Starting phenix.real_space_refine on Fri Jul 3 01:05:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8oxa_17262/07_2026/8oxa_17262.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oxa_17262/07_2026/8oxa_17262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8oxa_17262/07_2026/8oxa_17262.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oxa_17262/07_2026/8oxa_17262.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oxa_17262/07_2026/8oxa_17262.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oxa_17262/07_2026/8oxa_17262.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8oxa_17262/07_2026/8oxa_17262.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8oxa_17262/07_2026/8oxa_17262.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians V 1 8.30 5 P 1 5.49 5 Mg 1 5.21 5 S 54 5.16 5 C 7196 2.51 5 N 1833 2.21 5 O 2052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 11138 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8361 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 25, 'TRANS': 1009} Chain breaks: 5 Chain: "B" Number of atoms: 2642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2642 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 25, 'TRANS': 302} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' MG': 1, 'D39': 1, 'VN4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Time building chain proxies: 2.11, per 1000 atoms: 0.19 Number of scatterers: 11138 At special positions: 0 Unit cell: (90.4183, 90.4183, 178.734, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) V 1 22.97 S 54 16.00 P 1 15.00 Mg 1 11.99 O 2052 8.00 N 1833 7.00 C 7196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 102 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 401 " - " ASN B 107 " " NAG B 402 " - " ASN B 294 " " NAG C 1 " - " ASN B 180 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 450.9 milliseconds 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2572 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 10 sheets defined 52.1% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 110 through 118 removed outlier: 3.643A pdb=" N ARG A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 133 removed outlier: 3.853A pdb=" N LEU A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 175 removed outlier: 3.677A pdb=" N VAL A 146 " --> pdb=" O TYR A 142 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.780A pdb=" N THR A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 223 Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.569A pdb=" N GLN A 248 " --> pdb=" O GLU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 258 Processing helix chain 'A' and resid 289 through 291 No H-bonds generated for 'chain 'A' and resid 289 through 291' Processing helix chain 'A' and resid 317 through 322 Processing helix chain 'A' and resid 331 through 366 Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 380 through 396 removed outlier: 3.600A pdb=" N ILE A 388 " --> pdb=" O ARG A 384 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 389 " --> pdb=" O GLY A 385 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TRP A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 400 Processing helix chain 'A' and resid 401 through 421 removed outlier: 4.123A pdb=" N TYR A 405 " --> pdb=" O PRO A 401 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 409 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 447 removed outlier: 3.521A pdb=" N GLY A 446 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 519 Processing helix chain 'A' and resid 521 through 534 removed outlier: 4.067A pdb=" N ARG A 525 " --> pdb=" O GLU A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 565 Processing helix chain 'A' and resid 621 through 627 Processing helix chain 'A' and resid 635 through 649 removed outlier: 3.696A pdb=" N GLU A 649 " --> pdb=" O ILE A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 677 removed outlier: 3.817A pdb=" N PHE A 666 " --> pdb=" O GLU A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 695 Processing helix chain 'A' and resid 713 through 724 Processing helix chain 'A' and resid 735 through 746 Processing helix chain 'A' and resid 757 through 770 removed outlier: 3.562A pdb=" N SER A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 795 Processing helix chain 'A' and resid 803 through 811 Processing helix chain 'A' and resid 840 through 859 removed outlier: 3.623A pdb=" N GLU A 859 " --> pdb=" O ASP A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 885 removed outlier: 3.515A pdb=" N ALA A 874 " --> pdb=" O PRO A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 896 No H-bonds generated for 'chain 'A' and resid 894 through 896' Processing helix chain 'A' and resid 897 through 904 Processing helix chain 'A' and resid 916 through 921 Processing helix chain 'A' and resid 928 through 930 No H-bonds generated for 'chain 'A' and resid 928 through 930' Processing helix chain 'A' and resid 931 through 938 Processing helix chain 'A' and resid 938 through 963 removed outlier: 3.562A pdb=" N PHE A 961 " --> pdb=" O LYS A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 969 Processing helix chain 'A' and resid 970 through 972 No H-bonds generated for 'chain 'A' and resid 970 through 972' Processing helix chain 'A' and resid 981 through 988 removed outlier: 3.619A pdb=" N LEU A 987 " --> pdb=" O TRP A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1004 removed outlier: 3.711A pdb=" N ASP A1004 " --> pdb=" O MET A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1015 Processing helix chain 'A' and resid 1016 through 1018 No H-bonds generated for 'chain 'A' and resid 1016 through 1018' Processing helix chain 'A' and resid 1019 through 1024 