Starting phenix.real_space_refine on Fri Jul 3 07:56:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kya_23073/07_2026/7kya_23073.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kya_23073/07_2026/7kya_23073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kya_23073/07_2026/7kya_23073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kya_23073/07_2026/7kya_23073.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7kya_23073/07_2026/7kya_23073.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kya_23073/07_2026/7kya_23073.cif" model { file = "/net/cci-nas-00/data/ceres_data/7kya_23073/07_2026/7kya_23073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kya_23073/07_2026/7kya_23073.cif" } resolution = 3.5 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= 0.003 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: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 62 5.16 5 Be 1 3.05 5 C 8163 2.51 5 N 2074 2.21 5 O 2352 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12656 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1174, 9384 Classifications: {'peptide': 1174} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 1134} Chain breaks: 3 Chain: "B" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2989 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Unusual residues: {' MG': 1, 'BEF': 1, 'CLR': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'CLR': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.84, per 1000 atoms: 0.22 Number of scatterers: 12656 At special positions: 0 Unit cell: (139.594, 118.944, 138.768, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 62 16.00 Mg 1 11.99 F 3 9.00 O 2352 8.00 N 2074 7.00 C 8163 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 231 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG D 2 " - " MAN D 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG B2002 " - " ASN B 113 " " NAG C 1 " - " ASN B 298 " " NAG D 1 " - " ASN B 240 " " NAG E 1 " - " ASN B 256 " " NAG F 1 " - " ASN B 332 " Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 534.9 milliseconds 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2902 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 13 sheets defined 44.7% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 243 through 253 Processing helix chain 'A' and resid 255 through 270 removed outlier: 3.621A pdb=" N ILE A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 280 removed outlier: 3.778A pdb=" N PHE A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 277 through 280' Processing helix chain 'A' and resid 281 through 312 removed outlier: 4.310A pdb=" N LEU A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 removed outlier: 3.864A pdb=" N ILE A 500 " --> pdb=" O CYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'A' and resid 570 through 574 removed outlier: 3.526A pdb=" N THR A 574 " --> pdb=" O GLY A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 619 removed outlier: 3.808A pdb=" N GLU A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 615 " --> pdb=" O THR A 611 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY A 617 " --> pdb=" O GLY A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 622 No H-bonds generated for 'chain 'A' and resid 620 through 622' Processing helix chain 'A' and resid 640 through 654 removed outlier: 3.914A pdb=" N ILE A 652 " --> pdb=" O TRP A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 679 Processing helix chain 'A' and resid 680 through 682 No H-bonds generated for 'chain 'A' and resid 680 through 682' Processing helix chain 'A' and resid 701 through 704 Processing helix chain 'A' and resid 739 through 750 Processing helix chain 'A' and resid 753 through 779 removed outlier: 3.745A pdb=" N SER A 779 " --> pdb=" O LEU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 789 removed outlier: 3.519A pdb=" N ASP A 788 " --> pdb=" O CYS A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 802 removed outlier: 3.502A pdb=" N GLU A 798 " --> pdb=" O LYS A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 820 removed outlier: 3.781A pdb=" N GLN A 809 " --> pdb=" O GLY A 805 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 820 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 856 removed outlier: 3.667A pdb=" N LEU A 856 " --> pdb=" O THR A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 925 removed outlier: 3.593A pdb=" N ARG A 925 " --> pdb=" O VAL A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 948 removed outlier: 3.741A pdb=" N THR A 948 " --> pdb=" O GLU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 978 removed outlier: 3.812A pdb=" N ALA A 978 " --> pdb=" O ASP A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 removed outlier: 4.401A pdb=" N GLU A 986 " --> pdb=" O ASN A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1025 removed outlier: 3.656A pdb=" N ALA A1019 " --> pdb=" O PRO A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1046 removed outlier: 3.902A pdb=" N ALA A1039 " --> pdb=" O LYS A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1084 Processing helix chain 'A' and resid 1096 through 1101 Processing helix chain 'A' and resid 1102 through 1104 No H-bonds generated for 'chain 'A' and resid 1102 through 1104' Processing helix chain 'A' and resid 1116 through 1124 Processing helix chain 'A' and resid 1126 through 1139 removed outlier: 3.790A pdb=" N ASN A1139 " --> pdb=" O LEU A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1163 Processing helix chain 'A' and resid 1174 through 1176 No H-bonds generated for 'chain 'A' and resid 1174 through 1176' Processing helix chain 'A' and resid 1177 through 1183 Processing helix chain 'A' and resid 1208 through 1210 No H-bonds generated for 'chain 'A' and resid 1208 through 1210' Processing helix chain 'A' and resid 1211 through 1216 Processing helix chain 'A' and resid 1218 through 1248 Proline residue: A1232 - end of helix removed outlier: 3.691A pdb=" N ASN A1238 " --> pdb=" O PHE A1234 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A1239 " --> pdb=" O PHE A1235 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE A1241 " --> pdb=" O LYS A1237 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER A1244 " --> pdb=" O ILE A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1250 No H-bonds generated for 'chain 'A' and resid 1249 through 1250' Processing helix chain 'A' and resid 1251 through 1255 removed outlier: 4.007A pdb=" N PHE A1254 " --> pdb=" O TYR A1251 " (cutoff:3.500A) Processing helix chain 'A' and resid 1273 through 1283 removed outlier: 3.971A pdb=" N VAL A1277 " --> pdb=" O THR A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1295 Processing helix chain 'A' and resid 1296 through 1298 No H-bonds generated for 'chain 'A' and resid 1296 through 1298' Processing helix chain 'A' and resid 1299 through 1304 Processing helix chain 'A' and resid 1309 through 1336 Proline residue: A1331 - end of helix Processing helix chain 'A' and resid 1350 through 1373 Processing helix chain 'A' and resid 1380 through 1401 Processing helix chain 'A' and resid 1410 through 1416 Processing helix chain 'A' and resid 1418 through 1444 removed outlier: 3.849A pdb=" N TRP A1422 " --> pdb=" O GLN A1418 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A1427 " --> pdb=" O ALA A1423 " (cutoff:3.500A) Proline residue: A1435 - end of helix Processing helix chain 'A' and resid 1449 through 1461 Processing helix chain 'B' and resid 75 through 98 Processing helix chain 'B' and resid 109 through 114 removed outlier: 3.547A pdb=" N ALA B 114 " --> pdb=" O CYS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.800A pdb=" N LEU B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'B' and resid 231 through 237 removed outlier: 4.625A pdb=" N ALA B 235 " --> pdb=" O CYS B 231 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 272 Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.973A pdb=" N GLU B 290 " --> pdb=" O PRO B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 350 through 354 Processing helix chain 'B' and resid 372 through 399 Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 210 Processing sheet with id=AA2, first strand: chain 'A' and resid 437 through 441 removed outlier: 3.930A pdb=" N HIS A 316 " --> pdb=" O ARG A 453 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ILE A 451 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N MET A 564 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 458 through 459 removed outlier: 3.761A pdb=" N ASP A 458 " --> pdb=" O LEU A 557 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 684 through 685 Processing sheet with id=AA5, first strand: chain 'A' and resid 693 through 694 removed outlier: 3.919A pdb=" N THR A 693 " --> pdb=" O ALA A1205 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A1205 " --> pdb=" O THR A 693 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1027 through 1030 removed outlier: 6.667A pdb=" N MET A1167 " --> pdb=" O ILE A 706 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 732 through 734 removed outlier: 5.776A pdb=" N ARG A1009 " --> pdb=" O GLN A 719 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A 721 " --> pdb=" O GLU A1007 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLU A1007 " --> pdb=" O VAL A 721 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLU A 723 " --> pdb=" O ALA A1005 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ALA A1005 " --> pdb=" O GLU A 723 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N LYS A 725 " --> pdb=" O GLY A1003 " (cutoff:3.500A) removed outlier: 11.772A pdb=" N GLY A1003 " --> pdb=" O LYS A 725 " (cutoff:3.500A) removed outlier: 10.612A pdb=" N CYS A 727 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 11.895A pdb=" N LEU A1001 " --> pdb=" O CYS A 727 " (cutoff:3.500A) removed outlier: 11.741A pdb=" N ILE A 729 " --> pdb=" O ILE A 999 " (cutoff:3.500A) removed outlier: 14.739A pdb=" N ILE A 999 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LEU A1000 " --> pdb=" O GLN A 958 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLN A 958 " --> pdb=" O LEU A1000 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE A1006 " --> pdb=" O ARG A 952 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS A 899 " --> pdb=" O VAL A 881 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A 881 " --> pdb=" O LYS A 899 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 826 through 829 Processing sheet with id=AA9, first strand: chain 'A' and resid 858 through 861 Processing sheet with id=AB1, first strand: chain 'A' and resid 1054 through 1058 Processing sheet with id=AB2, first strand: chain 'A' and resid 1377 through 1378 Processing sheet with id=AB3, first strand: chain 'B' and resid 126 through 129 removed outlier: 6.345A pdb=" N TYR B 177 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU B 326 " --> pdb=" O TYR B 177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 119 through 120 removed outlier: 5.905A pdb=" N ASP B 343 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N GLN B 246 " --> pdb=" O ASP B 343 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1560 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: 2.53 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3984 1.34 - 1.46: 2013 1.46 - 1.57: 6858 1.57 - 1.69: 0 1.69 - 1.81: 93 Bond restraints: 12948 Sorted by residual: bond pdb=" F1 BEF A1703 " pdb="BE BEF A1703 " ideal model delta sigma weight residual 1.476 1.766 -0.290 2.00e-02 2.50e+03 2.10e+02 bond pdb=" F3 BEF A1703 " pdb="BE BEF A1703 " ideal model delta sigma weight residual 1.476 1.765 -0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" F2 BEF A1703 " pdb="BE BEF A1703 " ideal model delta sigma weight residual 1.476 1.765 -0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.97e+00 ... (remaining 12943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 17178 1.71 - 3.43: 325 3.43 - 5.14: 59 5.14 - 6.85: 25 6.85 - 8.57: 5 Bond angle restraints: 17592 Sorted by residual: angle pdb=" N HIS A1336 " pdb=" CA HIS A1336 " pdb=" C HIS A1336 " ideal model delta sigma weight residual 112.38 120.95 -8.57 1.22e+00 6.72e-01 4.93e+01 angle pdb=" N HIS A 254 " pdb=" CA HIS A 254 " pdb=" C HIS A 254 " ideal model delta sigma weight residual 111.36 104.98 6.38 1.09e+00 8.42e-01 3.43e+01 angle pdb=" C TYR A1251 " pdb=" N ASN A1252 " pdb=" CA ASN A1252 " ideal model delta sigma weight residual 126.45 119.14 7.31 1.77e+00 3.19e-01 1.70e+01 angle pdb=" N ASN A1252 " pdb=" CA ASN A1252 " pdb=" CB ASN A1252 " ideal model delta sigma weight residual 114.17 110.48 3.69 1.14e+00 7.69e-01 1.05e+01 angle pdb=" N LEU A1243 " pdb=" CA LEU A1243 " pdb=" C LEU A1243 " ideal model delta sigma weight residual 111.71 108.27 3.44 1.15e+00 7.56e-01 8.96e+00 ... (remaining 17587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6835 17.94 - 35.87: 600 35.87 - 53.81: 112 53.81 - 71.74: 23 71.74 - 89.68: 7 Dihedral angle restraints: 7577 sinusoidal: 3065 harmonic: 4512 Sorted by residual: dihedral pdb=" CA LYS B 170 " pdb=" C LYS B 170 " pdb=" N ASN B 171 " pdb=" CA ASN B 171 " ideal model delta harmonic sigma weight residual 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA ILE A1250 " pdb=" C ILE A1250 " pdb=" N TYR A1251 " pdb=" CA TYR A1251 " ideal model delta harmonic sigma weight residual 180.00 158.45 21.55 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA GLY A1347 " pdb=" C GLY A1347 " pdb=" N LEU A1348 " pdb=" CA LEU A1348 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 7574 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1815 0.075 - 0.150: 166 0.150 - 0.224: 7 0.224 - 0.299: 9 0.299 - 0.374: 7 Chirality restraints: 2004 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 9.61e+00 chirality pdb=" C14 CLR A1701 " pdb=" C13 CLR A1701 " pdb=" C15 CLR A1701 " pdb=" C8 CLR A1701 " both_signs ideal model delta sigma weight residual False -2.32 -2.69 0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" C14 CLR A1705 " pdb=" C13 CLR A1705 " pdb=" C15 CLR A1705 " pdb=" C8 CLR A1705 " both_signs ideal model delta sigma weight residual False -2.32 -2.67 0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 2001 not shown) Planarity restraints: 2202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.081 2.00e-02 2.50e+03 6.65e-02 5.53e+01 pdb=" C7 NAG D 1 " -0.022 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.061 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.105 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 240 " -0.017 2.00e-02 2.50e+03 6.23e-02 4.86e+01 pdb=" CG ASN B 240 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN B 240 " 0.061 2.00e-02 2.50e+03 pdb=" ND2 ASN B 240 " -0.100 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A1335 " 0.010 2.00e-02 2.50e+03 2.13e-02 4.52e+00 pdb=" C TYR A1335 " -0.037 2.00e-02 2.50e+03 pdb=" O TYR A1335 " 0.014 2.00e-02 2.50e+03 pdb=" N HIS A1336 " 0.013 2.00e-02 2.50e+03 ... (remaining 2199 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 1 2.19 - 2.86: 4694 2.86 - 3.54: 17327 3.54 - 4.22: 29035 4.22 - 4.90: 51447 Nonbonded interactions: 102504 Sorted by model distance: nonbonded pdb=" OG1 THR A 714 " pdb="MG MG A1702 " model vdw 1.508 2.170 nonbonded pdb=" CG2 ILE A 869 " pdb=" OE2 GLU A 878 " model vdw 2.199 3.460 nonbonded pdb=" OG SER A 779 " pdb=" O GLN A 873 " model vdw 2.215 3.040 nonbonded pdb=" O GLU A 997 " pdb=" CD1 LEU A 998 " model vdw 2.240 3.460 nonbonded pdb=" OH TYR A1264 " pdb=" OG1 THR A1396 " model vdw 2.252 3.040 ... (remaining 102499 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 Found NCS groups: ncs_group { reference = (chain 'C' and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 o \ r name C7 or name C8 or name N2 or name O3 or name O4 or name O5 or name O6 or n \ ame O7 )) selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.910 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 : 0.006 0.290 12960 Z= 0.275 Angle : 0.663 24.715 17626 Z= 0.336 Chirality : 0.050 0.374 2004 Planarity : 0.003 0.067 2197 Dihedral : 13.958 89.676 4669 Min Nonbonded Distance : 1.508 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.24 % Favored : 92.63 % Rotamer: Outliers : 1.03 % Allowed : 12.98 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -3.21 (0.19), residues: 1533 helix: -1.11 (0.19), residues: 615 sheet: -2.35 (0.33), residues: 208 loop : -3.00 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 316 TYR 0.013 0.001 TYR B 280 PHE 0.012 0.001 PHE A1357 TRP 0.012 0.001 TRP A1247 HIS 0.003 0.000 HIS A 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.27 (12948) covalent geometry : angle 0.62653 / 0.33 (17592) SS BOND : bond 0.00050 / 0.03 ( 2) SS BOND : angle 0.32047 / 0.19 ( 4) hydrogen bonds : bond 0.15655 / 9.91 ( 557) hydrogen bonds : angle 6.14207 / 4.33 ( 1560) link_ALPHA1-4 : bond 0.00458 / 0.24 ( 1) link_ALPHA1-4 : angle 2.22221 / 1.79 ( 3) link_BETA1-4 : bond 0.00616 / 0.31 ( 4) link_BETA1-4 : angle 1.48234 / 1.09 ( 12) link_NAG-ASN : bond 0.04567 / 2.18 ( 5) link_NAG-ASN : angle 7.26247 / 3.36 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 237 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 PHE cc_start: 0.7932 (t80) cc_final: 0.7633 (t80) REVERT: A 761 LYS cc_start: 0.8150 (tptp) cc_final: 0.7940 (tptp) REVERT: A 809 GLN cc_start: 0.6699 (tm-30) cc_final: 0.6403 (tm-30) REVERT: A 813 GLU cc_start: 0.6772 (tm-30) cc_final: 0.6314 (pt0) REVERT: A 928 ARG cc_start: 0.5214 (OUTLIER) cc_final: 0.3335 (mmt-90) REVERT: A 935 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7270 (pt) REVERT: B 111 MET cc_start: 0.7872 (ttp) cc_final: 0.7657 (ttp) outliers start: 14 outliers final: 9 residues processed: 247 average time/residue: 0.1222 time to fit residues: 43.0344 Evaluate side-chains 186 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 254 HIS Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 928 ARG Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1088 PHE Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1252 ASN Chi-restraints excluded: chain A residue 1336 HIS Chi-restraints excluded: chain A residue 1408 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN A 232 ASN A 248 ASN A 311 ASN ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 HIS A 527 GLN A 655 GLN A 720 ASN A 876 GLN A1176 ASN A1269 ASN A1374 GLN B 50 ASN B 60 GLN B 96 GLN B 186 HIS B 246 GLN B 341 GLN B 366 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.149286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.109098 restraints weight = 13908.