Starting phenix.real_space_refine on Wed Mar 4 14:21:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zgj_14707/03_2026/7zgj_14707_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zgj_14707/03_2026/7zgj_14707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zgj_14707/03_2026/7zgj_14707_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zgj_14707/03_2026/7zgj_14707_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zgj_14707/03_2026/7zgj_14707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zgj_14707/03_2026/7zgj_14707.map" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 9073 2.51 5 N 2434 2.21 5 O 2743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14314 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5014 Classifications: {'peptide': 643} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 604} Chain: "B" Number of atoms: 7765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 970, 7765 Classifications: {'peptide': 970} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 42, 'TRANS': 927} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1535 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 4, 'TRANS': 187} Chain breaks: 2 Time building chain proxies: 3.14, per 1000 atoms: 0.22 Number of scatterers: 14314 At special positions: 0 Unit cell: (92.02, 148.78, 159.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 2743 8.00 N 2434 7.00 C 9073 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 559 " - pdb=" SG CYS B 816 " distance=2.03 Simple disulfide: pdb=" SG CYS A 627 " - pdb=" SG CYS A 662 " distance=2.03 Simple disulfide: pdb=" SG CYS B 693 " - pdb=" SG CYS B 720 " distance=2.03 Simple disulfide: pdb=" SG CYS B 694 " - pdb=" SG CYS B 727 " distance=2.03 Simple disulfide: pdb=" SG CYS B 707 " - pdb=" SG CYS B 728 " distance=2.03 Simple disulfide: pdb=" SG CYS B 873 " - pdb=" SG CYS B1513 " distance=2.03 Simple disulfide: pdb=" SG CYS B1101 " - pdb=" SG CYS B1158 " distance=2.03 Simple disulfide: pdb=" SG CYS B1358 " - pdb=" SG CYS B1489 " distance=2.03 Simple disulfide: pdb=" SG CYS B1389 " - pdb=" SG CYS B1458 " distance=2.04 Simple disulfide: pdb=" SG CYS B1506 " - pdb=" SG CYS B1511 " distance=2.03 Simple disulfide: pdb=" SG CYS B1518 " - pdb=" SG CYS B1590 " distance=2.03 Simple disulfide: pdb=" SG CYS B1537 " - pdb=" SG CYS B1661 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 655.6 milliseconds 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3402 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 23 sheets defined 29.2% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 77 through 81 Processing helix chain 'A' and resid 303 through 311 removed outlier: 4.011A pdb=" N VAL A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 526 Processing helix chain 'A' and resid 600 through 606 Processing helix chain 'A' and resid 612 through 623 removed outlier: 3.755A pdb=" N ALA A 623 " --> pdb=" O VAL A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 643 removed outlier: 3.706A pdb=" N PHE A 639 " --> pdb=" O TYR A 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 685 removed outlier: 3.894A pdb=" N LYS B 685 " --> pdb=" O ASP B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 699 Processing helix chain 'B' and resid 706 through 712 removed outlier: 3.777A pdb=" N ARG B 712 " --> pdb=" O GLN B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 739 removed outlier: 4.165A pdb=" N LYS B 721 " --> pdb=" O GLY B 717 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS B 722 " --> pdb=" O GLU B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 996 removed outlier: 3.664A pdb=" N VAL B 995 " --> pdb=" O THR B 991 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP B 996 " --> pdb=" O GLU B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1004 removed outlier: 3.781A pdb=" N ILE B1004 " --> pdb=" O LYS B1001 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1017 removed outlier: 3.715A pdb=" N GLY B1017 " --> pdb=" O ASN B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1031 removed outlier: 3.582A pdb=" N THR B1031 " --> pdb=" O TYR B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1038 Processing helix chain 'B' and resid 1040 through 1057 removed outlier: 4.044A pdb=" N GLY B1044 " --> pdb=" O GLU B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1060 No H-bonds generated for 'chain 'B' and resid 1058 through 1060' Processing helix chain 'B' and resid 1075 through 1091 removed outlier: 4.546A pdb=" N ASN B1091 " --> pdb=" O SER B1087 " (cutoff:3.500A) Processing helix chain 'B' and resid 1096 through 1110 removed outlier: 3.723A pdb=" N LEU B1100 " --> pdb=" O ASP B1096 " (cutoff:3.500A) Processing helix chain 'B' and resid 1135 through 1154 removed outlier: 3.691A pdb=" N LYS B1139 " --> pdb=" O ASN B1135 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP B1140 " --> pdb=" O ASN B1136 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B1153 " --> pdb=" O ILE B1149 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B1154 " --> pdb=" O SER B1150 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1179 Processing helix chain 'B' and resid 1185 through 1200 Processing helix chain 'B' and resid 1204 through 1213 removed outlier: 3.516A pdb=" N ASN B1208 " --> pdb=" O GLY B1204 " (cutoff:3.500A) Processing helix chain 'B' and resid 1226 through 1244 removed outlier: 3.751A pdb=" N VAL B1230 " --> pdb=" O GLN B1226 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU B1231 " --> pdb=" O LEU B1227 " (cutoff:3.500A) Processing helix chain 'B' and resid 1248 through 1258 removed outlier: 4.250A pdb=" N VAL B1252 " --> pdb=" O PHE B1248 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TRP B1255 " --> pdb=" O PRO B1251 " (cutoff:3.500A) Processing helix chain 'B' and resid 1268 through 1285 Processing helix chain 'B' and resid 1414 through 1424 removed outlier: 3.610A pdb=" N LEU B1418 " --> pdb=" O ASP B1414 " (cutoff:3.500A) Processing helix chain 'B' and resid 1509 through 1515 Processing helix chain 'B' and resid 1528 through 1537 Processing helix chain 'B' and resid 1590 through 1595 removed outlier: 4.162A pdb=" N LYS B1595 " --> pdb=" O ARG B1591 " (cutoff:3.500A) Processing helix chain 'B' and resid 1609 through 1611 No H-bonds generated for 'chain 'B' and resid 1609 through 1611' Processing helix chain 'B' and resid 1644 through 1655 removed outlier: 3.646A pdb=" N SER B1655 " --> pdb=" O ALA B1651 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 