Processing helix chain 'A' and resid 1029 through 1057 Proline residue: A1051 - end of helix removed outlier: 4.266A pdb=" N GLN A1057 " --> pdb=" O GLY A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1092 removed outlier: 3.501A pdb=" N GLY A1089 " --> pdb=" O ASN A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1114 removed outlier: 3.564A pdb=" N ILE A1107 " --> pdb=" O ILE A1103 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET A1114 " --> pdb=" O TYR A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1140 removed outlier: 4.142A pdb=" N LEU A1140 " --> pdb=" O ALA A1136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1136 through 1140' Processing helix chain 'A' and resid 1142 through 1171 Proline residue: A1159 - end of helix Processing helix chain 'A' and resid 1173 through 1181 Processing helix chain 'B' and resid 46 through 74 Proline residue: B 52 - end of helix removed outlier: 3.943A pdb=" N GLY B 58 " --> pdb=" O PHE B 54 " (cutoff:3.500A) Proline residue: B 63 - end of helix Processing helix chain 'B' and resid 91 through 96 removed outlier: 3.588A pdb=" N LEU B 95 " --> pdb=" O ASN B 92 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER B 96 " --> pdb=" O LYS B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 136 removed outlier: 3.639A pdb=" N LYS B 136 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 144 Processing helix chain 'B' and resid 146 through 151 removed outlier: 3.719A pdb=" N LEU B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 161 Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 206 through 212 Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 239 through 243 removed outlier: 3.838A pdb=" N MET B 242 " --> pdb=" O PRO B 239 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU B 243 " --> pdb=" O VAL B 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 239 through 243' Processing helix chain 'B' and resid 246 through 253 removed outlier: 3.936A pdb=" N ASN B 250 " --> pdb=" O PRO B 247 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLY B 251 " --> pdb=" O ASP B 248 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE B 252 " --> pdb=" O ASN B 249 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE B 253 " --> pdb=" O ASN B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 322 through 350 removed outlier: 3.834A pdb=" N GLY B 326 " --> pdb=" O ASN B 322 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE B 337 " --> pdb=" O GLY B 333 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 67 removed outlier: 3.663A pdb=" N THR A 278 " --> pdb=" O GLU A 264 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY A 277 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 190 removed outlier: 11.856A pdb=" N THR A 177 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N LYS A 203 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU A 179 " --> pdb=" O ARG A 201 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N VAL A 199 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE A 305 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER A 217 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N HIS A 307 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP A 211 " --> pdb=" O ILE A 311 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 224 through 226 Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 436 Processing sheet with id=AA5, first strand: chain 'A' and resid 798 through 802 removed outlier: 6.482A pdb=" N LEU A 799 " --> pdb=" O ILE A 864 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N CYS A 866 " --> pdb=" O LEU A 799 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE A 801 " --> pdb=" O CYS A 866 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE A 728 " --> pdb=" O VAL A 863 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N CYS A 865 " --> pdb=" O ILE A 728 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL A 730 " --> pdb=" O CYS A 865 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE A 451 " --> pdb=" O TRP A 729 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU A 731 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N SER A 453 " --> pdb=" O LEU A 731 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR A 888 " --> pdb=" O ILE A 906 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N VAL A 908 " --> pdb=" O THR A 888 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ALA A 890 " --> pdb=" O VAL A 908 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 460 through 469 removed outlier: 5.242A pdb=" N ILE A 463 " --> pdb=" O LYS A 709 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA A 705 " --> pdb=" O LYS A 467 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N CYS A 469 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA A 703 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU A 656 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA A 703 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A 654 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA A 705 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ARG A 652 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ARG A 608 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VAL A 590 " --> pdb=" O ARG A 608 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER A 580 " --> pdb=" O PHE A 569 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N PHE A 569 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA8, first strand: chain 'A' and resid 1095 through 1096 Processing sheet with id=AA9, first strand: chain 'B' and resid 77 through 80 removed outlier: 3.511A pdb=" N ARG B 307 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL B 118 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU B 275 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N MET B 120 " --> pdb=" O TYR B 273 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 102 through 110 removed outlier: 4.073A pdb=" N CYS B 102 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG B 290 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR B 182 " --> pdb=" O THR B 296 " (cutoff:3.500A) 520 hydrogen bonds defined for protein. 