Starting phenix.real_space_refine on Fri Jul 3 03:23:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7oh7_12896/07_2026/7oh7_12896.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oh7_12896/07_2026/7oh7_12896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7oh7_12896/07_2026/7oh7_12896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oh7_12896/07_2026/7oh7_12896.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7oh7_12896/07_2026/7oh7_12896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oh7_12896/07_2026/7oh7_12896.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7oh7_12896/07_2026/7oh7_12896.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7oh7_12896/07_2026/7oh7_12896.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 48 5.16 5 C 7455 2.51 5 N 1863 2.21 5 O 2180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s 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: 11552 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8504 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 30, 'TRANS': 1033} Chain: "C" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2842 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 21, 'TRANS': 328} Chain: "B" 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: "D" 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: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 100 Unusual residues: {' MG': 1, '2Y5': 1, 'ACP': 1} Classifications: {'undetermined': 3, 'water': 3} Link IDs: {None: 5} Time building chain proxies: 2.10, per 1000 atoms: 0.18 Number of scatterers: 11552 At special positions: 0 Unit cell: (79.4024, 105.182, 171.179, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 5 15.00 Mg 1 11.99 O 2180 8.00 N 1863 7.00 C 7455 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 190 " 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 BETA1-3 " BMA E 3 " - " BMA E 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG B 1 " - " ASN C 288 " " NAG D 1 " - " ASN C 216 " " NAG E 1 " - " ASN C 199 " Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 375.7 milliseconds 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2676 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 10 sheets defined 44.8% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 192 through 196 removed outlier: 3.512A pdb=" N SER A 195 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 222 removed outlier: 4.211A pdb=" N PHE A 219 " --> pdb=" O PRO A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 237 Processing helix chain 'A' and resid 250 through 281 removed outlier: 3.700A pdb=" N SER A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.719A pdb=" N ASN A 365 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N MET A 366 " --> pdb=" O LEU A 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 366' Processing helix chain 'A' and resid 396 through 398 No H-bonds generated for 'chain 'A' and resid 396 through 398' Processing helix chain 'A' and resid 420 through 424 removed outlier: 4.051A pdb=" N THR A 424 " --> pdb=" O GLY A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 473 removed outlier: 3.555A pdb=" N LYS A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 503 removed outlier: 3.533A pdb=" N PHE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 506 No H-bonds generated for 'chain 'A' and resid 504 through 506' Processing helix chain 'A' and resid 509 through 526 removed outlier: 3.946A pdb=" N GLU A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 532 Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 604 through 614 removed outlier: 4.379A pdb=" N ASP A 614 " --> pdb=" O LYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 633 removed outlier: 3.609A pdb=" N ALA A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 Processing helix chain 'A' and resid 723 through 728 removed outlier: 3.565A pdb=" N ILE A 727 " --> pdb=" O ALA A 723 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 728 " --> pdb=" O ASP A 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 723 through 728' Processing helix chain 'A' and resid 729 through 731 No H-bonds generated for 'chain 'A' and resid 729 through 731' Processing helix chain 'A' and resid 738 through 751 Processing helix chain 'A' and resid 765 through 782 removed outlier: 3.643A pdb=" N THR A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 795 removed outlier: 4.044A pdb=" N GLU A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 827 removed outlier: 3.689A pdb=" N HIS A 822 " --> pdb=" O PRO A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 849 Processing helix chain 'A' and resid 865 through 882 removed outlier: 3.523A pdb=" N GLU A 882 " --> pdb=" O ASN A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 892 removed outlier: 3.612A pdb=" N ASN A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 905 Processing helix chain 'A' and resid 910 through 919 removed outlier: 3.683A pdb=" N LEU A 914 " --> pdb=" O LEU A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 932 No H-bonds generated for 'chain 'A' and resid 930 through 932' Processing helix chain 'A' and resid 933 through 944 removed outlier: 3.730A pdb=" N LYS A 944 " --> pdb=" O MET A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 957 No H-bonds generated for 'chain 'A' and resid 955 through 957' Processing helix chain 'A' and resid 958 through 963 removed outlier: 3.628A pdb=" N ILE A 962 " --> pdb=" O ASP A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 991 No H-bonds generated for 'chain 'A' and resid 989 through 991' Processing helix chain 'A' and resid 992 through 997 Processing helix chain 'A' and resid 1001 through 1021 removed outlier: 4.263A pdb=" N ILE A1008 " --> pdb=" O SER A1004 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER A1009 " --> pdb=" O TYR A1005 