55 Processing helix chain 'C' and resid 55 through 63 removed outlier: 3.520A pdb=" N ASP C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 85 removed outlier: 3.928A pdb=" N GLY C 69 " --> pdb=" O GLN C 65 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE C 73 " --> pdb=" O GLY C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 removed outlier: 3.649A pdb=" N ALA C 96 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 119 removed outlier: 3.572A pdb=" N GLU C 104 " --> pdb=" O ASP C 100 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 105 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS C 119 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 145 removed outlier: 3.569A pdb=" N ALA C 124 " --> pdb=" O GLN C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 211 removed outlier: 3.566A pdb=" N GLU C 206 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR C 209 " --> pdb=" O GLU C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 226 removed outlier: 4.372A pdb=" N ALA C 219 " --> pdb=" O ALA C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 300 removed outlier: 3.722A pdb=" N THR C 264 " --> pdb=" O PRO C 260 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL C 265 " --> pdb=" O TYR C 261 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLU C 266 " --> pdb=" O LYS C 262 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY C 287 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA C 292 " --> pdb=" O TYR C 288 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 312 removed outlier: 3.662A pdb=" N VAL C 308 " --> pdb=" O PRO C 304 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 88 removed outlier: 8.529A pdb=" N THR A 41 " --> pdb=" O PRO A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 35 removed outlier: 5.890A pdb=" N VAL A 59 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N SER A 70 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 134 Processing sheet with id=AA4, first strand: chain 'A' and resid 138 through 139 removed outlier: 6.701A pdb=" N VAL A 163 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER A 179 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL A 165 " --> pdb=" O GLN A 177 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLN A 177 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE A 167 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 233 through 238 Processing sheet with id=AA6, first strand: chain 'A' and resid 280 through 293 removed outlier: 5.379A pdb=" N PHE A 273 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 8.883A pdb=" N GLU A 286 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 10.655A pdb=" N VAL A 271 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 9.757A pdb=" N LEU A 288 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 11.059A pdb=" N ALA A 269 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.216A pdb=" N ARG A 290 " --> pdb=" O GLY A 267 " (cutoff:3.500A) removed outlier: 11.394A pdb=" N GLY A 267 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY A 345 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 339 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 363 through 364 Processing sheet with id=AA8, first strand: chain 'A' and resid 370 through 375 Processing sheet with id=AA9, first strand: chain 'A' and resid 455 through 460 removed outlier: 3.963A pdb=" N GLU A 469 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 521 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 499 through 507 removed outlier: 5.393A pdb=" N LEU A 500 " --> pdb=" O ASN A 496 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN A 496 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 502 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N TYR A 489 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N THR A 536 " --> pdb=" O TYR A 489 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 564 through 566 removed outlier: 3.513A pdb=" N GLY A 587 " --> pdb=" O SER B 787 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 580 through 581 Processing sheet with id=AB4, first strand: chain 'B' and resid 771 through 777 removed outlier: 5.481A pdb=" N LEU B 772 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA A 597 " --> pdb=" O LEU B 772 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN B 774 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 771 through 777 removed outlier: 5.481A pdb=" N LEU B 772 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA A 597 " --> pdb=" O LEU B 772 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN B 774 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 829 through 834 removed outlier: 3.685A pdb=" N ARG B 848 " --> pdb=" O ARG B 834 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN B 853 " --> pdb=" O SER B 892 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER B 892 " --> pdb=" O ASN B 853 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 839 through 840 removed outlier: 3.503A pdb=" N LEU B 866 " --> pdb=" O HIS B 882 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N HIS B 882 " --> pdb=" O LEU B 866 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 844 through 845 removed outlier: 3.628A pdb=" N GLN B 844 " --> pdb=" O GLU B1470 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 872 through 874 Processing sheet with id=AC1, first strand: chain 'B' and resid 936 through 947 removed outlier: 6.539A pdb=" N VAL B1344 " --> pdb=" O VAL B 942 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL B 944 " --> pdb=" O LEU B1342 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU B1342 " --> pdb=" O VAL B 944 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N THR B 946 " --> pdb=" O GLY B1340 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLY B1340 " --> pdb=" O THR B 946 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 958 through 962 removed outlier: 4.375A pdb=" N THR B1331 " --> pdb=" O GLN B1299 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN B1299 " --> pdb=" O THR B1331 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1364 through 1369 Processing sheet with id=AC4, first strand: chain 'B' and resid 1431 through 1432 removed outlier: 3.531A pdb=" N LYS B1431 " --> pdb=" O TYR B1447 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA B1476 " --> pdb=" O SER B1406 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1620 through 1621 removed outlier: 3.615A pdb=" N GLU B1560 " --> pdb=" O GLN B1553 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ALA B1564 " --> pdb=" O LEU B1549 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LEU B1549 " --> pdb=" O ALA B1564 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N GLU B1566 " --> pdb=" O THR B1547 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR B1547 " --> pdb=" O GLU B1566 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR B1568 " --> pdb=" O TYR B1545 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N TYR B1545 " --> pdb=" O THR B1568 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LYS B1570 " --> pdb=" O TYR B1543 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR B1543 " --> pdb=" O LYS B1570 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR B1543 " --> pdb=" O GLY B1606 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY B1606 " --> pdb=" O TYR B1543 " (cutoff:3.500A) 609 hydrogen bonds defined for protein. 