 673 PHE cc_start: 0.7036 (OUTLIER) cc_final: 0.5505 (p90) REVERT: B 709 LYS cc_start: 0.8186 (mmmt) cc_final: 0.7838 (tptm) REVERT: B 769 MET cc_start: 0.7349 (tmm) cc_final: 0.6983 (tmm) REVERT: B 834 MET cc_start: 0.3647 (mmm) cc_final: 0.3053 (mmm) outliers start: 24 outliers final: 16 residues processed: 117 average time/residue: 0.2583 time to fit residues: 44.0378 Evaluate side-chains 109 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 673 PHE Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain B residue 837 GLN Chi-restraints excluded: chain B residue 885 LYS Chi-restraints excluded: chain B residue 1011 LEU Chi-restraints excluded: chain B residue 1223 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 8 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 96 optimal weight: 30.0000 chunk 110 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.117421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.081615 restraints weight = 22291.465| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.48 r_work: 0.2785 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12725 Z= 0.119 Angle : 0.603 10.170 17284 Z= 0.303 Chirality : 0.042 0.305 1921 Planarity : 0.004 0.043 2184 Dihedral : 9.675 116.481 1943 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 1.53 % Allowed : 18.40 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.21), residues: 1512 helix: 0.49 (0.23), residues: 559 sheet: -0.61 (0.39), residues: 174 loop : -3.03 (0.19), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1191 HIS 0.006 0.001 HIS B 359 PHE 0.013 0.001 PHE B 262 TYR 0.016 0.001 TYR A 65 ARG 0.008 0.000 ARG B 631 Details of bonding type rmsd link_NAG-ASN : bond 0.00495 ( 4) link_NAG-ASN : angle 2.76556 ( 12) link_ALPHA1-4 : bond 0.01636 ( 2) link_ALPHA1-4 : angle 3.06648 ( 6) link_ALPHA1-6 : bond 0.01566 ( 2) link_ALPHA1-6 : angle 2.44727 ( 6) link_BETA1-4 : bond 0.00530 ( 3) link_BETA1-4 : angle 1.52283 ( 9) link_ALPHA1-3 : bond 0.01006 ( 2) link_ALPHA1-3 : angle 1.93168 ( 6) hydrogen bonds : bond 0.04117 ( 415) hydrogen bonds : angle 4.37239 ( 1149) SS BOND : bond 0.00544 ( 3) SS BOND : angle 3.38526 ( 6) covalent geometry : bond 0.00258 (12709) covalent geometry : angle 0.58930 (17239) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 1.263 Fit side-chains REVERT: A 104 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.5081 (m-80) REVERT: A 280 ARG cc_start: 0.8483 (ptt90) cc_final: 0.7571 (ttp80) REVERT: B 94 ASN cc_start: 0.7884 (t0) cc_final: 0.7292 (p0) REVERT: B 105 PHE cc_start: 0.8800 (p90) cc_final: 0.8585 (p90) REVERT: B 110 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8470 (mtp) REVERT: B 632 MET cc_start: 0.7825 (tpp) cc_final: 0.7608 (tpp) REVERT: B 640 GLN cc_start: 0.8981 (tp40) cc_final: 0.8748 (tp40) REVERT: B 652 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.6015 (ptm160) REVERT: B 673 PHE cc_start: 0.6955 (OUTLIER) cc_final: 0.5454 (p90) REVERT: B 709 LYS cc_start: 0.8071 (mmmt) cc_final: 0.7561 (tptm) REVERT: B 769 MET cc_start: 0.7305 (tmm) cc_final: 0.6700 (tmm) REVERT: B 834 MET cc_start: 0.3523 (mmm) cc_final: 0.2914 (mmm) REVERT: B 1062 ASP cc_start: 0.7287 (t0) cc_final: 0.6876 (t0) REVERT: B 1104 PHE cc_start: 0.8385 (m-10) cc_final: 0.7883 (m-80) outliers start: 20 outliers final: 10 residues processed: 125 average time/residue: 0.2877 time to fit residues: 52.5100 Evaluate side-chains 114 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 564 ASN Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 652 ARG Chi-restraints excluded: chain B residue 673 PHE Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain B residue 837 GLN Chi-restraints excluded: chain B residue 885 LYS Chi-restraints excluded: chain B residue 1083 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 26 optimal weight: 0.0170 chunk 83 optimal weight: 0.0770 chunk 101 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 121 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 ASN ** B1196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.118622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.082636 restraints weight = 22012.845| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.53 r_work: 0.2808 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12725 Z= 0.109 Angle : 0.589 