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A1010 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN A1019 " --> pdb=" O SER A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1029 Processing helix chain 'A' and resid 1030 through 1032 No H-bonds generated for 'chain 'A' and resid 1030 through 1032' Processing helix chain 'A' and resid 1043 through 1049 removed outlier: 3.687A pdb=" N SER A1047 " --> pdb=" O SER A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1064 Processing helix chain 'A' and resid 1078 through 1086 removed outlier: 4.002A pdb=" N LEU A1082 " --> pdb=" O GLN A1078 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY A1083 " --> pdb=" O LEU A1079 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A1086 " --> pdb=" O LEU A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1116 removed outlier: 3.622A pdb=" N ILE A1115 " --> pdb=" O GLY A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1154 removed outlier: 3.718A pdb=" N GLY A1135 " --> pdb=" O HIS A1131 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR A1137 " --> pdb=" O SER A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1183 removed outlier: 3.563A pdb=" N LEU A1169 " --> pdb=" O ILE A1165 " (cutoff:3.500A) Proline residue: A1177 - end of helix Processing helix chain 'A' and resid 1184 through 1187 removed outlier: 3.593A pdb=" N ASN A1187 " --> pdb=" O PRO A1184 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1184 through 1187' Processing helix chain 'A' and resid 1194 through 1200 removed outlier: 3.597A pdb=" N HIS A1198 " --> pdb=" O GLY A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1230 removed outlier: 4.017A pdb=" N ILE A1210 " --> pdb=" O TRP A1206 " (cutoff:3.500A) Proline residue: A1213 - end of helix removed outlier: 5.030A pdb=" N ARG A1219 " --> pdb=" O PHE A1215 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASP A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1245 Processing helix chain 'C' and resid 41 through 44 Processing helix chain 'C' and resid 45 through 69 Proline residue: C 58 - end of helix Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 150 through 155 removed outlier: 3.955A pdb=" N GLN C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 164 Processing helix chain 'C' and resid 181 through 185 removed outlier: 4.238A pdb=" N ASP C 184 " --> pdb=" O SER C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 Processing helix chain 'C' and resid 224 through 231 Processing helix chain 'C' and resid 244 through 248 removed outlier: 3.934A pdb=" N MET C 248 " --> pdb=" O PRO C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 274 removed outlier: 3.746A pdb=" N GLN C 270 " --> pdb=" O TRP C 266 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG C 274 " --> pdb=" O GLN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 357 removed outlier: 3.627A pdb=" N ILE C 348 " --> pdb=" O ALA C 344 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 186 removed outlier: 3.869A pdb=" N GLY A 384 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 283 through 288 removed outlier: 3.534A pdb=" N ASP A 293 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 307 through 310 removed outlier: 7.037A pdb=" N PHE A 414 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ASP A 319 " --> pdb=" O ILE A 418 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR A 320 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 401 " --> pdb=" O THR A 320 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 345 through 349 removed outlier: 3.858A pdb=" N TYR A 333 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 541 through 542 removed outlier: 6.701A pdb=" N LEU A 949 " --> pdb=" O VAL A 967 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL A 969 " --> pdb=" O LEU A 949 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ALA A 951 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE A 971 " --> pdb=" O ALA A 951 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLY A 953 " --> pdb=" O ILE A 971 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 952 " --> pdb=" O PHE A 558 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP A 560 " --> pdb=" O ILE A 952 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ILE A 557 " --> pdb=" O TRP A 832 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU A 834 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER A 559 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 923 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN A 857 " --> pdb=" O ALA A 894 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A 896 " --> pdb=" O ASN A 857 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N LEU A 859 " --> pdb=" O VAL A 896 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 566 through 577 removed outlier: 6.858A pdb=" N LYS A 812 " --> pdb=" O ARG A 567 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A 569 " --> pdb=" O GLU A 810 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLU A 810 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLU A 571 " --> pdb=" O ALA A 808 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ALA A 808 " --> pdb=" O GLU A 571 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N LYS A 573 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 11.993A pdb=" N ALA A 806 " --> pdb=" O LYS A 573 " (cutoff:3.500A) removed outlier: 10.538A pdb=" N CYS A 575 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 12.047A pdb=" N ILE A 804 " --> pdb=" O CYS A 575 " (cutoff:3.500A) removed outlier: 11.776A pdb=" N ILE A 577 " --> pdb=" O ILE A 802 " (cutoff:3.500A) removed outlier: 14.662A pdb=" N ILE A 802 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU A 759 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ALA A 806 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 757 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ALA