1473 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: 2.04 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1785 1.31 - 1.44: 3165 1.44 - 1.56: 6344 1.56 - 1.69: 6 1.69 - 1.82: 83 Bond restraints: 11383 Sorted by residual: bond pdb=" C21 D39 A1203 " pdb=" O6 D39 A1203 " ideal model delta sigma weight residual 1.330 1.409 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C5 D39 A1203 " pdb=" O4 D39 A1203 " ideal model delta sigma weight residual 1.326 1.402 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.563 -0.044 2.00e-02 2.50e+03 4.86e+00 bond pdb=" C28 D39 A1203 " pdb=" C29 D39 A1203 " ideal model delta sigma weight residual 1.497 1.535 -0.038 2.00e-02 2.50e+03 3.70e+00 bond pdb=" C30 D39 A1203 " pdb=" C31 D39 A1203 " ideal model delta sigma weight residual 1.497 1.535 -0.038 2.00e-02 2.50e+03 3.63e+00 ... (remaining 11378 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 15305 2.89 - 5.78: 96 5.78 - 8.67: 11 8.67 - 11.56: 3 11.56 - 14.45: 1 Bond angle restraints: 15416 Sorted by residual: angle pdb=" O D39 A1203 " pdb=" P D39 A1203 " pdb=" O3 D39 A1203 " ideal model delta sigma weight residual 95.08 109.53 -14.45 3.00e+00 1.11e-01 2.32e+01 angle pdb=" N PRO B 87 " pdb=" CD PRO B 87 " pdb=" CG PRO B 87 " ideal model delta sigma weight residual 103.20 97.78 5.42 1.50e+00 4.44e-01 1.31e+01 angle pdb=" CA PRO B 87 " pdb=" N PRO B 87 " pdb=" CD PRO B 87 " ideal model delta sigma weight residual 112.00 106.97 5.03 1.40e+00 5.10e-01 1.29e+01 angle pdb=" O1 D39 A1203 " pdb=" P D39 A1203 " pdb=" O2 D39 A1203 " ideal model delta sigma weight residual 119.87 109.58 10.29 3.00e+00 1.11e-01 1.18e+01 angle pdb=" OG1 THR A1152 " pdb=" CB THR A1152 " pdb=" CG2 THR A1152 " ideal model delta sigma weight residual 109.30 103.30 6.00 2.00e+00 2.50e-01 9.01e+00 ... (remaining 15411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.21: 6568 29.21 - 58.42: 226 58.42 - 87.64: 21 87.64 - 116.85: 2 116.85 - 146.06: 1 Dihedral angle restraints: 6818 sinusoidal: 2826 harmonic: 3992 Sorted by residual: dihedral pdb=" C33 D39 A1203 " pdb=" C34 D39 A1203 " pdb=" C35 D39 A1203 " pdb=" C36 D39 A1203 " ideal model delta sinusoidal sigma weight residual 180.82 34.76 146.06 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" CA THR A1058 " pdb=" C THR A1058 " pdb=" N VAL A1059 " pdb=" CA VAL A1059 " ideal model delta harmonic sigma weight residual 180.00 161.96 18.04 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ASP A1116 " pdb=" CB ASP A1116 " pdb=" CG ASP A1116 " pdb=" OD1 ASP A1116 " ideal model delta sinusoidal sigma weight residual -30.00 -89.43 59.43 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 6815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1476 0.054 - 0.107: 205 0.107 - 0.161: 43 0.161 - 0.215: 2 0.215 - 0.269: 1 Chirality restraints: 1727 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C3 D39 A1203 " pdb=" C2 D39 A1203 " pdb=" C4 D39 A1203 " pdb=" O6 D39 A1203 " both_signs ideal model delta sigma weight residual False -2.35 -2.55 0.20 2.00e-01 2.50e+01 9.78e-01 chirality pdb=" CB THR A1152 " pdb=" CA THR A1152 " pdb=" OG1 THR A1152 " pdb=" CG2 THR A1152 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.93e-01 ... (remaining 1724 not shown) Planarity restraints: 1942 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 792 " -0.040 5.00e-02 4.00e+02 6.10e-02 5.95e+00 pdb=" N PRO A 793 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 793 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 793 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 108 " 0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO A 109 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 109 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 109 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 195 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO B 196 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 196 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 196 " -0.022 5.00e-02 4.00e+02 ... (remaining 1939 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 75 2.51 - 3.11: 8393 3.11 - 3.70: 17047 3.70 - 4.30: 26134 4.30 - 4.90: 43206 Nonbonded interactions: 94855 Sorted by model distance: nonbonded pdb=" OD2 ASP A 454 " pdb=" O3 VN4 A1201 " model vdw 1.910 3.040 nonbonded pdb=" O GLN A 65 " pdb=" OH TYR A 92 " model vdw 1.995 3.040 nonbonded pdb=" OG1 THR A 732 " pdb=" O1 VN4 A1201 " model vdw 2.018 3.040 nonbonded pdb=" OD2 ASP A 454 " pdb="MG MG A1202 " model vdw 2.031 2.170 nonbonded pdb=" O THR A 456 " pdb="MG MG A1202 " model vdw 2.052 2.170 ... (remaining 94850 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.260 Find NCS groups from input model: 0.050 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:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 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 : 0.004 0.258 11392 Z= 0.280 Angle : 0.597 14.448 15437 Z= 0.287 Chirality : 0.040 0.269 1727 Planarity : 0.004 0.061 1939 Dihedral : 14.527 146.059 4237 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.27 (0.23), residues: 1349 helix: 0.45 (0.22), residues: 609 sheet: 0.12 (0.38), residues: 203 loop : -0.91 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 262 TYR 0.009 0.001 TYR A 225 PHE 0.012 0.001 PHE A 466 TRP 0.006 