10.160 17284 Z= 0.295 Chirality : 0.042 0.299 1921 Planarity : 0.004 0.048 2184 Dihedral : 9.302 113.669 1943 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 1.37 % Allowed : 18.70 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.22), residues: 1512 helix: 0.62 (0.24), residues: 561 sheet: -0.43 (0.39), residues: 173 loop : -2.92 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1191 HIS 0.006 0.001 HIS B 359 PHE 0.014 0.001 PHE B1101 TYR 0.014 0.001 TYR A 65 ARG 0.012 0.000 ARG B 563 Details of bonding type rmsd link_NAG-ASN : bond 0.00528 ( 4) link_NAG-ASN : angle 2.74707 ( 12) link_ALPHA1-4 : bond 0.01643 ( 2) link_ALPHA1-4 : angle 3.15152 ( 6) link_ALPHA1-6 : bond 0.01406 ( 2) link_ALPHA1-6 : angle 2.08955 ( 6) link_BETA1-4 : bond 0.00535 ( 3) link_BETA1-4 : angle 1.42333 ( 9) link_ALPHA1-3 : bond 0.00869 ( 2) link_ALPHA1-3 : angle 1.55542 ( 6) hydrogen bonds : bond 0.03847 ( 415) hydrogen bonds : angle 4.25563 ( 1149) SS BOND : bond 0.00252 ( 3) SS BOND : angle 2.39666 ( 6) covalent geometry : bond 0.00223 (12709) covalent geometry : angle 0.57740 (17239) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 1.414 Fit side-chains REVERT: A 280 ARG cc_start: 0.8436 (ptt90) cc_final: 0.7522 (ttp80) REVERT: B 94 ASN cc_start: 0.7866 (t0) cc_final: 0.7176 (p0) REVERT: B 105 PHE cc_start: 0.8795 (p90) cc_final: 0.8589 (p90) REVERT: B 110 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8468 (mtp) REVERT: B 640 GLN cc_start: 0.8968 (tp40) cc_final: 0.8726 (tp40) REVERT: B 652 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.6026 (ptm160) REVERT: B 673 PHE cc_start: 0.6938 (OUTLIER) cc_final: 0.5382 (p90) REVERT: B 709 LYS cc_start: 0.7910 (mmmt) cc_final: 0.7415 (tptm) REVERT: B 769 MET cc_start: 0.7318 (tmm) cc_final: 0.6665 (tmm) REVERT: B 834 MET cc_start: 0.3483 (mmm) cc_final: 0.2847 (mmm) REVERT: B 1057 GLN cc_start: 0.8240 (mm-40) cc_final: 0.8037 (tp-100) outliers start: 18 outliers final: 10 residues processed: 115 average time/residue: 0.2612 time to fit residues: 43.1699 Evaluate side-chains 106 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 652 ARG Chi-restraints excluded: chain B residue 673 PHE Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain B residue 837 GLN Chi-restraints excluded: chain B residue 885 LYS Chi-restraints excluded: chain B residue 1084 VAL Chi-restraints excluded: chain B residue 1223 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 15 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1196 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 = 0.3469 r_free = 0.3469 target = 0.116074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.079869 restraints weight = 22405.689| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.54 r_work: 0.2750 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12725 Z= 0.164 Angle : 0.620 10.577 17284 Z= 0.314 Chirality : 0.044 0.316 1921 Planarity : 0.004 0.045 2184 Dihedral : 9.290 111.552 1943 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.51 % Favored : 88.49 % Rotamer: Outliers : 1.37 % Allowed : 19.08 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.21), residues: 1512 helix: 0.59 (0.23), residues: 561 sheet: -0.46 (0.39), residues: 172 loop : -2.95 (0.20), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B1191 HIS 0.004 0.001 HIS B 417 PHE 0.018 0.001 PHE B 959 TYR 0.020 0.001 TYR A 65 ARG 0.007 0.000 ARG B 631 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 4) link_NAG-ASN : angle 3.00967 ( 12) link_ALPHA1-4 : bond 0.01429 ( 2) link_ALPHA1-4 : angle 3.24536 ( 6) link_ALPHA1-6 : bond 0.01117 ( 2) link_ALPHA1-6 : angle 1.94389 ( 6) link_BETA1-4 : bond 0.00470 ( 3) link_BETA1-4 : angle 1.52219 ( 9) link_ALPHA1-3 : bond 0.00721 ( 2) link_ALPHA1-3 : angle 1.36793 ( 6) hydrogen bonds : bond 0.04775 ( 415) hydrogen bonds : angle 4.36681 ( 1149) SS BOND : bond 0.00290 ( 3) SS BOND : angle 2.68054 ( 6) covalent geometry : bond 0.00389 (12709) covalent geometry : angle 0.60798 (17239) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 1.371 Fit side-chains REVERT: A 104 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.5069 (m-80) REVERT: B 94 ASN cc_start: 0.7942 (t0) cc_final: 0.7290 (p0) REVERT: B 110 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8528 (mtp) REVERT: B 632 