1689 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.91 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2697 1.33 - 1.45: 3460 1.45 - 1.57: 8335 1.57 - 1.70: 0 1.70 - 1.82: 101 Bond restraints: 14593 Sorted by residual: bond pdb=" N CYS B1389 " pdb=" CA CYS B1389 " ideal model delta sigma weight residual 1.454 1.490 -0.035 1.15e-02 7.56e+03 9.44e+00 bond pdb=" N ILE C 309 " pdb=" CA ILE C 309 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.70e+00 bond pdb=" N GLN C 301 " pdb=" CA GLN C 301 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.09e-02 8.42e+03 8.65e+00 bond pdb=" N ASP B1508 " pdb=" CA ASP B1508 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.14e-02 7.69e+03 8.38e+00 bond pdb=" N LYS C 303 " pdb=" CA LYS C 303 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.21e-02 6.83e+03 7.88e+00 ... (remaining 14588 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 19199 1.13 - 2.25: 359 2.25 - 3.38: 142 3.38 - 4.51: 43 4.51 - 5.63: 8 Bond angle restraints: 19751 Sorted by residual: angle pdb=" N LYS C 298 " pdb=" CA LYS C 298 " pdb=" C LYS C 298 " ideal model delta sigma weight residual 111.40 105.90 5.50 1.22e+00 6.72e-01 2.03e+01 angle pdb=" N VAL C 299 " pdb=" CA VAL C 299 " pdb=" C VAL C 299 " ideal model delta sigma weight residual 112.04 106.43 5.61 1.40e+00 5.10e-01 1.60e+01 angle pdb=" CA LEU C 305 " pdb=" C LEU C 305 " pdb=" O LEU C 305 " ideal model delta sigma weight residual 120.92 116.71 4.21 1.12e+00 7.97e-01 1.41e+01 angle pdb=" CA VAL C 295 " pdb=" C VAL C 295 " pdb=" O VAL C 295 " ideal model delta sigma weight residual 120.64 116.54 4.10 1.09e+00 8.42e-01 1.41e+01 angle pdb=" N PRO C 304 " pdb=" CA PRO C 304 " pdb=" C PRO C 304 " ideal model delta sigma weight residual 111.57 117.20 -5.63 1.52e+00 4.33e-01 1.37e+01 ... (remaining 19746 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 8183 17.87 - 35.74: 595 35.74 - 53.60: 132 53.60 - 71.47: 28 71.47 - 89.34: 13 Dihedral angle restraints: 8951 sinusoidal: 3684 harmonic: 5267 Sorted by residual: dihedral pdb=" CB CYS B1537 " pdb=" SG CYS B1537 " pdb=" SG CYS B1661 " pdb=" CB CYS B1661 " ideal model delta sinusoidal sigma weight residual 93.00 -178.37 -88.63 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS B1518 " pdb=" SG CYS B1518 " pdb=" SG CYS B1590 " pdb=" CB CYS B1590 " ideal model delta sinusoidal sigma weight residual 93.00 150.28 -57.28 1 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" CB CYS B1389 " pdb=" SG CYS B1389 " pdb=" SG CYS B1458 " pdb=" CB CYS B1458 " ideal model delta sinusoidal sigma weight residual -86.00 -29.44 -56.56 1 1.00e+01 1.00e-02 4.31e+01 ... (remaining 8948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1601 0.035 - 0.069: 350 0.069 - 0.104: 140 0.104 - 0.138: 121 0.138 - 0.173: 7 Chirality restraints: 2219 Sorted by residual: chirality pdb=" CA ILE B1388 " pdb=" N ILE B1388 " pdb=" C ILE B1388 " pdb=" CB ILE B1388 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CA VAL C 299 " pdb=" N VAL C 299 " pdb=" C VAL C 299 " pdb=" CB VAL C 299 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CA LEU B1459 " pdb=" N LEU B1459 " pdb=" C LEU B1459 " pdb=" CB LEU B1459 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.42e-01 ... (remaining 2216 not shown) Planarity restraints: 2551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 303 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.80e+00 pdb=" C LYS C 303 " 0.042 2.00e-02 2.50e+03 pdb=" O LYS C 303 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO C 304 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 223 " -0.015 2.00e-02 2.50e+03 1.51e-02 5.67e+00 pdb=" CG TRP C 223 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP C 223 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP C 223 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 223 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 223 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 223 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 223 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 223 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 223 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B1507 " -0.010 2.00e-02 2.50e+03 1.90e-02 3.60e+00 pdb=" C ARG B1507 " 0.033 2.00e-02 2.50e+03 pdb=" O ARG B1507 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP B1508 " -0.011 2.00e-02 2.50e+03 ... (remaining 2548 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 16 2.34 - 2.98: 6875 2.98 - 3.62: 19341 3.62 - 4.26: 28918 4.26 - 4.90: 50292 Nonbonded interactions: 105442 Sorted by model distance: nonbonded pdb=" SG CYS B1010 " pdb=" CD GLN B1013 " model vdw 1.696 3.630 nonbonded pdb=" O LEU B1109 " pdb=" NH2 ARG C 77 " model vdw 1.829 3.120 nonbonded pdb=" O ALA C 219 " pdb=" OG SER C 222 " model vdw 2.025 3.040 nonbonded pdb=" OD1 ASP C 210 " pdb=" OG SER C 212 " model vdw 2.025 3.040 nonbonded pdb=" OG1 THR C 35 " pdb=" OE1 GLU C 37 " model vdw 2.108 3.040 ... (remaining 105437 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.920 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 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 : 0.002 0.035 14605 Z= 0.165 Angle : 0.477 5.633 19775 Z= 0.278 Chirality : 0.043 0.173 2219 Planarity : 0.003 0.033 2551 Dihedral : 13.365 89.340 5513 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.23 % Favored : 97.71 % Rotamer: Outliers : 0.82 % Allowed : 0.32 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.20), residues: 1791 helix: 