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.110888 restraints weight = 9763.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.111969 restraints weight = 7115.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.112061 restraints weight = 5947.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.114248 restraints weight = 5353.683| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 12960 Z= 0.248 Angle : 0.677 9.495 17626 Z= 0.345 Chirality : 0.047 0.188 2004 Planarity : 0.004 0.048 2197 Dihedral : 6.424 59.595 1753 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 3.98 % Allowed : 16.52 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -2.57 (0.20), residues: 1533 helix: -0.62 (0.19), residues: 647 sheet: -1.98 (0.34), residues: 214 loop : -2.69 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 925 TYR 0.022 0.002 TYR A 678 PHE 0.019 0.002 PHE A1357 TRP 0.018 0.002 TRP A 648 HIS 0.005 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.25 (12948) covalent geometry : angle 0.67385 / 0.34 (17592) SS BOND : bond 0.00199 / 0.10 ( 2) SS BOND : angle 0.59147 / 0.53 ( 4) hydrogen bonds : bond 0.05119 / 3.25 ( 557) hydrogen bonds : angle 4.94847 / 3.40 ( 1560) link_ALPHA1-4 : bond 0.00727 / 0.38 ( 1) link_ALPHA1-4 : angle 2.07747 / 1.80 ( 3) link_BETA1-4 : bond 0.00682 / 0.33 ( 4) link_BETA1-4 : angle 1.43258 / 0.95 ( 12) link_NAG-ASN : bond 0.00244 / 0.12 ( 5) link_NAG-ASN : angle 2.05537 / 1.21 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 182 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 PHE cc_start: 0.7804 (t80) cc_final: 0.7547 (t80) REVERT: A 248 ASN cc_start: 0.8163 (t160) cc_final: 0.7839 (t0) REVERT: A 809 GLN cc_start: 0.6727 (tm-30) cc_final: 0.6236 (tm-30) REVERT: A 813 GLU cc_start: 0.6558 (tm-30) cc_final: 0.5847 (pp20) REVERT: A 928 ARG cc_start: 0.5670 (OUTLIER) cc_final: 0.3814 (mpt180) REVERT: A 1004 THR cc_start: 0.8546 (p) cc_final: 0.8296 (t) REVERT: B 111 MET cc_start: 0.8071 (ttp) cc_final: 0.7810 (ttp) outliers start: 54 outliers final: 32 residues processed: 222 average time/residue: 0.0939 time to fit residues: 30.5666 Evaluate side-chains 190 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 254 HIS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 928 ARG Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1088 PHE Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1185 ASP Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1252 ASN Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1336 HIS Chi-restraints excluded: chain A residue 1349 ASP Chi-restraints excluded: chain A residue 1370 VAL Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 373 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 134 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 433 ASN A 455 HIS A 579 ASN ** A 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.153269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.113611 restraints weight = 13796.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.114920 restraints weight = 9058.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.116341 restraints weight = 7763.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.116826 restraints weight = 6071.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.117582 restraints weight = 5667.882| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12960 Z= 0.133 Angle : 0.588 10.118 17626 Z= 0.298 Chirality : 0.043 0.236 2004 Planarity : 0.004 0.047 2197 Dihedral : 5.941 56.894 1744 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.61 % Allowed : 18.22 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -1.89 (0.21), residues: 1533 helix: -0.02 (0.20), residues: 642 sheet: -1.65 (0.35), residues: 210 loop : -2.35 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 162 TYR 0.019 0.001 TYR B 136 PHE 0.020 0.001 PHE A1313 TRP 0.014 0.001 TRP A 648 HIS 0.003 0.001 HIS A 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (12948) covalent geometry : angle 0.58372 / 0.30 (17592) SS BOND : bond 0.00110 / 0.05 ( 2) SS BOND : angle 0.32974 / 0.20 ( 4) hydrogen bonds : bond 0.04349 / 2.78 ( 557) hydrogen bonds : angle 4.64544 / 3.19 ( 1560) link_ALPHA1-4 : bond 0.00708 / 0.37 ( 1) link_ALPHA1-4 : angle 1.95055 / 1.59 ( 3) link_BETA1-4 : bond 0.00628 / 0.31 ( 4) link_BETA1-4 : angle 1.25844 / 0.83 ( 12) link_NAG-ASN : bond 0.00243 / 0.12 ( 5) link_NAG-ASN : angle 2.28659 / 1.27 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 171 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 ASN cc_start: 0.8091 (t160) cc_final: 0.7761 (t0) REVERT: A 566 MET cc_start: 0.8207 (ttm) cc_final: 0.7921 (ttm) REVERT: A 809 GLN cc_start: 0.6622 (tm-30) cc_final: 0.6169 (tm-30) REVERT: A 813 GLU cc_start: 0.6509 (tm-30) cc_final: 0.5879 (pp20) REVERT: A 928 ARG cc_start: 0.5724 (OUTLIER) cc_final: 0.3951 (mmt90) REVERT: B 111 MET cc_start: 0.7938 (ttp) cc_final: 0.7673 (ttp) outliers start: 49 outliers final: 30 residues processed: 209 average time/residue: 0.0886 time to fit residues: 27.4277 Evaluate side-chains 187 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 HIS Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 928 ARG Chi-restraints excluded: chain A residue 1088 PHE Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1252 ASN Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1336 HIS Chi-restraints excluded: chain A residue 1349 ASP Chi-restraints excluded: chain A residue 1378 ASP Chi-restraints excluded: chain A residue 1408 PHE Chi-restraints excluded: chain A residue 1480 ILE Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 342 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 128 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 145 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 ASN A 232 ASN A 873 GLN B 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.154434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.113937 restraints weight = 13570.