MET cc_start: 0.7442 (tpp) cc_final: 0.6922 (ppp) REVERT: B 640 GLN cc_start: 0.8975 (tp40) cc_final: 0.8740 (tp40) REVERT: B 652 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.5959 (ptm160) REVERT: B 673 PHE cc_start: 0.6975 (OUTLIER) cc_final: 0.5413 (p90) REVERT: B 709 LYS cc_start: 0.8021 (mmmt) cc_final: 0.7531 (tptm) REVERT: B 769 MET cc_start: 0.7422 (tmm) cc_final: 0.6745 (tmm) REVERT: B 834 MET cc_start: 0.3579 (mmm) cc_final: 0.2933 (mmm) outliers start: 18 outliers final: 12 residues processed: 109 average time/residue: 0.2563 time to fit residues: 41.4572 Evaluate side-chains 110 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 652 ARG Chi-restraints excluded: chain B residue 673 PHE Chi-restraints excluded: chain B residue 837 GLN Chi-restraints excluded: chain B residue 885 LYS Chi-restraints excluded: chain B residue 1083 THR Chi-restraints excluded: chain B residue 1084 VAL Chi-restraints excluded: chain B residue 1223 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 88 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 150 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 148 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1196 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 = 0.3489 r_free = 0.3489 target = 0.117452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.081373 restraints weight = 22080.844| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.53 r_work: 0.2780 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12725 Z= 0.123 Angle : 0.589 10.336 17284 Z= 0.297 Chirality : 0.042 0.301 1921 Planarity : 0.004 0.041 2184 Dihedral : 9.009 108.829 1943 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer: Outliers : 1.37 % Allowed : 19.47 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.21), residues: 1512 helix: 0.68 (0.23), residues: 561 sheet: -0.41 (0.39), residues: 172 loop : -2.90 (0.20), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1191 HIS 0.005 0.001 HIS B 359 PHE 0.014 0.001 PHE B 673 TYR 0.019 0.001 TYR A 65 ARG 0.006 0.000 ARG A 280 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 4) link_NAG-ASN : angle 2.84681 ( 12) link_ALPHA1-4 : bond 0.01497 ( 2) link_ALPHA1-4 : angle 3.22158 ( 6) link_ALPHA1-6 : bond 0.01050 ( 2) link_ALPHA1-6 : angle 1.64764 ( 6) link_BETA1-4 : bond 0.00492 ( 3) link_BETA1-4 : angle 1.47686 ( 9) link_ALPHA1-3 : bond 0.00633 ( 2) link_ALPHA1-3 : angle 1.39136 ( 6) hydrogen bonds : bond 0.04193 ( 415) hydrogen bonds : angle 4.27357 ( 1149) SS BOND : bond 0.00246 ( 3) SS BOND : angle 2.31437 ( 6) covalent geometry : bond 0.00278 (12709) covalent geometry : angle 0.57742 (17239) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 1.496 Fit side-chains REVERT: A 104 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.5004 (m-80) REVERT: A 280 ARG cc_start: 0.8421 (ptt90) cc_final: 0.7553 (ttp80) REVERT: B 94 ASN cc_start: 0.7884 (t0) cc_final: 0.7309 (p0) REVERT: B 110 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8522 (mtp) REVERT: B 632 MET cc_start: 0.7539 (tpp) cc_final: 0.6886 (ppp) REVERT: B 640 GLN cc_start: 0.8966 (tp40) cc_final: 0.8728 (tp40) REVERT: B 652 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.5843 (ptm160) REVERT: B 673 PHE cc_start: 0.6922 (OUTLIER) cc_final: 0.5335 (p90) REVERT: B 709 LYS cc_start: 0.7807 (mmmt) cc_final: 0.7307 (tptm) REVERT: B 769 MET cc_start: 0.7302 (tmm) cc_final: 0.6638 (tmm) REVERT: B 834 MET cc_start: 0.3404 (mmm) cc_final: 0.2771 (mmm) outliers start: 18 outliers final: 13 residues processed: 113 average time/residue: 0.2532 time to fit residues: 42.3425 Evaluate side-chains 114 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 652 ARG Chi-restraints excluded: chain B residue 673 PHE Chi-restraints excluded: chain B residue 837 GLN Chi-restraints excluded: chain B residue 885 LYS Chi-restraints excluded: chain B residue 1083 THR Chi-restraints excluded: chain B residue 1084 VAL Chi-restraints excluded: chain B residue 1223 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1196 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 = 0.3492 r_free = 0.3492 target = 0.117542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.081863 restraints weight = 22115.943| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.47 r_work: 0.2785 