3.10 (0.26), residues: 430 sheet: 0.94 (0.22), residues: 545 loop : -0.55 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1512 TYR 0.015 0.001 TYR A 385 PHE 0.005 0.001 PHE A 475 TRP 0.041 0.001 TRP C 223 HIS 0.003 0.000 HIS B1494 Details of bonding type rmsd covalent geometry : bond 0.00247 (14593) covalent geometry : angle 0.47536 (19751) SS BOND : bond 0.00185 ( 12) SS BOND : angle 1.18301 ( 24) hydrogen bonds : bond 0.15046 ( 598) hydrogen bonds : angle 5.57067 ( 1689) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 300 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1430 SER cc_start: 0.7870 (m) cc_final: 0.7427 (t) REVERT: C 257 TRP cc_start: 0.1945 (m-10) cc_final: 0.1735 (m-10) outliers start: 13 outliers final: 5 residues processed: 309 average time/residue: 0.1354 time to fit residues: 58.7845 Evaluate side-chains 176 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 171 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1013 GLN Chi-restraints excluded: chain B residue 1390 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 309 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN B 792 ASN B1119 GLN B1259 GLN C 58 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.100685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.072548 restraints weight = 39241.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.075294 restraints weight = 18284.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.077095 restraints weight = 11687.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.078223 restraints weight = 8872.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.078862 restraints weight = 7489.718| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14605 Z= 0.136 Angle : 0.590 12.274 19775 Z= 0.302 Chirality : 0.043 0.196 2219 Planarity : 0.004 0.053 2551 Dihedral : 3.802 63.650 1957 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.71 % Allowed : 8.46 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.20), residues: 1791 helix: 2.72 (0.24), residues: 452 sheet: 1.06 (0.22), residues: 537 loop : -0.65 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 736 TYR 0.019 0.001 TYR A 261 PHE 0.009 0.001 PHE A 475 TRP 0.012 0.001 TRP C 223 HIS 0.006 0.001 HIS A 483 Details of bonding type rmsd covalent geometry : bond 0.00316 (14593) covalent geometry : angle 0.58463 (19751) SS BOND : bond 0.00515 ( 12) SS BOND : angle 2.41860 ( 24) hydrogen bonds : bond 0.03814 ( 598) hydrogen bonds : angle 4.34238 ( 1689) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.7857 (m110) REVERT: A 178 ASP cc_start: 0.8259 (t70) cc_final: 0.8018 (t0) REVERT: A 372 LEU cc_start: 0.8517 (mp) cc_final: 0.8174 (mp) REVERT: A 549 ASP cc_start: 0.7937 (t70) cc_final: 0.7620 (t70) REVERT: B 698 MET cc_start: 0.7564 (mmp) cc_final: 0.7326 (mmp) REVERT: B 832 ASP cc_start: 0.8898 (t0) cc_final: 0.8637 (t0) REVERT: B 917 TYR cc_start: 0.7672 (m-10) cc_final: 0.7460 (m-80) REVERT: B 1388 ILE cc_start: 0.8793 (pt) cc_final: 0.8476 (pt) REVERT: B 1545 TYR cc_start: 0.7820 (m-80) cc_final: 0.7237 (m-10) REVERT: B 1551 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8093 (ptmm) REVERT: B 1620 TYR cc_start: 0.8075 (m-80) cc_final: 0.7439 (m-10) REVERT: C 210 ASP cc_start: 0.9552 (t0) cc_final: 0.9297 (p0) REVERT: C 296 ASN cc_start: 0.8632 (t0) cc_final: 0.8359 (t0) outliers start: 27 outliers final: 13 residues processed: 188 average time/residue: 0.1131 time to fit residues: 31.7764 Evaluate side-chains 154 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASN Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain B residue 1390 THR Chi-restraints excluded: chain B residue 1549 LEU Chi-restraints excluded: chain B residue 1551 LYS Chi-restraints excluded: chain B residue 1559 ASP Chi-restraints excluded: chain C residue 102 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 72 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 151 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 139 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS A 200 ASN A 579 GLN A 664 GLN B 858 GLN B1453 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.089970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.060752 restraints weight = 40394.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.063155 restraints weight = 19674.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.064780 restraints weight = 12927.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.065698 restraints weight = 9978.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.066380 restraints weight = 8583.586| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14605 Z= 0.226 Angle : 0.652 15.305 19775 Z= 0.343 Chirality : 0.045 0.266 2219 Planarity : 0.004 0.048 2551 Dihedral : 4.270 33.148 1949 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.72 % Allowed : 9.48 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.20), residues: 1791 helix: 2.34 (0.24), residues: 444 sheet: 0.73 (0.22), residues: 539 loop : -0.94 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 736 TYR 0.019 0.002 TYR B1261 PHE 0.020 0.002 PHE B1519 TRP 0.013 0.002 TRP C 223 HIS 0.009 0.001 HIS B1464 Details of bonding type rmsd covalent geometry : bond 0.00538 (14593) covalent geometry : angle 0.64517 (19751) SS BOND : bond 0.00759 ( 12) SS BOND : angle 2.86827 ( 24) hydrogen bonds : bond 0.05056 ( 598) hydrogen bonds : angle 4.65160 ( 1689) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 135 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.8296 (t0) REVERT: A 201 MET cc_start: 0.7989 (mmm) cc_final: 0.6085 (mmm) REVERT: A 237 GLU cc_start: 0.8344 (pt0) cc_final: 0.8131 (pm20) REVERT: B 698 MET cc_start: 0.8152 (mmp) cc_final: 0.7902 (mmp) REVERT: B 826 MET cc_start: 0.8385 (pmm) cc_final: 0.7663 (pmm) REVERT: B 832 ASP cc_start: 0.9113 (t0) cc_final: 0.8745 (t0) REVERT: B 917 TYR cc_start: 0.7935 (m-10) cc_final: 0.7666 (m-80) REVERT: B 1545 TYR cc_start: 0.7992 (m-80) cc_final: 0.7603 (m-10) REVERT: B 1597 GLU cc_start: 0.9106 (tt0) cc_final: 0.8828 (tm-30) REVERT: B 1610 ASP cc_start: 0.7948 (m-30) cc_final: 0.7728 (m-30) REVERT: C 56 ARG cc_start: 0.9200 (tpt170) cc_final: 0.8987 (tpp80) REVERT: C 58 GLN cc_start: 0.9261 (tp40) cc_final: 0.8805 (tp-100) REVERT: C 92 LYS cc_start: 0.4993 (tttt) cc_final: 0.4679 (tttp) REVERT: C 210 ASP cc_start: 0.9597 (t0) cc_final: 0.9278 (p0) REVERT: C 293 TYR cc_start: 0.8157 (t80) cc_final: 0.7946 (t80) outliers start: 43 outliers final: 26 residues processed: 170 average time/residue: 0.1123 time to fit residues: 28.7425 Evaluate side-chains 147 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASN Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1390 THR Chi-restraints excluded: chain B residue 1544 VAL Chi-restraints excluded: chain B residue 1557 ASP Chi-restraints excluded: chain B residue 1559 ASP Chi-restraints excluded: chain B residue 1594 LEU Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 102 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 96 optimal weight: 0.4980 chunk 122 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN A 457 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.089644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.059675 restraints weight = 40896.