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.116305 restraints weight = 9285.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.117295 restraints weight = 6618.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.117429 restraints weight = 5390.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.119455 restraints weight = 4946.508| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12960 Z= 0.121 Angle : 0.571 10.547 17626 Z= 0.289 Chirality : 0.042 0.198 2004 Planarity : 0.004 0.046 2197 Dihedral : 5.606 56.074 1742 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.69 % Allowed : 19.54 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -1.59 (0.22), residues: 1533 helix: 0.27 (0.21), residues: 640 sheet: -1.43 (0.36), residues: 216 loop : -2.25 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 162 TYR 0.023 0.001 TYR B 136 PHE 0.021 0.001 PHE B 320 TRP 0.019 0.001 TRP A 648 HIS 0.003 0.001 HIS A 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (12948) covalent geometry : angle 0.56731 / 0.29 (17592) SS BOND : bond 0.00092 / 0.05 ( 2) SS BOND : angle 0.29880 / 0.18 ( 4) hydrogen bonds : bond 0.04051 / 2.59 ( 557) hydrogen bonds : angle 4.46635 / 3.07 ( 1560) link_ALPHA1-4 : bond 0.00697 / 0.37 ( 1) link_ALPHA1-4 : angle 1.83504 / 1.50 ( 3) link_BETA1-4 : bond 0.00553 / 0.27 ( 4) link_BETA1-4 : angle 1.17895 / 0.79 ( 12) link_NAG-ASN : bond 0.00627 / 0.31 ( 5) link_NAG-ASN : angle 2.04919 / 1.17 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 178 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 ASN cc_start: 0.8111 (t160) cc_final: 0.7767 (t0) REVERT: A 566 MET cc_start: 0.8173 (ttm) cc_final: 0.7855 (ttm) REVERT: A 809 GLN cc_start: 0.6663 (tm-30) cc_final: 0.6227 (tm-30) REVERT: A 813 GLU cc_start: 0.6467 (tm-30) cc_final: 0.5862 (pp20) REVERT: B 111 MET cc_start: 0.7840 (ttp) cc_final: 0.7599 (ttp) REVERT: B 137 ASN cc_start: 0.5683 (OUTLIER) cc_final: 0.5319 (p0) REVERT: B 348 TRP cc_start: 0.8677 (OUTLIER) cc_final: 0.8268 (t60) outliers start: 50 outliers final: 34 residues processed: 218 average time/residue: 0.0914 time to fit residues: 29.8814 Evaluate side-chains 197 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 254 HIS Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1088 PHE Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1252 ASN Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1336 HIS Chi-restraints excluded: chain A residue 1343 GLU Chi-restraints excluded: chain A residue 1349 ASP Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1378 ASP Chi-restraints excluded: chain A residue 1408 PHE Chi-restraints excluded: chain A residue 1480 ILE Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 373 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 15 optimal weight: 4.9990 chunk 119 optimal weight: 0.1980 chunk 141 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 116 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 128 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 48 optimal weight: 0.5980 chunk 6 optimal weight: 6.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1336 HIS B 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.157113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.116595 restraints weight = 13545.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.117282 restraints weight = 9063.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.118651 restraints weight = 7266.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.119124 restraints weight = 5465.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.119525 restraints weight = 4944.619| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12960 Z= 0.105 Angle : 0.550 10.496 17626 Z= 0.278 Chirality : 0.042 0.225 2004 Planarity : 0.004 0.045 2197 Dihedral : 5.363 55.386 1738 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.17 % Allowed : 20.80 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -1.37 (0.22), residues: 1533 helix: 0.45 (0.21), residues: 651 sheet: -1.26 (0.36), residues: 215 loop : -2.19 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 162 TYR 0.022 0.001 TYR A1421 PHE 0.017 0.001 PHE A1313 TRP 0.021 0.001 TRP A 648 HIS 0.003 0.001 HIS A 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (12948) covalent geometry : angle 0.54628 / 0.28 (17592) SS BOND : bond 0.00088 / 0.04 ( 2) SS BOND : angle 0.32620 / 0.19 ( 4) hydrogen bonds : bond 0.03827 / 2.45 ( 557) hydrogen bonds : angle 4.38547 / 3.02 ( 1560) link_ALPHA1-4 : bond 0.00637 / 0.34 ( 1) link_ALPHA1-4 : angle 1.76700 / 1.48 ( 3) link_BETA1-4 : bond 0.00628 / 0.31 ( 4) link_BETA1-4 : angle 1.19729 / 0.79 ( 12) link_NAG-ASN : bond 0.00376 / 0.19 ( 5) link_NAG-ASN : angle 1.85870 / 1.05 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 178 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 ASN cc_start: 0.8827 (m-40) cc_final: 0.8304 (m-40) REVERT: A 502 LYS cc_start: 0.6823 (tptp) cc_final: 0.6215 (mttp) REVERT: A 566 MET cc_start: 0.8137 (ttm) cc_final: 0.7841 (ttm) REVERT: A 778 MET cc_start: 0.6828 (tmm) cc_final: 0.6595 (tmm) REVERT: A 809 GLN cc_start: 0.6543 (tm-30) cc_final: 0.6202 (tm-30) REVERT: A 813 GLU cc_start: 0.6418 (OUTLIER) cc_final: 0.5941 (pt0) REVERT: B 137 ASN cc_start: 0.5678 (OUTLIER) cc_final: 0.5320 (p0) REVERT: B 348 TRP cc_start: 0.8644 (OUTLIER) cc_final: 0.8247 (t60) outliers start: 43 outliers final: 30 residues processed: 208 average time/residue: 0.1000 time to fit residues: 31.1278 Evaluate side-chains 196 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 254 HIS Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1088 PHE Chi-restraints excluded: chain A residue 1185 ASP Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1252 ASN Chi-restraints excluded: chain A residue 1349 ASP Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1378 ASP Chi-restraints excluded: chain A residue 1408 PHE Chi-restraints excluded: chain A residue 1480 ILE Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 373 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 137 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 248 ASN ** A1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.151041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.111018 restraints weight = 13733.