0.001 TRP B 41 HIS 0.002 0.000 HIS A 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (11383) covalent geometry : angle 0.59431 / 0.29 (15416) SS BOND : bond 0.00288 / 0.12 ( 3) SS BOND : angle 0.79660 / 0.38 ( 6) hydrogen bonds : bond 0.23279 / 14.76 ( 520) hydrogen bonds : angle 8.07803 / 5.63 ( 1473) Misc. bond : bond 0.25775 / 13.57 ( 1) link_BETA1-4 : bond 0.01012 / 0.49 ( 2) link_BETA1-4 : angle 2.63864 / 1.72 ( 6) link_NAG-ASN : bond 0.00129 / 0.06 ( 3) link_NAG-ASN : angle 1.18262 / 0.65 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.8324 (ttpp) cc_final: 0.8110 (ttpt) REVERT: A 526 GLN cc_start: 0.7871 (mm110) cc_final: 0.7135 (mm110) REVERT: A 640 GLN cc_start: 0.8006 (tp-100) cc_final: 0.7642 (mm-40) REVERT: A 644 ASP cc_start: 0.7853 (m-30) cc_final: 0.7389 (m-30) REVERT: B 195 ILE cc_start: 0.7784 (mt) cc_final: 0.7447 (tt) REVERT: B 337 PHE cc_start: 0.7219 (m-80) cc_final: 0.7009 (m-80) outliers start: 0 outliers final: 1 residues processed: 152 average time/residue: 0.4488 time to fit residues: 74.7223 Evaluate side-chains 116 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.0040 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.0570 chunk 103 optimal weight: 0.0270 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 0.3968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 ASN A 917 GLN A1099 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.169177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.115823 restraints weight = 12205.804| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.05 r_work: 0.3289 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11392 Z= 0.138 Angle : 0.581 9.289 15437 Z= 0.302 Chirality : 0.042 0.225 1727 Planarity : 0.004 0.055 1939 Dihedral : 7.518 124.020 1621 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.50 % Allowed : 7.44 % Favored : 91.06 % 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: 0.18 (0.23), residues: 1349 helix: 0.98 (0.21), residues: 636 sheet: 0.19 (0.37), residues: 211 loop : -0.95 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 307 TYR 0.015 0.001 TYR A1144 PHE 0.016 0.001 PHE A 666 TRP 0.017 0.001 TRP A 669 HIS 0.003 0.001 HIS A 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (11383) covalent geometry : angle 0.57794 / 0.30 (15416) SS BOND : bond 0.00762 / 0.40 ( 3) SS BOND : angle 1.72890 / 0.84 ( 6) hydrogen bonds : bond 0.05022 / 3.16 ( 520) hydrogen bonds : angle 5.23899 / 3.66 ( 1473) Misc. bond : bond 0.00821 / 0.43 ( 1) link_BETA1-4 : bond 0.01161 / 0.55 ( 2) link_BETA1-4 : angle 2.15200 / 1.36 ( 6) link_NAG-ASN : bond 0.00195 / 0.09 ( 3) link_NAG-ASN : angle 1.16062 / 0.60 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.372 Fit side-chains REVERT: A 219 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7601 (pt0) REVERT: A 271 ARG cc_start: 0.7833 (mpp-170) cc_final: 0.7547 (mpp-170) REVERT: A 274 LYS cc_start: 0.8388 (ttpp) cc_final: 0.7980 (ttpt) REVERT: A 526 GLN cc_start: 0.7650 (mm110) cc_final: 0.6912 (mm110) REVERT: A 640 GLN cc_start: 0.7596 (tp-100) cc_final: 0.7187 (mm-40) REVERT: A 644 ASP cc_start: 0.7733 (m-30) cc_final: 0.7152 (m-30) REVERT: A 752 ASP cc_start: 0.8609 (t70) cc_final: 0.8049 (t0) REVERT: B 166 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.7349 (ptmt) REVERT: B 195 ILE cc_start: 0.7254 (mt) cc_final: 0.6936 (tt) REVERT: B 200 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7391 (ptpp) REVERT: B 261 MET cc_start: 0.8497 (mmm) cc_final: 0.8277 (mmm) outliers start: 18 outliers final: 7 residues processed: 139 average time/residue: 0.4072 time to fit residues: 62.6110 Evaluate side-chains 122 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 200 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 0.0270 chunk 20 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 61 optimal weight: 0.3980 chunk 48 optimal weight: 4.9990 chunk 103 optimal weight: 0.0270 chunk 104 optimal weight: 0.6980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.170772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.116973 restraints weight = 12147.337| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.07 r_work: 0.3313 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11392 Z= 0.119 Angle : 0.537 9.521 15437 Z= 0.275 Chirality : 0.041 0.249 1727 Planarity : 0.004 0.058 1939 Dihedral : 6.980 109.488 1619 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.75 % Allowed : 10.61 % Favored : 87.64 % 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: 0.42 (0.23), residues: 1349 helix: 1.27 (0.21), residues: 636 sheet: 0.27 (0.36), residues: 211 loop : -0.95 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 307 TYR 0.016 0.001 TYR A1144 PHE 0.015 0.001 PHE A 239 TRP 0.018 0.001 TRP A 669 HIS 0.002 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (11383) covalent geometry : angle 0.53315 / 0.27 (15416) SS BOND : bond 0.00880 / 0.46 ( 3) SS BOND : angle 1.47714 / 0.73 ( 6) hydrogen bonds : bond 0.04238 / 2.66 ( 520) hydrogen bonds : angle 4.81829 / 3.36 ( 1473) Misc. bond : bond 0.00056 / 0.03 ( 1) link_BETA1-4 : bond 0.01488 / 0.71 ( 2) link_BETA1-4 : angle 2.35892 / 1.51 ( 6) link_NAG-ASN : bond 0.00089 / 0.04 ( 3) link_NAG-ASN : angle 1.42532 / 0.74 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.376 Fit side-chains REVERT: A 71 ARG cc_start: 0.6750 (mpt180) cc_final: 0.6431 (mmm160) REVERT: A 172 GLU cc_start: 0.7951 (tp30) cc_final: 0.7567 (pt0) REVERT: A 271 ARG cc_start: 0.7832 (mpp-170) cc_final: 0.7536 (mpp-170) REVERT: A 274 LYS cc_start: 0.8413 (ttpp) cc_final: 0.8027 (ttpt) REVERT: A 526 GLN cc_start: 0.7662 (mm110) cc_final: 0.7057 (mm110) REVERT: A 570 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8036 (mm) REVERT: A 627 GLU cc_start: 0.7952 (tt0) cc_final: 0.7718 (pt0) REVERT: A 640 GLN cc_start: 0.7773 (tp-100) cc_final: 0.7400 (mm-40) REVERT: A 644 ASP cc_start: 0.7771 (m-30) cc_final: 0.7144 (m-30) REVERT: A 752 ASP cc_start: 0.8640 (t70) cc_final: 0.8074 (t0) REVERT: A 847 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6867 (tm-30) REVERT: A 848 GLN cc_start: 0.7633 (tp40) cc_final: 0.7357 (tp40) REVERT: A 916 MET cc_start: 0.7079 (mmt) cc_final: 0.6843 (mmp) REVERT: B 146 ASP cc_start: 0.7526 (t0) cc_final: 0.7238 (t0) REVERT: B 195 ILE cc_start: 0.7289 (mt) cc_final: 0.7055 (tt) REVERT: B 200 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7353 (ptpp) REVERT: B 201 LYS cc_start: 0.8143 (ptpt) cc_final: 0.7734 (ptmt) REVERT: B 261 MET cc_start: 0.8549 (mmm) cc_final: 0.8282 (mmm) outliers start: 21 outliers final: 8 residues processed: 140 average time/residue: 0.4454 time to fit residues: 68.9737 Evaluate side-chains 134 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 31 optimal weight: 0.9990 chunk 122 optimal weight: 0.0970 chunk 116 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 15 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 ASN A 547 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.170850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.120809 restraints weight = 12234.508| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.98 r_work: 0.3309 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11392 Z= 0.120 Angle : 0.518 9.575 15437 Z= 0.267 Chirality : 0.041 0.253 1727 Planarity : 0.004 0.057 1939 Dihedral : 6.725 98.597 1619 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.42 % Allowed : 12.36 % Favored : 85.21 % 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: 1349 helix: 1.34 (0.21), residues: 641 sheet: 0.39 (0.36), residues: 207 loop : -0.97 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 26 TYR 0.010 0.001 TYR A1144 PHE 0.016 0.001 PHE A 666 TRP 0.019 0.001 TRP A 669 HIS 0.003 0.001 HIS A 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (11383) covalent geometry : angle 0.51465 / 0.27 (15416) SS BOND : bond 0.00405 / 0.19 ( 3) SS BOND : angle 0.93208 / 0.46 ( 6) hydrogen bonds : bond 0.03871 / 2.44 ( 520) hydrogen bonds : angle 4.58581 / 3.24 ( 1473) Misc. bond : bond 0.00073 / 0.04 ( 1) link_BETA1-4 : bond 0.01426 / 0.68 ( 2) link_BETA1-4 : angle 2.34020 / 1.50 ( 6) link_NAG-ASN : bond 0.00072 / 0.03 ( 3) link_NAG-ASN : angle 1.53813 / 0.79 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.460 Fit side-chains REVERT: A 172 GLU cc_start: 0.8013 (tp30) cc_final: 0.7609 (pt0) REVERT: A 271 ARG cc_start: 0.7849 (mpp-170) cc_final: 0.7541 (mpp-170) REVERT: A 274 LYS cc_start: 0.8401 (ttpp) cc_final: 0.8007 (ttpt) REVERT: A 526 GLN cc_start: 0.7547 (mm110) cc_final: 0.6940 (mm110) REVERT: A 540 ASP cc_start: 0.7109 (t0) cc_final: 0.6822 (t70) REVERT: A 570 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8076 (mm) REVERT: A 640 GLN cc_start: 0.7733 (tp-100) cc_final: 0.7399 (mm-40) REVERT: A 644 ASP cc_start: 0.7712 (m-30) cc_final: 0.7134 (m-30) REVERT: A 752 ASP cc_start: 0.8646 (t70) cc_final: 0.8066 (t0) REVERT: A 847 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6811 (tm-30) REVERT: A 848 GLN cc_start: 0.7618 (tp40) cc_final: 0.7340 (tp40) REVERT: A 916 MET cc_start: 0.7025 (mmt) cc_final: 0.6784 (mmp) REVERT: B 42 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8484 (mm-40) REVERT: B 59 LEU cc_start: 0.7976 (tt) cc_final: 0.7725 (tm) REVERT: B 146 ASP cc_start: 0.7556 (t0) cc_final: 0.7211 (t0) REVERT: B 200 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7278 (ptpp) REVERT: B 201 LYS cc_start: 0.8132 (ptpt) cc_final: 0.7708 (ptmt) REVERT: B 244 ASP cc_start: 0.7907 (t0) cc_final: 0.7617 (t0) REVERT: B 246 ASP cc_start: 0.6920 (t0) cc_final: 0.6365 (t0) REVERT: B 250 ASN cc_start: 0.7692 (p0) cc_final: 0.7362 (p0) REVERT: B 261 MET cc_start: 0.8565 (mmm) cc_final: 0.8261 (mmm) REVERT: B 337 PHE cc_start: 0.7201 (m-80) cc_final: 0.6793 (t80) outliers start: 29 outliers final: 14 residues processed: 143 average time/residue: 0.4140 time to fit residues: 66.0600 Evaluate side-chains 131 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 122 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 633 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 = 0.3925 r_free = 0.3925 target = 0.164081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.109011 restraints weight = 12152.865| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.09 r_work: 0.3198 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 11392 Z= 0.291 Angle : 0.657 9.628 15437 Z= 0.335 Chirality : 0.046 0.248 1727 Planarity : 0.005 0.058 1939 Dihedral : 7.360 105.509 1619 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.01 % Allowed : 13.20 % Favored : 83.79 % 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: -0.05 (0.22), residues: 1349 helix: 0.85 (0.20), residues: 635 sheet: 0.21 (0.36), residues: 204 loop : -1.22 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 412 TYR 0.022 0.002 TYR A 92 PHE 0.020 0.002 PHE A 959 TRP 0.020 0.002 TRP A 669 HIS 0.005 0.001 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00716 / 0.29 (11383) covalent geometry : angle 0.65359 / 0.33 (15416) SS BOND : bond 0.00180 / 0.09 ( 3) SS BOND : angle 1.09516 / 0.56 ( 6) hydrogen bonds : bond 0.04941 / 3.13 ( 520) hydrogen bonds : angle 4.85744 / 3.37 ( 1473) Misc. bond : bond 0.00316 / 0.17 ( 1) link_BETA1-4 : bond 0.01206 / 0.57 ( 2) link_BETA1-4 : angle 2.85915 / 1.79 ( 6) link_NAG-ASN : bond 0.00345 / 0.16 ( 3) link_NAG-ASN : angle 1.70502 / 0.85 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 0.343 Fit side-chains REVERT: A 136 ILE cc_start: 0.7014 (OUTLIER) cc_final: 0.6805 (pp) REVERT: A 172 GLU cc_start: 0.8100 (tp30) cc_final: 0.7619 (pt0) REVERT: A 271 ARG cc_start: 0.7995 (mpp-170) cc_final: 0.7423 (mpp-170) REVERT: A 274 LYS cc_start: 0.8473 (ttpp) cc_final: 0.8264 (ttpp) REVERT: A 526 GLN cc_start: 0.7585 (mm110) cc_final: 0.6959 (mm110) REVERT: A 570 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8071 (mm) REVERT: A 604 SER cc_start: 0.8718 (OUTLIER) cc_final: 0.8411 (m) REVERT: A 640 GLN cc_start: 0.7735 (tp-100) cc_final: 0.7340 (mm-40) REVERT: A 644 ASP cc_start: 0.7665 (m-30) cc_final: 0.7055 (m-30) REVERT: A 752 ASP cc_start: 0.8737 (t70) cc_final: 0.8108 (t0) REVERT: A 847 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6915 (tm-30) REVERT: A 1097 PHE cc_start: 0.8051 (t80) cc_final: 0.7793 (t80) REVERT: B 42 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8562 (mm-40) REVERT: B 200 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7232 (ptpp) REVERT: B 201 LYS cc_start: 0.8144 (ptpt) cc_final: 0.7625 (ptmt) REVERT: B 337 PHE cc_start: 0.7411 (m-80) cc_final: 0.7027 (t80) outliers start: 36 outliers final: 15 residues processed: 139 average time/residue: 0.5173 time to fit residues: 78.5408 Evaluate side-chains 137 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 19 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 16 optimal weight: 0.0020 chunk 2 optimal weight: 0.4980 chunk 81 optimal weight: 0.5980 chunk 117 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 ASN ** A 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1179 GLN B 129 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.168365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.114195 restraints weight = 12273.940| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.08 r_work: 0.3268 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11392 Z= 0.121 Angle : 0.535 9.579 15437 Z= 0.277 Chirality : 0.041 0.249 1727 Planarity : 0.004 0.059 1939 Dihedral : 6.923 93.245 1619 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.34 % Allowed : 14.79 % Favored : 82.87 % 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: 0.29 (0.23), residues: 1349 helix: 1.15 (0.21), residues: 637 sheet: 0.37 (0.37), residues: 194 loop : -1.04 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 841 TYR 0.014 0.001 TYR A1144 PHE 0.022 0.001 PHE A 666 TRP 0.018 0.001 TRP A 669 HIS 0.002 0.001 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (11383) covalent geometry : angle 0.53181 / 0.28 (15416) SS BOND : bond 0.00385 / 0.17 ( 3) SS BOND : angle 0.81504 / 0.39 ( 6) hydrogen bonds : bond 0.03823 / 2.42 ( 520) hydrogen bonds : angle 4.53691 / 3.17 ( 1473) Misc. bond : bond 0.00090 / 0.05 ( 1) link_BETA1-4 : bond 0.01225 / 0.59 ( 2) link_BETA1-4 : angle 2.35725 / 1.51 ( 6) link_NAG-ASN : bond 0.00113 / 0.05 ( 3) link_NAG-ASN : angle 1.44244 / 0.73 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.430 Fit side-chains REVERT: A 271 ARG cc_start: 0.8110 (mpp-170) cc_final: 0.7560 (mpp-170) REVERT: A 274 LYS cc_start: 0.8444 (ttpp) cc_final: 0.8208 (ttpp) REVERT: A 526 GLN cc_start: 0.7585 (mm110) cc_final: 0.6938 (mm110) REVERT: A 570 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8122 (mm) REVERT: A 627 GLU cc_start: 0.7893 (pt0) cc_final: 0.7678 (pt0) REVERT: A 640 GLN cc_start: 0.7756 (tp-100) cc_final: 0.7421 (mm-40) REVERT: A 644 ASP cc_start: 0.7687 (m-30) cc_final: 0.7079 (m-30) REVERT: A 700 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7875 (tp) REVERT: A 752 ASP cc_start: 0.8777 (t70) cc_final: 0.8143 (t0) REVERT: A 848 GLN cc_start: 0.7670 (tp40) cc_final: 0.7383 (tp40) REVERT: A 916 MET cc_start: 0.6993 (mmt) cc_final: 0.6735 (mmp) REVERT: B 42 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8496 (mm-40) REVERT: B 59 LEU cc_start: 0.8145 (tt) cc_final: 0.7818 (tp) REVERT: B 146 ASP cc_start: 0.7599 (t0) cc_final: 0.7090 (p0) REVERT: B 200 LYS cc_start: 0.7724 (mtpp) cc_final: 0.7298 (ptpp) REVERT: B 201 LYS cc_start: 0.8175 (ptpt) cc_final: 0.7718 (ptmt) REVERT: B 261 MET cc_start: 0.8557 (mmm) cc_final: 0.8215 (mmm) REVERT: B 337 PHE cc_start: 0.7407 (m-80) cc_final: 0.7052 (t80) outliers start: 28 outliers final: 14 residues processed: 134 average time/residue: 0.4683 time to fit residues: 69.5383 Evaluate side-chains 128 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 116 optimal weight: 0.0980 chunk 10 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 633 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 = 0.3969 r_free = 0.3969 target = 0.168230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.113904 restraints weight = 12057.044| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.06 r_work: 0.3256 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11392 Z= 0.135 Angle : 0.548 9.592 15437 Z= 0.282 Chirality : 0.041 0.251 1727 Planarity : 0.004 0.058 1939 Dihedral : 6.749 93.046 1619 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.01 % Allowed : 14.70 % Favored : 82.29 % 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: 0.37 (0.23), residues: 1349 helix: 1.26 (0.21), residues: 635 sheet: 0.35 (0.37), residues: 198 loop : -1.06 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 525 TYR 0.012 0.001 TYR A1144 PHE 0.032 0.001 PHE A 666 TRP 0.019 0.001 TRP A 669 HIS 0.003 0.001 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (11383) covalent geometry : angle 0.54476 / 0.28 (15416) SS BOND : bond 0.00371 / 0.18 ( 3) SS BOND : angle 0.75211 / 0.36 ( 6) hydrogen bonds : bond 0.03817 / 2.40 ( 520) hydrogen bonds : angle 4.46202 / 3.12 ( 1473) Misc. bond : bond 0.00122 / 0.06 ( 1) link_BETA1-4 : bond 0.01267 / 0.61 ( 2) link_BETA1-4 : angle 2.38085 / 1.52 ( 6) link_NAG-ASN : bond 0.00035 / 0.01 ( 