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.062222 restraints weight = 19198.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.063925 restraints weight = 12435.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.064998 restraints weight = 9544.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.065603 restraints weight = 8126.237| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14605 Z= 0.160 Angle : 0.565 12.264 19775 Z= 0.294 Chirality : 0.043 0.239 2219 Planarity : 0.004 0.048 2551 Dihedral : 3.999 29.047 1949 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.34 % Allowed : 11.24 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.20), residues: 1791 helix: 2.52 (0.24), residues: 442 sheet: 0.75 (0.22), residues: 540 loop : -0.93 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 736 TYR 0.016 0.001 TYR A 261 PHE 0.024 0.001 PHE B1519 TRP 0.015 0.001 TRP C 223 HIS 0.005 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00381 (14593) covalent geometry : angle 0.55611 (19751) SS BOND : bond 0.00388 ( 12) SS BOND : angle 2.93788 ( 24) hydrogen bonds : bond 0.03964 ( 598) hydrogen bonds : angle 4.39711 ( 1689) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.7807 (ptp) cc_final: 0.7260 (ptp) REVERT: A 237 GLU cc_start: 0.8395 (pt0) cc_final: 0.8041 (pm20) REVERT: A 624 ASP cc_start: 0.8307 (t0) cc_final: 0.7911 (t0) REVERT: B 826 MET cc_start: 0.8516 (pmm) cc_final: 0.8032 (pmm) REVERT: B 832 ASP cc_start: 0.9170 (t0) cc_final: 0.8736 (t0) REVERT: B 917 TYR cc_start: 0.8064 (m-10) cc_final: 0.7761 (m-80) REVERT: B 1545 TYR cc_start: 0.7973 (m-80) cc_final: 0.7454 (m-10) REVERT: B 1597 GLU cc_start: 0.9186 (tt0) cc_final: 0.8849 (tp30) REVERT: B 1610 ASP cc_start: 0.7978 (m-30) cc_final: 0.7719 (m-30) REVERT: B 1659 PHE cc_start: 0.8670 (t80) cc_final: 0.8046 (t80) REVERT: C 56 ARG cc_start: 0.9201 (tpt170) cc_final: 0.8920 (tpp80) REVERT: C 58 GLN cc_start: 0.9304 (tp40) cc_final: 0.8965 (tp40) REVERT: C 92 LYS cc_start: 0.5055 (tttt) cc_final: 0.4754 (tttp) REVERT: C 111 ASN cc_start: 0.9277 (m-40) cc_final: 0.9044 (p0) REVERT: C 210 ASP cc_start: 0.9616 (t0) cc_final: 0.9269 (p0) outliers start: 37 outliers final: 27 residues processed: 160 average time/residue: 0.1147 time to fit residues: 27.6506 Evaluate side-chains 145 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 1390 THR Chi-restraints excluded: chain B residue 1479 VAL Chi-restraints excluded: chain B residue 1544 VAL Chi-restraints excluded: chain B residue 1549 LEU Chi-restraints excluded: chain B residue 1557 ASP Chi-restraints excluded: chain B residue 1559 ASP Chi-restraints excluded: chain B residue 1594 LEU Chi-restraints excluded: chain B residue 1595 LYS Chi-restraints excluded: chain B residue 1626 THR Chi-restraints excluded: chain B residue 1652 PHE Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 89 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 108 optimal weight: 0.2980 chunk 133 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 170 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 20 optimal weight: 0.3980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1423 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.089433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.059374 restraints weight = 40402.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.061920 restraints weight = 18985.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.063594 restraints weight = 12290.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.064680 restraints weight = 9445.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.065338 restraints weight = 8043.755| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14605 Z= 0.135 Angle : 0.548 10.726 19775 Z= 0.283 Chirality : 0.042 0.210 2219 Planarity : 0.003 0.045 2551 Dihedral : 3.879 25.944 1949 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.72 % Allowed : 12.26 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.20), residues: 1791 helix: 2.57 (0.24), residues: 442 sheet: 0.77 (0.22), residues: 545 loop : -0.93 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 102 TYR 0.014 0.001 TYR A 261 PHE 0.026 0.001 PHE B1519 TRP 0.020 0.001 TRP C 223 HIS 0.005 0.001 HIS B 918 Details of bonding type rmsd covalent geometry : bond 0.00318 (14593) covalent geometry : angle 0.53987 (19751) SS BOND : bond 0.00277 ( 12) SS BOND : angle 2.71694 ( 24) hydrogen bonds : bond 0.03777 ( 598) hydrogen bonds : angle 4.26212 ( 1689) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.7869 (tpp) cc_final: 0.7603 (tpp) REVERT: A 32 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.7746 (m-40) REVERT: A 164 MET cc_start: 0.7800 (ptp) cc_final: 0.7260 (ptp) REVERT: A 201 MET cc_start: 0.7999 (mmm) cc_final: 0.6531 (mmm) REVERT: A 237 GLU cc_start: 0.8375 (pt0) cc_final: 0.8030 (pm20) REVERT: A 624 ASP cc_start: 0.8289 (t0) cc_final: 0.7802 (t0) REVERT: B 826 MET cc_start: 0.8503 (pmm) cc_final: 0.8017 (pmm) REVERT: B 832 ASP cc_start: 0.9190 (t0) cc_final: 0.8740 (t0) REVERT: B 917 TYR cc_start: 0.8062 (m-10) cc_final: 0.7775 (m-80) REVERT: B 937 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8444 (ttm-80) REVERT: B 1592 GLU cc_start: 0.8784 (pp20) cc_final: 0.8552 (pp20) REVERT: B 1597 GLU cc_start: 0.9169 (tt0) cc_final: 0.8870 (tp30) REVERT: B 1610 ASP cc_start: 0.7832 (m-30) cc_final: 0.7617 (m-30) REVERT: B 1659 PHE cc_start: 0.8768 (t80) cc_final: 0.8147 (t80) REVERT: C 56 ARG cc_start: 0.9161 (tpt170) cc_final: 0.8928 (tpp80) REVERT: C 58 GLN cc_start: 0.9337 (tp40) cc_final: 0.8971 (tp40) REVERT: C 92 LYS cc_start: 0.5126 (tttt) cc_final: 0.4810 (tttp) REVERT: C 111 ASN