A 808 " --> pdb=" O ARG A 755 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ARG A 755 " --> pdb=" O ALA A 808 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE A 716 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N SER A 706 " --> pdb=" O ILE A 695 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE A 695 " --> pdb=" O SER A 706 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE A 708 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N SER A 676 " --> pdb=" O ARG A 672 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ARG A 672 " --> pdb=" O SER A 676 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR A 678 " --> pdb=" O ILE A 670 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 637 through 639 Processing sheet with id=AA8, first strand: chain 'C' and resid 98 through 100 removed outlier: 6.771A pdb=" N TYR C 141 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU C 284 " --> pdb=" O TYR C 141 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 90 through 91 removed outlier: 4.408A pdb=" N LYS C 297 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ASN C 301 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL C 205 " --> pdb=" O ASN C 301 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 186 through 187 removed outlier: 6.941A pdb=" N ILE C 186 " --> pdb=" O VAL C 242 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 481 hydrogen bonds defined for protein. 1365 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: 2.11 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1865 1.32 - 1.45: 3461 1.45 - 1.59: 6402 1.59 - 1.73: 7 1.73 - 1.86: 79 Bond restraints: 11814 Sorted by residual: bond pdb=" C1' ACP A1502 " pdb=" O4' ACP A1502 " ideal model delta sigma weight residual 1.390 1.618 -0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C1' ACP A1502 " pdb=" C2' ACP A1502 " ideal model delta sigma weight residual 1.527 1.309 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C4' ACP A1502 " pdb=" O4' ACP A1502 " ideal model delta sigma weight residual 1.428 1.302 0.126 2.00e-02 2.50e+03 3.94e+01 bond pdb=" C6 ACP A1502 " pdb=" N6 ACP A1502 " ideal model delta sigma weight residual 1.335 1.452 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" C2' ACP A1502 " pdb=" O2' ACP A1502 " ideal model delta sigma weight residual 1.401 1.494 -0.093 2.00e-02 2.50e+03 2.17e+01 ... (remaining 11809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 15893 3.18 - 6.35: 108 6.35 - 9.53: 13 9.53 - 12.70: 6 12.70 - 15.88: 3 Bond angle restraints: 16023 Sorted by residual: angle pdb=" O3A ACP A1502 " pdb=" PA ACP A1502 " pdb=" O5' ACP A1502 " ideal model delta sigma weight residual 93.75 109.63 -15.88 3.00e+00 1.11e-01 2.80e+01 angle pdb=" N1 ACP A1502 " pdb=" C6 ACP A1502 " pdb=" N6 ACP A1502 " ideal model delta sigma weight residual 119.32 104.44 14.88 3.00e+00 1.11e-01 2.46e+01 angle pdb=" C5 ACP A1502 " pdb=" C6 ACP A1502 " pdb=" N6 ACP A1502 " ideal model delta sigma weight residual 122.65 135.54 -12.89 3.00e+00 1.11e-01 1.85e+01 angle pdb=" O1 2Y5 A1501 " pdb=" P1 2Y5 A1501 " pdb=" O13 2Y5 A1501 " ideal model delta sigma weight residual 97.01 109.02 -12.01 3.00e+00 1.11e-01 1.60e+01 angle pdb=" O11 2Y5 A1501 " pdb=" P1 2Y5 A1501 " pdb=" O12 2Y5 A1501 " ideal model delta sigma weight residual 121.15 109.67 11.48 3.00e+00 1.11e-01 1.46e+01 ... (remaining 16018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.15: 6807 27.15 - 54.30: 165 54.30 - 81.45: 22 81.45 - 108.60: 8 108.60 - 135.74: 2 Dihedral angle restraints: 7004 sinusoidal: 2854 harmonic: 4150 Sorted by residual: dihedral pdb=" CA ILE A 670 " pdb=" C ILE A 670 " pdb=" N ILE A 671 " pdb=" CA ILE A 671 " ideal model delta harmonic sigma weight residual -180.00 -153.80 -26.20 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" C33 2Y5 A1501 " pdb=" C34 2Y5 A1501 " pdb=" C35 2Y5 A1501 " pdb=" C36 2Y5 A1501 " ideal model delta sinusoidal sigma weight residual 56.12 -168.14 -135.74 1 3.00e+01 1.11e-03 1.83e+01 dihedral pdb=" CA ILE A 187 " pdb=" C ILE A 187 " pdb=" N ASN A 188 " pdb=" CA ASN A 188 " ideal model delta harmonic sigma weight residual 180.00 -159.90 -20.10 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 7001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.993: 1833 0.993 - 1.986: 0 1.986 - 2.979: 0 2.979 - 3.972: 0 3.972 - 4.965: 1 Chirality restraints: 1834 Sorted by residual: chirality pdb=" C1 2Y5 A1501 " pdb=" C2 2Y5 A1501 " pdb=" C6 2Y5 A1501 " pdb=" O1 2Y5 A1501 " both_signs ideal model delta sigma weight residual False -2.53 2.43 -4.97 2.00e-01 2.50e+01 6.16e+02 chirality pdb=" C2' ACP A1502 " pdb=" C1' ACP A1502 " pdb=" C3' ACP A1502 " pdb=" O2' ACP A1502 " both_signs ideal model delta sigma weight residual False -2.75 -2.38 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" C5 BMA E 4 " pdb=" C4 BMA E 4 " pdb=" C6 BMA E 4 " pdb=" O5 BMA E 4 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 1831 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 621 " 0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C PRO A 621 " -0.065 2.00e-02 2.50e+03 pdb=" O PRO A 621 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE A 622 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 745 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C HIS A 745 " 0.059 2.00e-02 2.50e+03 pdb=" O HIS A 745 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU A 746 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 746 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.28e+00 pdb=" C LEU A 746 " -0.050 2.00e-02 2.50e+03 pdb=" O LEU A 746 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU A 747 " 0.017 2.00e-02 2.50e+03 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 166 2.65 - 3.21: 10665 3.21 - 3.77: 17238 3.77 - 4.34: 23955 4.34 - 4.90: 39098 Nonbonded interactions: 91122 Sorted by model distance: nonbonded pdb=" OD1 ASP A 954 " pdb="MG MG A1503 " model vdw 2.086 2.170 nonbonded pdb=" O THR A 562 " pdb="MG MG A1503 " model vdw 2.088 2.170 nonbonded pdb="MG MG A1503 " pdb=" O HOH A1601 " model vdw 2.089 2.170 nonbonded pdb=" OD2 ASP A 560 " pdb="MG MG A1503 " model vdw 2.089 2.170 nonbonded pdb="MG MG A1503 " pdb=" O HOH A1603 " model vdw 2.102 2.170 ... (remaining 91117 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 'B' selection = chain 'D' } 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.550 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.228 11824 Z= 0.229 Angle : 0.704 15.881 16051 Z= 0.333 Chirality : 0.123 4.965 1834 Planarity : 0.005 0.064 1995 Dihedral : 12.483 135.745 4322 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.20 % Allowed : 5.51 % Favored : 93.