3) link_NAG-ASN : angle 1.54623 / 0.78 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 0.466 Fit side-chains REVERT: A 198 ASP cc_start: 0.7680 (t0) cc_final: 0.7432 (t70) REVERT: A 274 LYS cc_start: 0.8395 (ttpp) cc_final: 0.7975 (ttpt) REVERT: A 526 GLN cc_start: 0.7495 (mm110) cc_final: 0.6898 (mm110) REVERT: A 570 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8044 (mm) REVERT: A 640 GLN cc_start: 0.7617 (tp-100) cc_final: 0.7269 (mm-40) REVERT: A 644 ASP cc_start: 0.7573 (m-30) cc_final: 0.6974 (m-30) REVERT: A 700 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7932 (tp) REVERT: A 752 ASP cc_start: 0.8744 (t70) cc_final: 0.8099 (t0) REVERT: A 916 MET cc_start: 0.6840 (mmt) cc_final: 0.6580 (mmp) REVERT: B 42 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8484 (mm-40) REVERT: B 200 LYS cc_start: 0.7639 (mtpp) cc_final: 0.7180 (ptpp) REVERT: B 201 LYS cc_start: 0.8112 (ptpt) cc_final: 0.7558 (ptmt) REVERT: B 261 MET cc_start: 0.8522 (mmm) cc_final: 0.8185 (mmm) REVERT: B 337 PHE cc_start: 0.7353 (m-80) cc_final: 0.7016 (t80) outliers start: 36 outliers final: 18 residues processed: 134 average time/residue: 0.5118 time to fit residues: 75.5605 Evaluate side-chains 135 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 633 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 = 0.3966 r_free = 0.3966 target = 0.167967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.113641 restraints weight = 12097.627| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.06 r_work: 0.3255 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11392 Z= 0.142 Angle : 0.560 12.961 15437 Z= 0.285 Chirality : 0.041 0.250 1727 Planarity : 0.004 0.057 1939 Dihedral : 6.674 92.497 1619 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.51 % Allowed : 15.71 % Favored : 81.79 % 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: 0.38 (0.23), residues: 1349 helix: 1.26 (0.21), residues: 636 sheet: 0.44 (0.38), residues: 188 loop : -1.06 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 841 TYR 0.013 0.001 TYR A1144 PHE 0.023 0.001 PHE A 239 TRP 0.018 0.001 TRP A 669 HIS 0.003 0.001 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (11383) covalent geometry : angle 0.55619 / 0.28 (15416) SS BOND : bond 0.00313 / 0.15 ( 3) SS BOND : angle 1.58631 / 0.86 ( 6) hydrogen bonds : bond 0.03785 / 2.39 ( 520) hydrogen bonds : angle 4.45183 / 3.11 ( 1473) Misc. bond : bond 0.00140 / 0.07 ( 1) link_BETA1-4 : bond 0.01137 / 0.54 ( 2) link_BETA1-4 : angle 2.33652 / 1.48 ( 6) link_NAG-ASN : bond 0.00085 / 0.03 ( 3) link_NAG-ASN : angle 1.54990 / 0.77 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.440 Fit side-chains REVERT: A 274 LYS cc_start: 0.8412 (ttpp) cc_final: 0.8000 (ttpt) REVERT: A 526 GLN cc_start: 0.7478 (mm110) cc_final: 0.6872 (mm110) REVERT: A 546 LEU cc_start: 0.7912 (tp) cc_final: 0.7654 (tp) REVERT: A 570 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8040 (mm) REVERT: A 640 GLN cc_start: 0.7627 (tp-100) cc_final: 0.7270 (mm-40) REVERT: A 644 ASP cc_start: 0.7547 (m-30) cc_final: 0.6948 (m-30) REVERT: A 700 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7888 (tp) REVERT: A 752 ASP cc_start: 0.8746 (t70) cc_final: 0.8087 (t0) REVERT: A 847 GLU cc_start: 0.7238 (tm-30) cc_final: 0.6758 (tp30) REVERT: A 916 MET cc_start: 0.6836 (mmt) cc_final: 0.6584 (mmp) REVERT: B 42 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8447 (mm-40) REVERT: B 200 LYS cc_start: 0.7625 (mtpp) cc_final: 0.7159 (ptpp) REVERT: B 201 LYS cc_start: 0.8094 (ptpt) cc_final: 0.7519 (ptmt) REVERT: B 261 MET cc_start: 0.8535 (mmm) cc_final: 0.8188 (mmm) REVERT: B 337 PHE cc_start: 0.7338 (m-80) cc_final: 0.7013 (t80) outliers start: 30 outliers final: 17 residues processed: 132 average time/residue: 0.5115 time to fit residues: 74.3818 Evaluate side-chains 134 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.0670 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 overall best weight: 1.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 633 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 = 0.3956 r_free = 0.3956 target = 0.166859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.112355 restraints weight = 12059.222| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.06 r_work: 0.3250 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11392 Z= 0.171 Angle : 0.574 12.569 15437 Z= 0.292 Chirality : 0.042 0.249 1727 Planarity : 0.004 0.057 1939 Dihedral : 6.743 92.311 1619 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.84 % Allowed : 16.46 % Favored : 81.70 % 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: 0.30 (0.23), residues: 1349 helix: 1.20 (0.21), residues: 636 sheet: 0.32 (0.38), residues: 191 loop : -1.09 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 412 TYR 0.015 0.002 TYR A1144 PHE 0.031 0.002 PHE A 666 TRP 0.018 0.001 TRP A 669 HIS 0.003 0.001 HIS A 939 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 (11383) covalent geometry : angle 0.56989 / 0.29 (15416) SS BOND : bond 0.00142 / 0.05 ( 3) SS BOND : angle 1.84252 / 1.04 ( 6) hydrogen bonds : bond 0.03975 / 2.51 ( 520) hydrogen bonds : angle 4.48135 / 3.13 ( 1473) Misc. bond : bond 0.00180 / 0.09 ( 1) link_BETA1-4 : bond 0.01161 / 0.56 ( 2) link_BETA1-4 : angle 2.39665 / 1.52 ( 6) link_NAG-ASN : bond 0.00084 / 0.04 ( 3) link_NAG-ASN : angle 1.53809 / 0.76 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.460 Fit side-chains REVERT: A 172 GLU cc_start: 0.7936 (tp30) cc_final: 0.7416 (pt0) REVERT: A 271 ARG cc_start: 0.7861 (mpp-170) cc_final: 0.7435 (mpp-170) REVERT: A 274 LYS cc_start: 0.8476 (ttpp) cc_final: 0.8193 (ttpp) REVERT: A 526 GLN cc_start: 0.7588 (mm110) cc_final: 0.6972 (mm110) REVERT: A 546 