cc_start: 0.9276 (m-40) cc_final: 0.9063 (p0) REVERT: C 210 ASP cc_start: 0.9615 (t0) cc_final: 0.9263 (p0) outliers start: 43 outliers final: 29 residues processed: 165 average time/residue: 0.1108 time to fit residues: 27.5442 Evaluate side-chains 148 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASN Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 937 ARG Chi-restraints excluded: chain B residue 1390 THR Chi-restraints excluded: chain B residue 1458 CYS Chi-restraints excluded: chain B residue 1479 VAL Chi-restraints excluded: chain B residue 1515 GLU Chi-restraints excluded: chain B residue 1544 VAL Chi-restraints excluded: chain B residue 1557 ASP Chi-restraints excluded: chain B residue 1559 ASP Chi-restraints excluded: chain B residue 1594 LEU Chi-restraints excluded: chain B residue 1626 THR Chi-restraints excluded: chain B residue 1652 PHE Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 89 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 123 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1420 GLN ** B1494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.087115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.056882 restraints weight = 41285.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.059270 restraints weight = 19906.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.060884 restraints weight = 13112.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.061893 restraints weight = 10171.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.062546 restraints weight = 8732.542| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14605 Z= 0.242 Angle : 0.630 11.154 19775 Z= 0.329 Chirality : 0.044 0.237 2219 Planarity : 0.004 0.044 2551 Dihedral : 4.323 28.799 1949 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.84 % Allowed : 12.44 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.20), residues: 1791 helix: 2.35 (0.24), residues: 440 sheet: 0.52 (0.22), residues: 551 loop : -1.02 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 148 TYR 0.015 0.002 TYR B1261 PHE 0.025 0.002 PHE B1519 TRP 0.022 0.001 TRP C 223 HIS 0.007 0.001 HIS B1464 Details of bonding type rmsd covalent geometry : bond 0.00577 (14593) covalent geometry : angle 0.62192 (19751) SS BOND : bond 0.00355 ( 12) SS BOND : angle 3.02652 ( 24) hydrogen bonds : bond 0.04840 ( 598) hydrogen bonds : angle 4.67441 ( 1689) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 128 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.7956 (ptp) cc_final: 0.7601 (ptp) REVERT: A 201 MET cc_start: 0.7654 (mmm) cc_final: 0.7212 (mmm) REVERT: A 237 GLU cc_start: 0.8422 (pt0) cc_final: 0.8062 (pm20) REVERT: A 493 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8881 (mt) REVERT: A 624 ASP cc_start: 0.8449 (t0) cc_final: 0.7960 (t0) REVERT: B 826 MET cc_start: 0.8498 (pmm) cc_final: 0.7949 (pmm) REVERT: B 832 ASP cc_start: 0.9221 (t0) cc_final: 0.8739 (t0) REVERT: B 917 TYR cc_start: 0.8179 (m-10) cc_final: 0.7901 (m-80) REVERT: B 937 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8510 (ttm-80) REVERT: B 1567 GLN cc_start: 0.8312 (tm-30) cc_final: 0.7774 (tm-30) REVERT: B 1597 GLU cc_start: 0.9205 (tt0) cc_final: 0.8935 (tp30) REVERT: C 45 MET cc_start: 0.9295 (mmt) cc_final: 0.9081 (mmm) REVERT: C 56 ARG cc_start: 0.9166 (tpt170) cc_final: 0.8913 (tpp80) REVERT: C 65 GLN cc_start: 0.9219 (mt0) cc_final: 0.8979 (mm-40) REVERT: C 92 LYS cc_start: 0.5193 (tttt) cc_final: 0.4941 (tttp) REVERT: C 210 ASP cc_start: 0.9641 (t0) cc_final: 0.9260 (p0) outliers start: 45 outliers final: 34 residues processed: 163 average time/residue: 0.1161 time to fit residues: 28.3635 Evaluate side-chains 155 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 937 ARG Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1390 THR Chi-restraints excluded: chain B residue 1458 CYS Chi-restraints excluded: chain B residue 1479 VAL Chi-restraints excluded: chain B residue 1544 VAL Chi-restraints excluded: chain B residue 1549 LEU Chi-restraints excluded: chain B residue 1557 ASP Chi-restraints excluded: chain B residue 1559 ASP Chi-restraints excluded: chain B residue 1594 LEU Chi-restraints excluded: chain B residue 1595 LYS Chi-restraints excluded: chain B residue 1626 THR Chi-restraints excluded: chain B residue 1652 PHE Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 259 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 125 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 149 optimal weight: 20.0000 chunk 22 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 4 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 173 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1494 HIS C 111 ASN ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.088977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.059005 restraints weight = 40150.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.061521 restraints weight = 18956.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.063214 restraints weight = 12304.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.064246 restraints weight = 9458.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.064945 restraints weight = 8080.707| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14605 Z= 0.114 Angle : 0.540 10.142 19775 Z= 0.280 Chirality : 0.042 0.200 2219 Planarity : 0.004 0.042 2551 Dihedral : 3.959 25.904 1949 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.34 % Allowed : 13.14 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.20), residues: 1791 helix: 2.50 (0.24), residues: 448 sheet: 0.76 (0.23), residues: 515 loop : -0.96 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 573 TYR 0.013 0.001 TYR A 261 PHE 0.028 0.001 PHE B1519 TRP 0.026 0.001 TRP C 223 HIS 0.004 0.001 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.00261 (14593) covalent geometry : angle 0.53298 (19751) SS BOND : bond 0.00295 ( 12) SS BOND : angle 2.62601 ( 24) hydrogen bonds : bond 0.03614 ( 598) hydrogen bonds : angle 4.21575 ( 1689) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.8007 (tpp) cc_final: 0.7705 (tpp) REVERT: A 164 MET cc_start: 0.7760 (ptp) cc_final: 0.7220 (ptp) REVERT: A 201 MET cc_start: 0.6953 (mmm) cc_final: 0.6479 (mtp) REVERT: A 237 GLU cc_start: 0.8387 (pt0) cc_final: 0.8041 (pm20) REVERT: A 624 ASP cc_start: 0.8357 (t0) cc_final: 0.7772 (t0) REVERT: B 826 MET cc_start: 0.8703 (pmm) cc_final: 0.8213 (pmm) REVERT: B 832 ASP cc_start: 0.9198 (t0) cc_final: 0.8847 (t0) REVERT: B 917 TYR cc_start: 0.8197 (m-10) cc_final: 0.7927 (m-80) REVERT: B 937 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8496 (ttm-80) REVERT: B 990 MET cc_start: 0.7978 (mtm) cc_final: 0.7765 (mtt) REVERT: B 1597 GLU cc_start: 0.9210 (tt0) cc_final: 0.8953 (tp30) REVERT: B 1659 PHE cc_start: 0.8945 (t80) cc_final: 0.8464 (t80) REVERT: C 45 MET cc_start: 0.9321 (mmt) cc_final: 0.8833 (mmm) REVERT: C 58 GLN cc_start: 0.9332 (tp40) cc_final: 0.8941 (tp40) REVERT: C 210 ASP cc_start: 0.9629 (t0) cc_final: 0.9247 (p0) outliers start: 37 outliers final: 28 residues processed: 162 average time/residue: 0.1119 time to fit residues: 27.2156 Evaluate side-chains 154 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 937 ARG Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1390 THR Chi-restraints excluded: chain B residue 1458 CYS Chi-restraints excluded: chain B residue 1515 GLU Chi-restraints excluded: chain B residue 1544 VAL Chi-restraints excluded: chain B residue 1557 ASP Chi-restraints excluded: chain B residue 1559 ASP Chi-restraints excluded: chain B residue 1594 LEU Chi-restraints excluded: chain B residue 1626 THR Chi-restraints excluded: chain B residue 1652 PHE Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 259 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 95 optimal weight: 0.0980 chunk 68 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.087949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.058141 restraints weight = 40469.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.060599 restraints weight = 19094.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.062257 restraints weight = 12420.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.063302 restraints weight = 9558.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.063953 restraints weight = 8150.878| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14605 Z= 0.156 Angle : 0.564 10.049 19775 Z= 0.294 Chirality : 0.043 0.202 2219 Planarity : 0.004 0.041 2551 Dihedral : 4.033 23.192 1949 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.34 % Allowed : 13.83 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.20), residues: 1791 helix: 2.48 (0.24), residues: 443 sheet: 0.66 (0.22), residues: 528 loop : -0.97 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 63 TYR 0.012 0.001 TYR A 261 PHE 0.028 0.001 PHE B1519 TRP 0.028 0.001 TRP C 223 HIS 0.005 0.001 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.00369 (14593) covalent geometry : angle 0.55691 (19751) SS BOND : bond 0.00297 ( 12) SS BOND : angle 2.70300 ( 24) hydrogen bonds : bond 0.04009 ( 598) hydrogen bonds : angle 4.30033 ( 1689) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.7812 (ptp) cc_final: 0.7470 (ptp) REVERT: A 237 GLU cc_start: 0.8411 (pt0) cc_final: 0.8062 (pm20) REVERT: A 373 MET cc_start: 0.8624 (mmm) cc_final: 0.8245 (mmt) REVERT: A 624 ASP cc_start: 0.8404 (t0) cc_final: 0.7804 (t0) REVERT: B 826 MET cc_start: 0.8627 (pmm) cc_final: 0.8322 (pmm) REVERT: B 832 ASP cc_start: 0.9198 (t0) cc_final: 0.8753 (t0) REVERT: B 917 TYR cc_start: 0.8175 (m-10) cc_final: 0.7906 (m-80) REVERT: B 937 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8536 (ttm-80) REVERT: B 990 MET cc_start: 0.8030 (mtm) cc_final: 0.7766 (mtt) REVERT: B 1521 GLN cc_start: 0.8267 (mm-40) cc_final: 0.7800 (mm-40) REVERT: B 1597 GLU cc_start: 0.9213 (tt0) cc_final: 0.8964 (tp30) REVERT: B 1599 LYS cc_start: 0.9289 (mttt) cc_final: 0.9060 (mmmt) REVERT: C 45 MET cc_start: 0.9314 (mmt) cc_final: 0.8882 (mmm) REVERT: C 58 GLN cc_start: 0.9321 (tp40) cc_final: 0.8929 (tp40) REVERT: C 65 GLN cc_start: 0.9171 (mt0) cc_final: 0.8939 (mm-40) outliers start: 37 outliers final: 33 residues processed: 158 average time/residue: 0.1127 time to fit residues: 26.6999 Evaluate side-chains 155 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 937 ARG Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain B residue 1390 THR Chi-restraints excluded: chain B residue 1399 THR Chi-restraints excluded: chain B residue 1458 CYS Chi-restraints excluded: chain B residue 1479 VAL Chi-restraints excluded: chain B residue 1515 GLU Chi-restraints excluded: chain B residue 1544 VAL Chi-restraints excluded: chain B residue 1557 ASP Chi-restraints excluded: chain B residue 1559 ASP Chi-restraints excluded: chain B residue 1594 LEU Chi-restraints excluded: chain B residue 1595 LYS Chi-restraints excluded: chain B residue 1626 THR Chi-restraints excluded: chain B residue 1652 PHE Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 259 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 22 optimal weight: 0.0000 chunk 163 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 135 optimal weight: 0.0980 chunk 1 optimal weight: 1.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.088565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.058631 restraints weight = 40810.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.061144 restraints weight = 19135.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.062823 restraints weight = 12410.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.063890 restraints weight = 9534.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.064519 restraints weight = 8121.496| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14605 Z= 0.126 Angle : 0.555 9.653 19775 Z= 0.287 Chirality : 0.042 0.196 2219 Planarity : 0.004 0.041 2551 Dihedral : 3.946 25.410 1949 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.08 % Allowed : 14.53 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.20), residues: 1791 helix: 2.48 (0.24), residues: 449 sheet: 0.74 (0.22), residues: 526 loop : -0.99 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 63 TYR 0.012 0.001 TYR A 261 PHE 0.029 0.001 PHE B1519 TRP 0.034 0.001 TRP C 223 HIS 0.005 0.001 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.00294 (14593) covalent geometry : angle 0.54708 (19751) SS BOND : bond 0.00283 ( 12) SS BOND : angle 2.65980 ( 24) hydrogen bonds : bond 0.03673 ( 598) hydrogen bonds : angle 4.17752 ( 1689) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.7757 (ptp) cc_final: 0.7210 (ptp) REVERT: A 237 GLU cc_start: 0.8374 (pt0) cc_final: 0.8049 (pm20) REVERT: A 624 ASP cc_start: 0.8358 (t0) cc_final: 0.7778 (t0) REVERT: B 826 MET cc_start: 0.8883 (pmm) cc_final: 0.8343 (pmm) REVERT: B 832 ASP cc_start: 0.9174 (t0) cc_final: 0.8700 (t0) REVERT: B 917 TYR cc_start: 0.8212 (m-10) cc_final: 