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.20), residues: 1410 helix: -1.63 (0.19), residues: 571 sheet: -2.02 (0.31), residues: 218 loop : -2.23 (0.22), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 183 TYR 0.013 0.001 TYR C 140 PHE 0.009 0.001 PHE A1205 TRP 0.007 0.001 TRP A1132 HIS 0.003 0.000 HIS A 745 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.23 (11814) covalent geometry : angle 0.70276 / 0.33 (16023) SS BOND : bond 0.00156 / 0.11 ( 2) SS BOND : angle 0.50486 / 0.33 ( 4) hydrogen bonds : bond 0.12299 / 7.87 ( 481) hydrogen bonds : angle 6.29966 / 4.30 ( 1365) link_BETA1-3 : bond 0.00503 / 0.34 ( 1) link_BETA1-3 : angle 1.52702 / 0.94 ( 3) link_BETA1-4 : bond 0.00324 / 0.21 ( 4) link_BETA1-4 : angle 1.18149 / 0.85 ( 12) link_NAG-ASN : bond 0.00226 / 0.14 ( 3) link_NAG-ASN : angle 0.99043 / 0.56 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 277 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 ASP cc_start: 0.7367 (t70) cc_final: 0.6549 (t0) REVERT: A 386 MET cc_start: 0.6339 (ttm) cc_final: 0.6114 (tmm) REVERT: A 528 ASP cc_start: 0.6644 (t0) cc_final: 0.6361 (t0) REVERT: A 565 LEU cc_start: 0.8193 (mt) cc_final: 0.7956 (mt) REVERT: A 585 LYS cc_start: 0.8514 (mtpt) cc_final: 0.8206 (tptp) REVERT: A 648 TYR cc_start: 0.7613 (m-80) cc_final: 0.7245 (m-10) REVERT: A 649 GLN cc_start: 0.8409 (mt0) cc_final: 0.7873 (mt0) REVERT: A 672 ARG cc_start: 0.8360 (ttt180) cc_final: 0.7641 (tpt170) REVERT: A 703 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7256 (mmmt) REVERT: A 948 LEU cc_start: 0.5891 (mt) cc_final: 0.5320 (mt) REVERT: C 74 THR cc_start: 0.6374 (m) cc_final: 0.6153 (p) REVERT: C 297 LYS cc_start: 0.7509 (mttt) cc_final: 0.7062 (tttt) outliers start: 15 outliers final: 4 residues processed: 289 average time/residue: 0.1113 time to fit residues: 43.9334 Evaluate side-chains 155 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 150 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain C residue 365 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 237 GLN A 777 ASN A 862 ASN A 891 ASN C 221 HIS ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.152277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.116992 restraints weight = 28645.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.118887 restraints weight = 17268.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.119072 restraints weight = 11118.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.119648 restraints weight = 11436.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.119964 restraints weight = 9899.173| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11824 Z= 0.133 Angle : 0.624 8.935 16051 Z= 0.314 Chirality : 0.045 0.269 1834 Planarity : 0.005 0.047 1995 Dihedral : 9.622 97.723 1621 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.47 % Allowed : 11.89 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.22), residues: 1410 helix: -0.58 (0.21), residues: 582 sheet: -1.45 (0.33), residues: 213 loop : -1.76 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 228 TYR 0.021 0.001 TYR C 77 PHE 0.015 0.001 PHE A 605 TRP 0.029 0.001 TRP A 299 HIS 0.008 0.001 HIS A 883 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (11814) covalent geometry : angle 0.62208 / 0.31 (16023) SS BOND : bond 0.00202 / 0.14 ( 2) SS BOND : angle 0.69627 / 0.46 ( 4) hydrogen bonds : bond 0.03602 / 2.36 ( 481) hydrogen bonds : angle 5.04432 / 3.44 ( 1365) link_BETA1-3 : bond 0.00793 / 0.53 ( 1) link_BETA1-3 : angle 1.45961 / 0.97 ( 3) link_BETA1-4 : bond 0.00342 / 0.23 ( 4) link_BETA1-4 : angle 1.42804 / 0.91 ( 12) link_NAG-ASN : bond 0.00411 / 0.26 ( 3) link_NAG-ASN : angle 1.46897 / 0.74 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7671 (pt0) REVERT: A 533 TYR cc_start: 0.6902 (OUTLIER) cc_final: 0.6394 (t80) REVERT: A 585 LYS cc_start: 0.8500 (mtpt) cc_final: 0.8072 (tptp) REVERT: A 672 ARG cc_start: 0.8396 (ttt180) cc_final: 0.7693 (tpt170) REVERT: A 703 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7144 (mmmt) REVERT: C 273 MET cc_start: 0.7872 (mmp) cc_final: 0.7643 (mmm) REVERT: C 297 LYS cc_start: 0.7566 (mttt) cc_final: 0.7025 (tttt) outliers start: 31 outliers final: 17 residues processed: 176 average time/residue: 0.0949 time to fit residues: 24.1061 Evaluate side-chains 152 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 333 TYR Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 891 ASN Chi-restraints excluded: chain A residue 922 LYS Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain C residue 115 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 136 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 chunk 47 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 822 HIS C 161 GLN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.143656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.105556 restraints weight = 28415.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.107071 restraints weight = 18167.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.107275 restraints weight = 12066.