LEU cc_start: 0.7939 (tp) cc_final: 0.7683 (tp) REVERT: A 570 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8124 (mm) REVERT: A 640 GLN cc_start: 0.7718 (tp-100) cc_final: 0.7353 (mm-40) REVERT: A 644 ASP cc_start: 0.7643 (m-30) cc_final: 0.7044 (m-30) REVERT: A 700 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8036 (tp) REVERT: A 752 ASP cc_start: 0.8757 (t70) cc_final: 0.8114 (t0) REVERT: A 1055 TYR cc_start: 0.8427 (m-80) cc_final: 0.7910 (m-80) REVERT: B 42 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8462 (mm-40) REVERT: B 146 ASP cc_start: 0.7730 (t0) cc_final: 0.7314 (p0) REVERT: B 200 LYS cc_start: 0.7705 (mtpp) cc_final: 0.7262 (ptpp) REVERT: B 201 LYS cc_start: 0.8177 (ptpt) cc_final: 0.7634 (ptmt) REVERT: B 261 MET cc_start: 0.8630 (mmm) cc_final: 0.8390 (mmm) REVERT: B 337 PHE cc_start: 0.7434 (m-80) cc_final: 0.7113 (t80) outliers start: 22 outliers final: 18 residues processed: 130 average time/residue: 0.5025 time to fit residues: 72.1077 Evaluate side-chains 144 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 80 optimal weight: 0.6980 chunk 115 optimal weight: 8.9990 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 59 optimal weight: 0.0060 chunk 88 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 36 optimal weight: 0.3980 chunk 60 optimal weight: 5.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 633 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 = 0.3982 r_free = 0.3982 target = 0.169306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.115436 restraints weight = 12145.085| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.06 r_work: 0.3275 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11392 Z= 0.119 Angle : 0.544 12.502 15437 Z= 0.277 Chirality : 0.040 0.249 1727 Planarity : 0.004 0.057 1939 Dihedral : 6.530 92.135 1619 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.75 % Allowed : 16.79 % Favored : 81.45 % 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: 0.49 (0.23), residues: 1349 helix: 1.38 (0.21), residues: 636 sheet: 0.42 (0.38), residues: 191 loop : -1.03 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 849 TYR 0.014 0.001 TYR A 339 PHE 0.028 0.001 PHE A 666 TRP 0.017 0.001 TRP A 669 HIS 0.002 0.000 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (11383) covalent geometry : angle 0.54041 / 0.28 (15416) SS BOND : bond 0.00346 / 0.16 ( 3) SS BOND : angle 1.58058 / 0.86 ( 6) hydrogen bonds : bond 0.03562 / 2.24 ( 520) hydrogen bonds : angle 4.36599 / 3.06 ( 1473) Misc. bond : bond 0.00119 / 0.06 ( 1) link_BETA1-4 : bond 0.01120 / 0.54 ( 2) link_BETA1-4 : angle 2.18501 / 1.40 ( 6) link_NAG-ASN : bond 0.00090 / 0.04 ( 3) link_NAG-ASN : angle 1.46463 / 0.73 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.460 Fit side-chains REVERT: A 172 GLU cc_start: 0.7865 (tp30) cc_final: 0.7309 (pt0) REVERT: A 274 LYS cc_start: 0.8376 (ttpp) cc_final: 0.7955 (ttpt) REVERT: A 546 LEU cc_start: 0.7813 (tp) cc_final: 0.7552 (tp) REVERT: A 570 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8028 (mm) REVERT: A 640 GLN cc_start: 0.7619 (tp-100) cc_final: 0.7272 (mm-40) REVERT: A 644 ASP cc_start: 0.7555 (m-30) cc_final: 0.6963 (m-30) REVERT: A 700 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7873 (tp) REVERT: A 752 ASP cc_start: 0.8747 (t70) cc_final: 0.8076 (t0) REVERT: A 847 GLU cc_start: 0.7209 (tm-30) cc_final: 0.6763 (tp30) REVERT: A 916 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.7049 (mmt) REVERT: A 1055 TYR cc_start: 0.8403 (m-80) cc_final: 0.7841 (m-80) REVERT: B 42 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8331 (mm-40) REVERT: B 146 ASP cc_start: 0.7719 (t0) cc_final: 0.7252 (p0) REVERT: B 200 LYS cc_start: 0.7643 (mtpp) cc_final: 0.7155 (ptpp) REVERT: B 201 LYS cc_start: 0.8081 (ptpt) cc_final: 0.7497 (ptmt) REVERT: B 261 MET cc_start: 0.8484 (mmm) cc_final: 0.8218 (mmm) REVERT: B 337 PHE cc_start: 0.7326 (m-80) cc_final: 0.7021 (t80) outliers start: 21 outliers final: 16 residues processed: 136 average time/residue: 0.4561 time to fit residues: 69.2927 Evaluate side-chains 137 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 916 MET Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 52 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 633 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 = 0.3956 r_free = 0.3956 target = 0.166839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.116689 restraints weight = 12230.160| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.98 r_work: 0.3239 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11392 Z= 0.186 Angle : 0.585 12.459 15437 Z= 0.297 Chirality : 0.042 0.247 1727 Planarity : 0.004 0.057 1939 Dihedral : 6.672 91.120 1619 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.75 % Allowed : 17.29 % Favored : 80.95 % 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: 0.34 (0.23), residues: 1349 helix: 1.25 (0.21), residues: 636 sheet: 0.29 (0.39), residues: 186 loop : -1.05 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 412 TYR 0.013 0.002 TYR A1144 PHE 0.026 0.002 PHE A 666 TRP 0.017 0.001 TRP A 669 HIS 0.003 0.001 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (11383) covalent geometry : angle 0.58162 / 0.30 (15416) SS BOND : bond 0.00141 / 0.06 ( 3) SS BOND : angle 1.62392 / 0.90 ( 6) hydrogen bonds : bond 0.03951 / 2.50 ( 520) hydrogen bonds : angle 4.45336 / 3.11 ( 1473) Misc. bond : bond 0.00274 / 0.14 ( 1) link_BETA1-4 : bond 0.01124 / 0.54 ( 2) link_BETA1-4 : angle 2.36314 / 1.49 ( 6) link_NAG-ASN : bond 0.00105 / 0.05 ( 3) link_NAG-ASN : angle 1.56432 / 0.78 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4029.95 seconds wall clock time: 69 minutes 36.53 seconds (4176.53 seconds total)