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.113010 restraints weight = 9251.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.114407 restraints weight = 6717.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.114699 restraints weight = 5442.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.114841 restraints weight = 4921.251| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12960 Z= 0.221 Angle : 0.646 8.262 17626 Z= 0.328 Chirality : 0.045 0.193 2004 Planarity : 0.004 0.048 2197 Dihedral : 5.603 57.382 1736 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.76 % Favored : 92.17 % Rotamer: Outliers : 4.28 % Allowed : 21.02 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -1.55 (0.22), residues: 1533 helix: 0.24 (0.20), residues: 648 sheet: -1.33 (0.37), residues: 214 loop : -2.20 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 925 TYR 0.021 0.002 TYR A 678 PHE 0.021 0.002 PHE A1313 TRP 0.021 0.002 TRP A 648 HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.22 (12948) covalent geometry : angle 0.64183 / 0.33 (17592) SS BOND : bond 0.00185 / 0.09 ( 2) SS BOND : angle 0.69713 / 0.64 ( 4) hydrogen bonds : bond 0.04520 / 2.85 ( 557) hydrogen bonds : angle 4.59649 / 3.16 ( 1560) link_ALPHA1-4 : bond 0.00586 / 0.31 ( 1) link_ALPHA1-4 : angle 1.78017 / 1.54 ( 3) link_BETA1-4 : bond 0.00552 / 0.27 ( 4) link_BETA1-4 : angle 1.37930 / 0.92 ( 12) link_NAG-ASN : bond 0.00263 / 0.13 ( 5) link_NAG-ASN : angle 2.31030 / 1.28 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 156 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 248 ASN cc_start: 0.8191 (t160) cc_final: 0.7981 (t0) REVERT: A 809 GLN cc_start: 0.6707 (tm-30) cc_final: 0.6469 (tm-30) REVERT: A 813 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.5899 (pp20) REVERT: A 873 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7624 (mm-40) REVERT: A 926 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6857 (mp) REVERT: A 1111 PHE cc_start: 0.7936 (m-80) cc_final: 0.7715 (m-80) REVERT: A 1310 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7665 (mp10) outliers start: 58 outliers final: 42 residues processed: 200 average time/residue: 0.0964 time to fit residues: 29.1395 Evaluate side-chains 194 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 148 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 254 HIS Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 873 GLN Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1088 PHE Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1185 ASP Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1252 ASN Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1310 GLN Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1370 VAL Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1408 PHE Chi-restraints excluded: chain A residue 1480 ILE Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 373 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 110 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.150827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.110771 restraints weight = 13823.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.113409 restraints weight = 9392.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.114236 restraints weight = 6908.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.114871 restraints weight = 5146.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.114964 restraints weight = 4688.979| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12960 Z= 0.173 Angle : 0.616 8.421 17626 Z= 0.312 Chirality : 0.044 0.246 2004 Planarity : 0.004 0.047 2197 Dihedral : 5.608 57.484 1736 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.85 % Favored : 93.09 % Rotamer: Outliers : 4.13 % Allowed : 21.53 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -1.48 (0.22), residues: 1533 helix: 0.27 (0.21), residues: 651 sheet: -1.37 (0.37), residues: 209 loop : -2.12 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 925 TYR 0.021 0.002 TYR B 136 PHE 0.020 0.002 PHE A1313 TRP 0.019 0.001 TRP A 648 HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (12948) covalent geometry : angle 0.61102 / 0.31 (17592) SS BOND : bond 0.00174 / 0.08 ( 2) SS BOND : angle 0.84619 / 0.75 ( 4) hydrogen bonds : bond 0.04337 / 2.75 ( 557) hydrogen bonds : angle 4.55441 / 3.13 ( 1560) link_ALPHA1-4 : bond 0.00661 / 0.35 ( 1) link_ALPHA1-4 : angle 1.92461 / 1.60 ( 3) link_BETA1-4 : bond 0.00585 / 0.29 ( 4) link_BETA1-4 : angle 1.36632 / 0.92 ( 12) link_NAG-ASN : bond 0.00227 / 0.11 ( 5) link_NAG-ASN : angle 2.25849 / 1.28 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 160 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 532 TRP cc_start: 0.8020 (p90) cc_final: 0.7573 (p90) REVERT: A 809 GLN cc_start: 0.6655 (tm-30) cc_final: 0.6417 (tm-30) REVERT: A 813 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.5838 (pp20) REVERT: A 926 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6857 (mp) REVERT: A 1111 PHE cc_start: 0.7904 (m-80) cc_final: 0.7664 (m-80) REVERT: A 1124 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.6313 (pp) REVERT: A 1310 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7594 (mp10) outliers start: 56 outliers final: 44 residues processed: 205 average time/residue: 0.0935 time to fit residues: 29.0174 Evaluate side-chains 193 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 145 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 254 HIS Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 738 TYR Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1088 PHE Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1185 ASP Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1252 ASN Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1310 GLN Chi-restraints excluded: chain A residue 1343 GLU Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1378 ASP Chi-restraints excluded: chain A residue 1408 PHE Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1480 ILE Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 15 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.148877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.108897 restraints weight = 13876.