0.7950 (m-80) REVERT: B 937 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8515 (ttm-80) REVERT: B 990 MET cc_start: 0.8012 (mtm) cc_final: 0.7779 (mtt) REVERT: B 1521 GLN cc_start: 0.8370 (mm-40) cc_final: 0.7904 (mm-40) REVERT: B 1597 GLU cc_start: 0.9186 (tt0) cc_final: 0.8960 (tp30) REVERT: B 1599 LYS cc_start: 0.9310 (mttt) cc_final: 0.9063 (mmmt) REVERT: C 45 MET cc_start: 0.9322 (mmt) cc_final: 0.8779 (mmm) REVERT: C 56 ARG cc_start: 0.8441 (tpp80) cc_final: 0.8188 (ttm-80) REVERT: C 58 GLN cc_start: 0.9316 (tp40) cc_final: 0.8925 (tp40) REVERT: C 65 GLN cc_start: 0.9164 (mt0) cc_final: 0.8942 (mm-40) REVERT: C 111 ASN cc_start: 0.9261 (m-40) cc_final: 0.9014 (p0) outliers start: 33 outliers final: 30 residues processed: 157 average time/residue: 0.1202 time to fit residues: 28.2619 Evaluate side-chains 158 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 937 ARG Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1390 THR Chi-restraints excluded: chain B residue 1399 THR Chi-restraints excluded: chain B residue 1458 CYS Chi-restraints excluded: chain B residue 1479 VAL Chi-restraints excluded: chain B residue 1515 GLU Chi-restraints excluded: chain B residue 1544 VAL Chi-restraints excluded: chain B residue 1557 ASP Chi-restraints excluded: chain B residue 1594 LEU Chi-restraints excluded: chain B residue 1626 THR Chi-restraints excluded: chain B residue 1652 PHE Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 259 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 8 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.087882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.058008 restraints weight = 40625.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.060487 restraints weight = 19075.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.062136 restraints weight = 12381.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.063151 restraints weight = 9538.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.063823 restraints weight = 8156.890| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14605 Z= 0.156 Angle : 0.587 10.577 19775 Z= 0.304 Chirality : 0.043 0.227 2219 Planarity : 0.004 0.042 2551 Dihedral : 4.058 27.529 1949 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.15 % Allowed : 14.53 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.20), residues: 1791 helix: 2.40 (0.24), residues: 450 sheet: 0.71 (0.22), residues: 526 loop : -1.00 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 63 TYR 0.012 0.001 TYR A 261 PHE 0.028 0.001 PHE B1519 TRP 0.039 0.001 TRP C 223 HIS 0.006 0.001 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.00372 (14593) covalent geometry : angle 0.57953 (19751) SS BOND : bond 0.00269 ( 12) SS BOND : angle 2.71746 ( 24) hydrogen bonds : bond 0.03930 ( 598) hydrogen bonds : angle 4.24979 ( 1689) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.7957 (tpp) cc_final: 0.7499 (tpp) REVERT: A 164 MET cc_start: 0.7835 (ptp) cc_final: 0.7493 (ptp) REVERT: A 237 GLU cc_start: 0.8384 (pt0) cc_final: 0.8032 (pm20) REVERT: A 624 ASP cc_start: 0.8389 (t0) cc_final: 0.7803 (t0) REVERT: B 826 MET cc_start: 0.8816 (pmm) cc_final: 0.8276 (pmm) REVERT: B 832 ASP cc_start: 0.9187 (t0) cc_final: 0.8745 (t0) REVERT: B 917 TYR cc_start: 0.8217 (m-10) cc_final: 0.7962 (m-80) REVERT: B 937 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8522 (ttm-80) REVERT: B 990 MET cc_start: 0.8033 (mtm) cc_final: 0.7761 (mtt) REVERT: B 1521 GLN cc_start: 0.8398 (mm-40) cc_final: 0.7952 (mm-40) REVERT: B 1563 MET cc_start: 0.6362 (ttm) cc_final: 0.5886 (tpp) REVERT: B 1567 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8152 (tm-30) REVERT: B 1597 GLU cc_start: 0.9179 (tt0) cc_final: 0.8960 (tp30) REVERT: C 45 MET cc_start: 0.9323 (mmt) cc_final: 0.8781 (mmm) REVERT: C 56 ARG cc_start: 0.8435 (tpp80) cc_final: 0.8168 (ttm-80) REVERT: C 65 GLN cc_start: 0.9157 (mt0) cc_final: 0.8955 (mm-40) REVERT: C 111 ASN cc_start: 0.9267 (m-40) cc_final: 0.9012 (p0) REVERT: C 225 ASP cc_start: 0.8938 (m-30) cc_final: 0.8632 (p0) outliers start: 34 outliers final: 32 residues processed: 155 average time/residue: 0.1168 time to fit residues: 27.4021 Evaluate side-chains 157 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 937 ARG Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain B residue 1390 THR Chi-restraints excluded: chain B residue 1399 THR Chi-restraints excluded: chain B residue 1458 CYS Chi-restraints excluded: chain B residue 1479 VAL Chi-restraints excluded: chain B residue 1515 GLU Chi-restraints excluded: chain B residue 1544 VAL Chi-restraints excluded: chain B residue 1557 ASP Chi-restraints excluded: chain B residue 1594 LEU Chi-restraints excluded: chain B residue 1626 THR Chi-restraints excluded: chain B residue 1652 PHE Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 259 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 17 optimal weight: 0.5980 chunk 154 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 68 optimal weight: 0.0020 chunk 27 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.088740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.058979 restraints weight = 40505.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.061503 restraints weight = 18866.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.063199 restraints weight = 12178.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.064250 restraints weight = 9330.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.064783 restraints weight = 7948.170| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14605 Z= 0.121 Angle : 0.570 11.161 19775 Z= 0.295 Chirality : 0.042 0.197 2219 Planarity : 0.004 0.046 2551 Dihedral : 3.925 28.273 1949 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.02 % Allowed : 14.72 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.20), residues: 1791 helix: 2.43 (0.24), residues: 450 sheet: 0.76 (0.23), residues: 527 loop : -0.98 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 573 TYR 0.013 0.001 TYR A 261 PHE 0.029 0.001 PHE B1519 TRP 0.039 0.001 TRP C 223 HIS 0.006 0.001 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.00282 (14593) covalent geometry : angle 0.56286 (19751) SS BOND : bond 0.00261 ( 12) SS BOND : angle 2.56122 ( 24) hydrogen bonds : bond 0.03639 ( 598) hydrogen bonds : angle 4.17215 ( 1689) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2620.36 seconds wall clock time: 45 minutes 50.66 seconds (2750.66 seconds total)