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.107859 restraints weight = 10872.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.108946 restraints weight = 9593.351| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11824 Z= 0.142 Angle : 0.599 9.328 16051 Z= 0.302 Chirality : 0.043 0.169 1834 Planarity : 0.004 0.038 1995 Dihedral : 8.829 87.900 1620 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.87 % Allowed : 13.09 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.22), residues: 1410 helix: -0.24 (0.22), residues: 583 sheet: -1.20 (0.34), residues: 224 loop : -1.54 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 704 TYR 0.018 0.001 TYR A1116 PHE 0.020 0.002 PHE A1175 TRP 0.011 0.001 TRP A1044 HIS 0.006 0.001 HIS A 883 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (11814) covalent geometry : angle 0.59691 / 0.30 (16023) SS BOND : bond 0.00229 / 0.16 ( 2) SS BOND : angle 0.84739 / 0.53 ( 4) hydrogen bonds : bond 0.03494 / 2.31 ( 481) hydrogen bonds : angle 4.76126 / 3.24 ( 1365) link_BETA1-3 : bond 0.00508 / 0.34 ( 1) link_BETA1-3 : angle 1.49255 / 0.92 ( 3) link_BETA1-4 : bond 0.00491 / 0.32 ( 4) link_BETA1-4 : angle 1.42993 / 0.96 ( 12) link_NAG-ASN : bond 0.00508 / 0.33 ( 3) link_NAG-ASN : angle 1.55865 / 0.92 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7650 (pt0) REVERT: A 533 TYR cc_start: 0.6988 (OUTLIER) cc_final: 0.6434 (t80) REVERT: A 570 MET cc_start: 0.6814 (mmt) cc_final: 0.6449 (mmm) REVERT: A 585 LYS cc_start: 0.8605 (mtpt) cc_final: 0.8115 (tptp) REVERT: A 672 ARG cc_start: 0.8439 (ttt180) cc_final: 0.7639 (tpt170) REVERT: A 703 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7360 (mmmt) REVERT: A 1041 MET cc_start: 0.5741 (mtt) cc_final: 0.5510 (mtt) REVERT: A 1114 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8060 (mp) REVERT: C 297 LYS cc_start: 0.7465 (mttt) cc_final: 0.6762 (tttt) outliers start: 36 outliers final: 27 residues processed: 161 average time/residue: 0.0885 time to fit residues: 21.0378 Evaluate side-chains 156 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 333 TYR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 891 ASN Chi-restraints excluded: chain A residue 922 LYS Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 179 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 83 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 129 optimal weight: 0.0980 chunk 69 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 891 ASN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.150099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.114230 restraints weight = 28751.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.116988 restraints weight = 17298.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.118263 restraints weight = 11934.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.119177 restraints weight = 8851.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.119308 restraints weight = 7633.084| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11824 Z= 0.105 Angle : 0.562 10.999 16051 Z= 0.279 Chirality : 0.043 0.188 1834 Planarity : 0.003 0.041 1995 Dihedral : 8.493 86.939 1620 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.31 % Allowed : 13.97 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.23), residues: 1410 helix: 0.05 (0.22), residues: 591 sheet: -1.05 (0.33), residues: 223 loop : -1.33 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 704 TYR 0.022 0.001 TYR A 208 PHE 0.016 0.001 PHE C 278 TRP 0.010 0.001 TRP A 772 HIS 0.006 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (11814) covalent geometry : angle 0.56013 / 0.28 (16023) SS BOND : bond 0.00227 / 0.16 ( 2) SS BOND : angle 0.83280 / 0.51 ( 4) hydrogen bonds : bond 0.03105 / 2.07 ( 481) hydrogen bonds : angle 4.51130 / 3.06 ( 1365) link_BETA1-3 : bond 0.00610 / 0.41 ( 1) link_BETA1-3 : angle 1.42019 / 0.88 ( 3) link_BETA1-4 : bond 0.00307 / 0.21 ( 4) link_BETA1-4 : angle 1.22299 / 0.82 ( 12) link_NAG-ASN : bond 0.00356 / 0.22 ( 3) link_NAG-ASN : angle 1.44052 / 0.77 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7845 (pt0) REVERT: A 533 TYR cc_start: 0.6553 (OUTLIER) cc_final: 0.6118 (t80) REVERT: A 570 MET cc_start: 0.6867 (mmt) cc_final: 0.6580 (mmm) REVERT: A 585 LYS cc_start: 0.8652 (mtpt) cc_final: 0.8118 (tptp) REVERT: A 672 ARG cc_start: 0.8389 (ttt180) cc_final: 0.7596 (tpt170) REVERT: A 703 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7236 (mmmt) REVERT: A 1024 MET cc_start: 0.6422 (tpt) cc_final: 0.6153 (tpp) REVERT: A 1041 MET cc_start: 0.6160 (mtt) cc_final: 0.5880 (mtt) REVERT: C 248 MET cc_start: 0.8757 (mmp) cc_final: 0.8548 (mmp) REVERT: C 297 LYS cc_start: 0.7545 (mttt) cc_final: 0.7040 (tttt) outliers start: 29 outliers final: 17 residues processed: 157 average time/residue: 0.1052 time to fit residues: 24.6043 Evaluate side-chains 144 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 333 TYR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 891 ASN Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 115 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 97 optimal weight: 0.0770 chunk 87 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 46 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 overall best weight: 1.6944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 825 GLN A 891 ASN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.148254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.115894 restraints weight = 28899.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.114768 restraints weight = 21726.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.115929 restraints weight = 15515.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.116622 restraints weight = 13029.