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12725 Z= 0.122 Angle : 0.586 10.352 17284 Z= 0.296 Chirality : 0.042 0.299 1921 Planarity : 0.004 0.040 2184 Dihedral : 8.894 107.941 1943 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 1.45 % Allowed : 19.54 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.22), residues: 1512 helix: 0.73 (0.23), residues: 561 sheet: -0.33 (0.39), residues: 171 loop : -2.88 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1191 HIS 0.005 0.001 HIS B 359 PHE 0.015 0.001 PHE B 673 TYR 0.026 0.001 TYR A 65 ARG 0.008 0.000 ARG B 480 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 4) link_NAG-ASN : angle 2.87357 ( 12) link_ALPHA1-4 : bond 0.01482 ( 2) link_ALPHA1-4 : angle 3.23139 ( 6) link_ALPHA1-6 : bond 0.00974 ( 2) link_ALPHA1-6 : angle 1.58973 ( 6) link_BETA1-4 : bond 0.00483 ( 3) link_BETA1-4 : angle 1.43518 ( 9) link_ALPHA1-3 : bond 0.00564 ( 2) link_ALPHA1-3 : angle 1.46206 ( 6) hydrogen bonds : bond 0.04162 ( 415) hydrogen bonds : angle 4.24693 ( 1149) SS BOND : bond 0.00212 ( 3) SS BOND : angle 2.29808 ( 6) covalent geometry : bond 0.00276 (12709) covalent geometry : angle 0.57518 (17239) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 1.353 Fit side-chains REVERT: A 104 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.4991 (m-80) REVERT: A 280 ARG cc_start: 0.8430 (ptt90) cc_final: 0.7544 (ttp80) REVERT: B 94 ASN cc_start: 0.7947 (t0) cc_final: 0.7304 (p0) REVERT: B 110 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8502 (mtp) REVERT: B 266 GLU cc_start: 0.8472 (pt0) cc_final: 0.8236 (pm20) REVERT: B 632 MET cc_start: 0.7506 (tpp) cc_final: 0.6895 (ppp) REVERT: B 640 GLN cc_start: 0.8969 (tp40) cc_final: 0.8733 (tp40) REVERT: B 652 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.5890 (ptm160) REVERT: B 673 PHE cc_start: 0.6914 (OUTLIER) cc_final: 0.5322 (p90) REVERT: B 709 LYS cc_start: 0.7780 (mmmt) cc_final: 0.7430 (tptm) REVERT: B 769 MET cc_start: 0.7301 (tmm) cc_final: 0.6576 (tmm) REVERT: B 834 MET cc_start: 0.3388 (mmm) cc_final: 0.2746 (mmm) outliers start: 19 outliers final: 13 residues processed: 115 average time/residue: 0.2698 time to fit residues: 46.0343 Evaluate side-chains 113 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 652 ARG Chi-restraints excluded: chain B residue 673 PHE Chi-restraints excluded: chain B residue 837 GLN Chi-restraints excluded: chain B residue 885 LYS Chi-restraints excluded: chain B residue 1083 THR Chi-restraints excluded: chain B residue 1084 VAL Chi-restraints excluded: chain B residue 1223 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 28 optimal weight: 0.2980 chunk 139 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 112 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 HIS ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.116790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.080816 restraints weight = 22227.198| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.54 r_work: 0.2759 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12725 Z= 0.140 Angle : 0.600 10.479 17284 Z= 0.304 Chirality : 0.043 0.303 1921 Planarity : 0.004 0.091 2184 Dihedral : 8.896 108.126 1943 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 1.37 % Allowed : 19.85 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.21), residues: 1512 helix: 0.68 (0.23), residues: 562 sheet: -0.35 (0.39), residues: 172 loop : -2.88 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B1191 HIS 0.004 0.001 HIS B 359 PHE 0.015 0.001 PHE B 673 TYR 0.025 0.001 TYR A 65 ARG 0.007 0.000 ARG A 280 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 4) link_NAG-ASN : angle 2.89789 ( 12) link_ALPHA1-4 : bond 0.01419 ( 2) link_ALPHA1-4 : angle 3.19864 ( 6) link_ALPHA1-6 : bond 0.00908 ( 2) link_ALPHA1-6 : angle 1.58415 ( 6) link_BETA1-4 : bond 0.00465 ( 3) link_BETA1-4 : angle 1.45289 ( 9) link_ALPHA1-3 : bond 0.00541 ( 2) link_ALPHA1-3 : angle 1.48927 ( 6) hydrogen bonds : bond 0.04449 ( 415) hydrogen bonds : angle 4.28895 ( 1149) SS BOND : bond 0.00153 ( 3) SS BOND : angle 2.53820 ( 6) covalent geometry : bond 0.00326 (12709) covalent geometry : angle 0.58822 (17239) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7262.58 seconds wall clock time: 127 minutes 56.80 seconds (7676.80 seconds total)