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.110681 restraints weight = 9660.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.111605 restraints weight = 7103.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.111901 restraints weight = 6092.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.112262 restraints weight = 5555.674| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12960 Z= 0.209 Angle : 0.649 8.516 17626 Z= 0.329 Chirality : 0.046 0.257 2004 Planarity : 0.004 0.048 2197 Dihedral : 5.749 57.901 1736 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.09 % Favored : 91.85 % Rotamer: Outliers : 4.72 % Allowed : 21.17 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -1.58 (0.22), residues: 1533 helix: 0.17 (0.20), residues: 651 sheet: -1.40 (0.37), residues: 209 loop : -2.15 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 925 TYR 0.019 0.002 TYR B 136 PHE 0.021 0.002 PHE A1313 TRP 0.021 0.002 TRP A 648 HIS 0.004 0.001 HIS A1336 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.21 (12948) covalent geometry : angle 0.64389 / 0.33 (17592) SS BOND : bond 0.00219 / 0.11 ( 2) SS BOND : angle 0.74176 / 0.64 ( 4) hydrogen bonds : bond 0.04541 / 2.87 ( 557) hydrogen bonds : angle 4.63974 / 3.20 ( 1560) link_ALPHA1-4 : bond 0.00787 / 0.41 ( 1) link_ALPHA1-4 : angle 2.03746 / 1.70 ( 3) link_BETA1-4 : bond 0.00559 / 0.27 ( 4) link_BETA1-4 : angle 1.42779 / 0.97 ( 12) link_NAG-ASN : bond 0.00230 / 0.12 ( 5) link_NAG-ASN : angle 2.33995 / 1.33 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 155 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 809 GLN cc_start: 0.6718 (tm-30) cc_final: 0.6462 (tm-30) REVERT: A 813 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.5936 (pp20) REVERT: A 926 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6897 (mp) REVERT: A 1111 PHE cc_start: 0.7935 (m-80) cc_final: 0.7710 (m-80) REVERT: A 1124 LEU cc_start: 0.6602 (OUTLIER) cc_final: 0.6326 (pp) REVERT: A 1243 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7808 (mp) REVERT: A 1310 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7601 (mp10) outliers start: 64 outliers final: 47 residues processed: 206 average time/residue: 0.0828 time to fit residues: 26.6691 Evaluate side-chains 198 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 146 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 254 HIS Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 738 TYR Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1088 PHE Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1252 ASN Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1310 GLN Chi-restraints excluded: chain A residue 1343 GLU Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1408 PHE Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1480 ILE Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 403 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 92 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 137 optimal weight: 0.0980 chunk 87 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 873 GLN A1238 ASN B 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.154636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.114690 restraints weight = 13521.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.115183 restraints weight = 9337.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.116629 restraints weight = 7436.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.117017 restraints weight = 5496.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.117530 restraints weight = 4940.017| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12960 Z= 0.121 Angle : 0.585 8.546 17626 Z= 0.294 Chirality : 0.043 0.260 2004 Planarity : 0.004 0.049 2197 Dihedral : 5.492 56.445 1736 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.47 % Allowed : 22.49 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -1.27 (0.22), residues: 1533 helix: 0.44 (0.21), residues: 651 sheet: -1.20 (0.37), residues: 208 loop : -2.03 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 925 TYR 0.028 0.001 TYR B 293 PHE 0.023 0.001 PHE A1313 TRP 0.021 0.001 TRP A 648 HIS 0.003 0.001 HIS A 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (12948) covalent geometry : angle 0.58046 / 0.29 (17592) SS BOND : bond 0.00097 / 0.05 ( 2) SS BOND : angle 0.87359 / 0.75 ( 4) hydrogen bonds : bond 0.04038 / 2.58 ( 557) hydrogen bonds : angle 4.44986 / 3.07 ( 1560) link_ALPHA1-4 : bond 0.00981 / 0.52 ( 1) link_ALPHA1-4 : angle 2.05075 / 1.68 ( 3) link_BETA1-4 : bond 0.00605 / 0.30 ( 4) link_BETA1-4 : angle 1.33971 / 0.93 ( 12) link_NAG-ASN : bond 0.00220 / 0.11 ( 5) link_NAG-ASN : angle 2.02390 / 1.16 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 163 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 502 LYS cc_start: 0.6907 (tptp) cc_final: 0.6198 (tptp) REVERT: A 809 GLN cc_start: 0.6609 (tm-30) cc_final: 0.6390 (tm-30) REVERT: A 813 GLU cc_start: 0.6465 (OUTLIER) cc_final: 0.5833 (pp20) REVERT: A 873 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7687 (mm-40) REVERT: A 1111 PHE cc_start: 0.7838 (m-80) cc_final: 0.7592 (m-80) REVERT: A 1243 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7669 (mp) REVERT: A 1310 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7514 (mp10) outliers