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.116743 restraints weight = 11491.847| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11824 Z= 0.136 Angle : 0.596 9.588 16051 Z= 0.296 Chirality : 0.043 0.189 1834 Planarity : 0.003 0.036 1995 Dihedral : 8.500 87.194 1620 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.95 % Allowed : 15.24 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.23), residues: 1410 helix: 0.14 (0.22), residues: 583 sheet: -0.92 (0.33), residues: 223 loop : -1.31 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 704 TYR 0.022 0.001 TYR A 208 PHE 0.020 0.001 PHE C 278 TRP 0.010 0.001 TRP A1044 HIS 0.006 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (11814) covalent geometry : angle 0.59389 / 0.30 (16023) SS BOND : bond 0.00269 / 0.19 ( 2) SS BOND : angle 0.85964 / 0.53 ( 4) hydrogen bonds : bond 0.03299 / 2.18 ( 481) hydrogen bonds : angle 4.46991 / 3.03 ( 1365) link_BETA1-3 : bond 0.00542 / 0.36 ( 1) link_BETA1-3 : angle 1.41367 / 0.86 ( 3) link_BETA1-4 : bond 0.00453 / 0.27 ( 4) link_BETA1-4 : angle 1.34818 / 0.92 ( 12) link_NAG-ASN : bond 0.00374 / 0.24 ( 3) link_NAG-ASN : angle 1.55488 / 0.88 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.6979 (pttt) cc_final: 0.6728 (tttm) REVERT: A 220 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8017 (pt0) REVERT: A 399 GLN cc_start: 0.3082 (OUTLIER) cc_final: 0.2600 (mp-120) REVERT: A 533 TYR cc_start: 0.6846 (OUTLIER) cc_final: 0.6411 (t80) REVERT: A 640 PHE cc_start: 0.7097 (m-10) cc_final: 0.5795 (t80) REVERT: A 672 ARG cc_start: 0.7955 (ttt180) cc_final: 0.7550 (tpt170) REVERT: A 703 LYS cc_start: 0.7099 (OUTLIER) cc_final: 0.6801 (mmmt) REVERT: A 784 ASP cc_start: 0.7969 (t0) cc_final: 0.7641 (t70) REVERT: A 1041 MET cc_start: 0.6269 (mtt) cc_final: 0.5984 (mtt) REVERT: C 297 LYS cc_start: 0.7582 (mttt) cc_final: 0.7071 (tttt) REVERT: C 337 LEU cc_start: 0.7018 (mt) cc_final: 0.6734 (tp) outliers start: 37 outliers final: 23 residues processed: 153 average time/residue: 0.1017 time to fit residues: 23.1859 Evaluate side-chains 150 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 333 TYR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 345 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 79 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 chunk 13 optimal weight: 0.0770 chunk 81 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 68 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 overall best weight: 1.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 989 GLN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 364 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.140908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.105729 restraints weight = 28474.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.104631 restraints weight = 18727.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.105804 restraints weight = 13288.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.106212 restraints weight = 10584.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.106433 restraints weight = 9680.131| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11824 Z= 0.148 Angle : 0.615 11.040 16051 Z= 0.305 Chirality : 0.043 0.178 1834 Planarity : 0.003 0.035 1995 Dihedral : 8.563 84.596 1620 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.03 % Allowed : 15.56 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.23), residues: 1410 helix: 0.19 (0.22), residues: 576 sheet: -0.65 (0.35), residues: 213 loop : -1.34 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 943 TYR 0.022 0.001 TYR A 208 PHE 0.024 0.002 PHE C 278 TRP 0.011 0.001 TRP A1044 HIS 0.006 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (11814) covalent geometry : angle 0.61302 / 0.30 (16023) SS BOND : bond 0.00249 / 0.18 ( 2) SS BOND : angle 0.93412 / 0.60 ( 4) hydrogen bonds : bond 0.03472 / 2.28 ( 481) hydrogen bonds : angle 4.44669 / 3.01 ( 1365) link_BETA1-3 : bond 0.00731 / 0.49 ( 1) link_BETA1-3 : angle 1.44938 / 0.87 ( 3) link_BETA1-4 : bond 0.00404 / 0.25 ( 4) link_BETA1-4 : angle 1.36592 / 0.93 ( 12) link_NAG-ASN : bond 0.00397 / 0.26 ( 3) link_NAG-ASN : angle 1.59713 / 0.92 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8017 (pt0) REVERT: A 399 GLN cc_start: 0.3369 (OUTLIER) cc_final: 0.3069 (mp10) REVERT: A 533 TYR cc_start: 0.6838 (OUTLIER) cc_final: 0.6471 (t80) REVERT: A 640 PHE cc_start: 0.7593 (m-10) cc_final: 0.6170 (t80) REVERT: A 703 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7303 (mmmt) REVERT: A 1041 MET cc_start: 0.6143 (mtt) cc_final: 0.5928 (mtt) REVERT: C 297 LYS cc_start: 0.7486 (mttt) cc_final: 0.6836 (tttt) REVERT: C 337 LEU cc_start: 0.7197 (mt) cc_final: 0.6936 (tp) outliers start: 38 outliers final: 29 residues processed: 151 average time/residue: 0.1023 time to fit residues: 22.9156 Evaluate side-chains 147 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 333 TYR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 193 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 77 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.146897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.115661 restraints weight = 28726.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.113308 restraints weight = 21723.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.114530 restraints weight = 17334.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.114927 restraints weight = 13748.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.115099 restraints weight = 12561.820| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11824 Z= 0.131 Angle : 0.608 12.224 16051 Z= 0.302 Chirality : 0.043 0.182 1834 Planarity : 0.003 0.040 1995 Dihedral : 8.524 84.538 1620 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.19 % Allowed : 15.80 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.23), residues: 1410 helix: 0.30 (0.22), residues: 575 sheet: -0.56 (0.35), residues: 213 loop : -1.26 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 943 TYR 0.021 0.001 TYR C 140 PHE 0.023 0.001 PHE C 278 TRP 0.009 0.001 TRP A1044 HIS 0.007 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (11814) covalent geometry : angle 0.60612 / 0.30 (16023) SS BOND : bond 0.00227 / 0.16 ( 2) SS BOND : angle 0.90979 / 0.57 ( 4) hydrogen bonds : bond 0.03364 / 2.23 ( 481) hydrogen bonds : angle 4.39790 / 2.97 ( 1365) link_BETA1-3 : bond 0.00432 / 0.29 ( 1) link_BETA1-3 : angle 1.31408 / 0.79 ( 3) link_BETA1-4 : bond 0.00451 / 0.28 ( 4) link_BETA1-4 : angle 1.22958 / 0.85 ( 12) link_NAG-ASN : bond 0.00358 / 0.23 ( 3) link_NAG-ASN : angle 1.62605 / 0.92 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 119 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8069 (pt0) REVERT: A 399 GLN cc_start: 0.3365 (OUTLIER) cc_final: 0.3096 (mp10) REVERT: A 533 TYR cc_start: 0.6813 (OUTLIER) cc_final: 0.6431 (t80) REVERT: A 570 MET cc_start: 0.6629 (mmt) cc_final: 0.6397 (mmm) REVERT: A 640 PHE cc_start: 0.7159 (m-10) cc_final: 0.5880 (t80) REVERT: A 703 LYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6860 (mmmt) REVERT: C 248 MET cc_start: 0.8892 (mmp) cc_final: 0.8658 (mmp) REVERT: C 297 LYS cc_start: 0.7546 (mttt) cc_final: 0.6950 (tttt) outliers start: 40 outliers final: 25 residues processed: 148 average time/residue: 0.1050 time to fit residues: 23.2597 Evaluate side-chains 144 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 333 TYR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 345 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 25 optimal weight: 0.0030 chunk 21 optimal weight: 0.0870 chunk 40 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 overall best weight: 0.8172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 GLN ** A 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.142691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.107366 restraints weight = 28112.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.106845 restraints weight = 17971.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.107922 restraints weight = 12715.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.108181 restraints weight = 10999.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.108389 restraints weight = 9825.570| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11824 Z= 0.110 Angle : 0.608 12.524 16051 Z= 0.299 Chirality : 0.043 0.190 1834 Planarity : 0.003 0.040 1995 Dihedral : 8.375 87.808 1620 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.39 % Allowed : 16.20 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.23), residues: 1410 helix: 0.54 (0.23), residues: 566 sheet: -0.51 (0.36), residues: 205 loop : -1.00 (0.26), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 272 TYR 0.018 0.001 TYR C 140 PHE 0.022 0.001 PHE C 278 TRP 0.014 0.001 TRP A 772 HIS 0.007 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (11814) covalent geometry : angle 0.60673 / 0.30 (16023) SS BOND : bond 0.00204 / 0.15 ( 2) SS BOND : angle 0.89226 / 0.53 ( 4) hydrogen bonds : bond 0.03126 / 2.08 ( 481) hydrogen bonds : angle 4.30816 / 2.90 ( 1365) link_BETA1-3 : bond 0.00589 / 0.39 ( 1) link_BETA1-3 : angle 1.33611 / 0.81 ( 3) link_BETA1-4 : bond 0.00278 / 0.19 ( 4) link_BETA1-4 : angle 1.13904 / 0.78 ( 12) link_NAG-ASN : bond 0.00329 / 0.19 ( 3) link_NAG-ASN : angle 1.41363 / 0.73 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8092 (pt0) REVERT: A 265 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6946 (mt-10) REVERT: A 399 GLN cc_start: 0.3547 (OUTLIER) cc_final: 0.3208 (mp10) REVERT: A 533 TYR cc_start: 0.6711 (OUTLIER) cc_final: 0.6423 (t80) REVERT: A 570 MET cc_start: 0.6672 (mmt) cc_final: 0.6326 (mmm) REVERT: A 640 PHE cc_start: 0.7654 (m-10) cc_final: 0.6324 (t80) REVERT: A 790 LEU cc_start: 0.7488 (mm) cc_final: 0.6758 (tp) REVERT: A 1024 MET cc_start: 0.6505 (tpt) cc_final: 0.6152 (tpp) REVERT: A 1225 TYR cc_start: 0.8067 (t80) cc_final: 0.7809 (t80) REVERT: C 115 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8265 (mp0) REVERT: C 248 MET cc_start: 0.9042 (mmp) cc_final: 0.8791 (mmp) REVERT: C 297 LYS cc_start: 0.7371 (mttt) cc_final: 0.6661 (tttt) outliers start: 30 outliers final: 19 residues processed: 148 average time/residue: 0.0934 time to fit residues: 21.1641 Evaluate side-chains 140 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 333 TYR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 193 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 37 optimal weight: 4.9990 chunk 11 optimal weight: 20.0000 chunk 110 optimal weight: 10.0000 chunk 25 optimal weight: 0.0020 chunk 38 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 19 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 128 optimal weight: 0.0370 overall best weight: 1.4070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.147850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.114909 restraints weight = 28492.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.113892 restraints weight = 20971.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.115117 restraints weight = 15421.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.115626 restraints weight = 12473.