start: 47 outliers final: 37 residues processed: 201 average time/residue: 0.0896 time to fit residues: 26.9365 Evaluate side-chains 194 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 254 HIS Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 738 TYR Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 873 GLN Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1088 PHE Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1252 ASN Chi-restraints excluded: chain A residue 1310 GLN Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1378 ASP Chi-restraints excluded: chain A residue 1408 PHE Chi-restraints excluded: chain A residue 1480 ILE Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 120 optimal weight: 2.9990 chunk 95 optimal weight: 0.2980 chunk 114 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 134 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 873 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.155464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.116080 restraints weight = 13493.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.116087 restraints weight = 8263.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.116908 restraints weight = 7053.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.117277 restraints weight = 5502.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.119175 restraints weight = 5116.997| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12960 Z= 0.122 Angle : 0.593 11.315 17626 Z= 0.296 Chirality : 0.043 0.273 2004 Planarity : 0.004 0.048 2197 Dihedral : 5.392 55.770 1736 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.83 % Allowed : 22.35 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -1.18 (0.22), residues: 1533 helix: 0.51 (0.21), residues: 651 sheet: -1.14 (0.37), residues: 208 loop : -1.97 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 401 TYR 0.033 0.001 TYR B 293 PHE 0.024 0.001 PHE A1313 TRP 0.022 0.001 TRP A 648 HIS 0.003 0.001 HIS A 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (12948) covalent geometry : angle 0.58877 / 0.30 (17592) SS BOND : bond 0.00095 / 0.05 ( 2) SS BOND : angle 0.74870 / 0.64 ( 4) hydrogen bonds : bond 0.03981 / 2.54 ( 557) hydrogen bonds : angle 4.40151 / 3.04 ( 1560) link_ALPHA1-4 : bond 0.00784 / 0.41 ( 1) link_ALPHA1-4 : angle 1.98149 / 1.61 ( 3) link_BETA1-4 : bond 0.00585 / 0.29 ( 4) link_BETA1-4 : angle 1.34444 / 0.93 ( 12) link_NAG-ASN : bond 0.00227 / 0.12 ( 5) link_NAG-ASN : angle 1.95426 / 1.12 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 159 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 309 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7305 (tt0) REVERT: A 314 ARG cc_start: 0.7157 (mmt180) cc_final: 0.6839 (tpp-160) REVERT: A 502 LYS cc_start: 0.6922 (tptp) cc_final: 0.6226 (tptp) REVERT: A 809 GLN cc_start: 0.6539 (tm-30) cc_final: 0.6311 (tm-30) REVERT: A 813 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.5774 (pp20) REVERT: A 873 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7701 (mm-40) REVERT: A 1243 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7540 (mp) REVERT: A 1310 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7519 (mp10) REVERT: B 118 TRP cc_start: 0.7039 (m100) cc_final: 0.6761 (m100) outliers start: 52 outliers final: 41 residues processed: 202 average time/residue: 0.0942 time to fit residues: 29.0285 Evaluate side-chains 203 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 254 HIS Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 738 TYR Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 873 GLN Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1088 PHE Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1252 ASN Chi-restraints excluded: chain A residue 1310 GLN Chi-restraints excluded: chain A residue 1343 GLU Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1378 ASP Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1408 PHE Chi-restraints excluded: chain A residue 1480 ILE Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 373 PHE Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 99 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 chunk 117 optimal weight: 8.9990 chunk 134 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 873 GLN B 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.156421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116935 restraints weight = 13497.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.116879 restraints weight = 8230.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.117656 restraints weight = 7367.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.118533 restraints weight = 5617.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.119090 restraints weight = 5106.193| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12960 Z= 0.122 Angle : 0.594 11.102 17626 Z= 0.296 Chirality : 0.043 0.274 2004 Planarity : 0.004 0.047 2197 Dihedral : 5.358 55.518 1736 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.61 % Allowed : 22.42 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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 (0.22), residues: 1533 helix: 0.55 (0.21), residues: 659 sheet: -1.13 (0.36), residues: 208 loop : -1.97 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 401 TYR 0.029 0.001 TYR B 293 PHE 0.025 0.001 PHE A1313 TRP 0.024 0.001 TRP A 648 HIS 0.003 0.001 HIS A 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (12948) covalent geometry : angle 0.58942 / 0.29 (17592) SS BOND : bond 0.00133 / 0.07 ( 2) SS BOND : angle 1.59537 / 1.00 ( 4) hydrogen bonds : bond 0.03980 / 2.56 ( 557) hydrogen bonds : angle 4.39089 / 3.03 ( 1560) link_ALPHA1-4 : bond 0.00742 / 0.39 ( 1) link_ALPHA1-4 : angle 1.94842 / 1.60 ( 3) link_BETA1-4 : bond 0.00588 / 0.29 ( 4) link_BETA1-4 : angle 1.34157 / 0.93 ( 12) link_NAG-ASN : bond 0.00234 / 0.12 ( 5) link_NAG-ASN : angle 1.94256 / 1.11 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4927.70 seconds wall clock time: 84 minutes 29.46 seconds (5069.46 seconds total)