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.115865 restraints weight = 10804.025| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11824 Z= 0.126 Angle : 0.630 19.911 16051 Z= 0.308 Chirality : 0.044 0.207 1834 Planarity : 0.003 0.039 1995 Dihedral : 8.420 89.491 1618 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.79 % Allowed : 16.04 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.23), residues: 1410 helix: 0.47 (0.23), residues: 570 sheet: -0.51 (0.36), residues: 205 loop : -1.00 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 943 TYR 0.019 0.001 TYR C 140 PHE 0.024 0.001 PHE C 278 TRP 0.010 0.001 TRP A 772 HIS 0.005 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (11814) covalent geometry : angle 0.62872 / 0.31 (16023) SS BOND : bond 0.00239 / 0.17 ( 2) SS BOND : angle 0.82696 / 0.51 ( 4) hydrogen bonds : bond 0.03251 / 2.16 ( 481) hydrogen bonds : angle 4.35286 / 2.92 ( 1365) link_BETA1-3 : bond 0.00571 / 0.38 ( 1) link_BETA1-3 : angle 1.34350 / 0.81 ( 3) link_BETA1-4 : bond 0.00347 / 0.21 ( 4) link_BETA1-4 : angle 1.18513 / 0.83 ( 12) link_NAG-ASN : bond 0.00318 / 0.20 ( 3) link_NAG-ASN : angle 1.53236 / 0.85 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 GLN cc_start: 0.3514 (OUTLIER) cc_final: 0.3222 (mp10) REVERT: A 533 TYR cc_start: 0.6750 (OUTLIER) cc_final: 0.6439 (t80) REVERT: A 640 PHE cc_start: 0.7042 (m-10) cc_final: 0.6040 (t80) REVERT: A 790 LEU cc_start: 0.7225 (mm) cc_final: 0.6390 (tt) REVERT: A 1107 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8513 (mm) REVERT: C 297 LYS cc_start: 0.7553 (mttt) cc_final: 0.6961 (tttt) outliers start: 35 outliers final: 24 residues processed: 141 average time/residue: 0.1016 time to fit residues: 21.6425 Evaluate side-chains 144 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 333 TYR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 345 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 64 optimal weight: 0.0870 chunk 7 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 GLN ** A 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.141322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.105184 restraints weight = 28391.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.105407 restraints weight = 18131.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.106315 restraints weight = 12159.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.106711 restraints weight = 10602.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.106867 restraints weight = 9507.941| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11824 Z= 0.129 Angle : 0.643 17.924 16051 Z= 0.314 Chirality : 0.043 0.179 1834 Planarity : 0.003 0.039 1995 Dihedral : 8.412 88.974 1618 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.55 % Allowed : 16.36 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.23), residues: 1410 helix: 0.49 (0.23), residues: 571 sheet: -0.50 (0.36), residues: 211 loop : -0.99 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 943 TYR 0.015 0.001 TYR C 140 PHE 0.025 0.001 PHE C 278 TRP 0.009 0.001 TRP A 772 HIS 0.006 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (11814) covalent geometry : angle 0.64081 / 0.31 (16023) SS BOND : bond 0.00247 / 0.18 ( 2) SS BOND : angle 0.91704 / 0.57 ( 4) hydrogen bonds : bond 0.03290 / 2.18 ( 481) hydrogen bonds : angle 4.36527 / 2.93 ( 1365) link_BETA1-3 : bond 0.00732 / 0.49 ( 1) link_BETA1-3 : angle 1.42400 / 0.85 ( 3) link_BETA1-4 : bond 0.00312 / 0.20 ( 4) link_BETA1-4 : angle 1.21351 / 0.85 ( 12) link_NAG-ASN : bond 0.00317 / 0.19 ( 3) link_NAG-ASN : angle 1.48352 / 0.84 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8133 (pt0) REVERT: A 399 GLN cc_start: 0.3688 (OUTLIER) cc_final: 0.3282 (mp10) REVERT: A 533 TYR cc_start: 0.6821 (OUTLIER) cc_final: 0.6501 (t80) REVERT: A 640 PHE cc_start: 0.7564 (m-10) cc_final: 0.6425 (t80) REVERT: A 790 LEU cc_start: 0.7463 (mm) cc_final: 0.6605 (tt) REVERT: A 940 MET cc_start: 0.8139 (mmm) cc_final: 0.7823 (tpt) REVERT: A 1107 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8508 (mm) REVERT: C 297 LYS cc_start: 0.7431 (mttt) cc_final: 0.6724 (tttt) outliers start: 32 outliers final: 23 residues processed: 144 average time/residue: 0.1004 time to fit residues: 22.0256 Evaluate side-chains 147 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 333 TYR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 345 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 137 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 79 optimal weight: 0.0070 chunk 117 optimal weight: 0.0050 chunk 140 optimal weight: 0.6980 chunk 112 optimal weight: 7.9990 overall best weight: 0.5214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 GLN ** A 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.146716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.114334 restraints weight = 28769.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.112764 restraints weight = 20585.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.114510 restraints weight = 14546.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.114788 restraints weight = 11178.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.115035 restraints weight = 10508.536| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11824 Z= 0.109 Angle : 0.640 17.953 16051 Z= 0.310 Chirality : 0.043 0.196 1834 Planarity : 0.003 0.038 1995 Dihedral : 8.286 86.293 1618 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.76 % Allowed : 16.84 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.23), residues: 1410 helix: 0.62 (0.23), residues: 563 sheet: -0.36 (0.36), residues: 210 loop : -0.90 (0.26), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 272 TYR 0.016 0.001 TYR C 140 PHE 0.025 0.001 PHE A 605 TRP 0.010 0.001 TRP A1172 HIS 0.006 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (11814) covalent geometry : angle 0.63831 / 0.31 (16023) SS BOND : bond 0.00191 / 0.14 ( 2) SS BOND : angle 0.82572 / 0.47 ( 4) hydrogen bonds : bond 0.03064 / 2.05 ( 481) hydrogen bonds : angle 4.30830 / 2.90 ( 1365) link_BETA1-3 : bond 0.00668 / 0.45 ( 1) link_BETA1-3 : angle 1.40403 / 0.84 ( 3) link_BETA1-4 : bond 0.00325 / 0.23 ( 4) link_BETA1-4 : angle 1.10002 / 0.76 ( 12) link_NAG-ASN : bond 0.00331 / 0.20 ( 3) link_NAG-ASN : angle 1.39685 / 0.73 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1838.03 seconds wall clock time: 32 minutes 47.82 seconds (1967.82 seconds total)