Starting phenix.real_space_refine on Tue Jul 29 11:18:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oxa_17262/07_2025/8oxa_17262.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oxa_17262/07_2025/8oxa_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8oxa_17262/07_2025/8oxa_17262.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oxa_17262/07_2025/8oxa_17262.map" model { file = "/net/cci-nas-00/data/ceres_data/8oxa_17262/07_2025/8oxa_17262.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oxa_17262/07_2025/8oxa_17262.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 9 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: 7.46, per 1000 atoms: 0.67 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: 2.95 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.48 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: 4.42 Time building geometry restraints manager: 3.41 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: 6577 29.21 - 58.42: 226 58.42 - 87.64: 27 87.64 - 116.85: 6 116.85 - 146.06: 1 Dihedral angle restraints: 6837 sinusoidal: 2845 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=" O4 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.66 108.37 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" C3 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual 47.62 -58.71 106.33 1 3.00e+01 1.11e-03 1.37e+01 ... (remaining 6834 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 30.270 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 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 : 15.163 146.059 4256 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.77 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.006 0.001 TRP B 41 HIS 0.002 0.000 HIS A 479 PHE 0.012 0.001 PHE A 466 TYR 0.009 0.001 TYR A 225 ARG 0.003 0.000 ARG B 262 Details of bonding type rmsd link_NAG-ASN : bond 0.00129 ( 3) link_NAG-ASN : angle 1.18262 ( 9) link_BETA1-4 : bond 0.01012 ( 2) link_BETA1-4 : angle 2.63864 ( 6) hydrogen bonds : bond 0.23279 ( 520) hydrogen bonds : angle 8.07803 ( 1473) SS BOND : bond 0.00288 ( 3) SS BOND : angle 0.79660 ( 6) covalent geometry : bond 0.00321 (11383) covalent geometry : angle 0.59431 (15416) Misc. bond : bond 0.25775 ( 1) *********************** 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 : 1.236 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: 0.7872 (mm110) cc_final: 0.7136 (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: 0.7388 (m-30) REVERT: B 195 ILE cc_start: 0.7783 (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: 1.0703 time to fit residues: 178.3596 Evaluate side-chains 117 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 113 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 ASN A 447 GLN A 917 GLN A1099 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.168173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.114883 restraints weight = 12006.857| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.01 r_work: 0.3253 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11392 Z= 0.171 Angle : 0.613 9.227 15437 Z= 0.316 Chirality : 0.043 0.245 1727 Planarity : 0.005 0.057 1939 Dihedral : 9.199 125.631 1640 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.67 % Allowed : 8.02 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.23), residues: 1349 helix: 0.84 (0.21), residues: 636 sheet: 0.16 (0.37), residues: 211 loop : -1.01 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 669 HIS 0.004 0.001 HIS A 939 PHE 0.016 0.002 PHE A 666 TYR 0.015 0.002 TYR A1144 ARG 0.007 0.001 ARG B 307 Details of bonding type rmsd link_NAG-ASN : bond 0.00075 ( 3) link_NAG-ASN : angle 1.26001 ( 9) link_BETA1-4 : bond 0.01701 ( 2) link_BETA1-4 : angle 2.67396 ( 6) hydrogen bonds : bond 0.05056 ( 520) hydrogen bonds : angle 5.27228 ( 1473) SS BOND : bond 0.00747 ( 3) SS BOND : angle 1.79581 ( 6) covalent geometry : bond 0.00403 (11383) covalent geometry : angle 0.60930 (15416) Misc. bond : bond 0.00355 ( 1) *********************** 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 151 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 1.141 Fit side-chains REVERT: A 271 ARG cc_start: 0.7867 (mpp-170) cc_final: 0.7591 (mpp-170) REVERT: A 274 LYS cc_start: 0.8405 (ttpp) cc_final: 0.8001 (ttpt) REVERT: A 526 GLN cc_start: 0.7666 (mm110) cc_final: 0.6930 (mm110) REVERT: A 640 GLN cc_start: 0.7668 (tp-100) cc_final: 0.7295 (mm-40) REVERT: A 644 ASP cc_start: 0.7750 (m-30) cc_final: 0.7179 (m-30) REVERT: A 752 ASP cc_start: 0.8609 (t70) cc_final: 0.8042 (t0) REVERT: A 847 GLU cc_start: 0.7235 (tp30) cc_final: 0.6867 (tm-30) REVERT: B 166 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7386 (ptmt) REVERT: B 195 ILE cc_start: 0.7286 (mt) cc_final: 0.6934 (tt) REVERT: B 200 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7382 (ptpp) outliers start: 20 outliers final: 8 residues processed: 139 average time/residue: 1.0426 time to fit residues: 159.5564 Evaluate side-chains 113 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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 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 66 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 7 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A1138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.168452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.114092 restraints weight = 12201.707| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.07 r_work: 0.3265 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11392 Z= 0.152 Angle : 0.566 9.526 15437 Z= 0.290 Chirality : 0.042 0.248 1727 Planarity : 0.004 0.059 1939 Dihedral : 8.138 115.280 1638 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.26 % Allowed : 10.94 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.23), residues: 1349 helix: 1.05 (0.21), residues: 637 sheet: 0.15 (0.36), residues: 212 loop : -1.08 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 669 HIS 0.003 0.001 HIS A 939 PHE 0.016 0.001 PHE A 239 TYR 0.016 0.001 TYR A1144 ARG 0.004 0.000 ARG B 307 Details of bonding type rmsd link_NAG-ASN : bond 0.00070 ( 3) link_NAG-ASN : angle 1.48924 ( 9) link_BETA1-4 : bond 0.01676 ( 2) link_BETA1-4 : angle 2.79913 ( 6) hydrogen bonds : bond 0.04513 ( 520) hydrogen bonds : angle 4.92605 ( 1473) SS BOND : bond 0.00189 ( 3) SS BOND : angle 0.90007 ( 6) covalent geometry : bond 0.00361 (11383) covalent geometry : angle 0.56184 (15416) Misc. bond : bond 0.00087 ( 1) *********************** 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 148 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 1.139 Fit side-chains REVERT: A 71 ARG cc_start: 0.6733 (mpt180) cc_final: 0.6401 (mmm160) REVERT: A 172 GLU cc_start: 0.7956 (tp30) cc_final: 0.7499 (pt0) REVERT: A 271 ARG cc_start: 0.7856 (mpp-170) cc_final: 0.7564 (mpp-170) REVERT: A 274 LYS cc_start: 0.8392 (ttpp) cc_final: 0.7994 (ttpt) REVERT: A 526 GLN cc_start: 0.7541 (mm110) cc_final: 0.6950 (mm110) REVERT: A 627 GLU cc_start: 0.7959 (tt0) cc_final: 0.7701 (pt0) REVERT: A 635 THR cc_start: 0.7023 (OUTLIER) cc_final: 0.6819 (m) REVERT: A 640 GLN cc_start: 0.7750 (tp-100) cc_final: 0.7371 (mm-40) REVERT: A 644 ASP cc_start: 0.7673 (m-30) cc_final: 0.7105 (m-30) REVERT: A 752 ASP cc_start: 0.8676 (t70) cc_final: 0.8064 (t0) REVERT: A 843 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7747 (tm-30) REVERT: A 847 GLU cc_start: 0.7323 (tp30) cc_final: 0.6933 (tm-30) REVERT: A 848 GLN cc_start: 0.7581 (tp40) cc_final: 0.7293 (tp40) REVERT: B 42 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.7591 (mp10) REVERT: B 195 ILE cc_start: 0.7250 (mt) cc_final: 0.6990 (tt) REVERT: B 200 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7304 (ptpp) REVERT: B 201 LYS cc_start: 0.8170 (ptpt) cc_final: 0.7672 (ptmt) REVERT: B 261 MET cc_start: 0.8501 (mmm) cc_final: 0.8236 (mmm) REVERT: B 337 PHE cc_start: 0.7146 (m-80) cc_final: 0.6729 (t80) outliers start: 27 outliers final: 13 residues processed: 135 average time/residue: 1.0409 time to fit residues: 155.3813 Evaluate side-chains 135 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 276 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 337 MET 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 A residue 635 THR 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 200 LYS Chi-restraints excluded: chain B residue 237 LEU 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 38 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3969 r_free = 0.3969 target = 0.168447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.113991 restraints weight = 12138.725| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.06 r_work: 0.3261 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11392 Z= 0.146 Angle : 0.544 9.574 15437 Z= 0.279 Chirality : 0.041 0.250 1727 Planarity : 0.004 0.060 1939 Dihedral : 7.352 104.477 1638 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.67 % Allowed : 12.87 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.23), residues: 1349 helix: 1.14 (0.21), residues: 640 sheet: 0.14 (0.36), residues: 216 loop : -1.08 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 669 HIS 0.002 0.001 HIS A 630 PHE 0.018 0.001 PHE A 666 TYR 0.013 0.001 TYR A1144 ARG 0.004 0.000 ARG B 26 Details of bonding type rmsd link_NAG-ASN : bond 0.00050 ( 3) link_NAG-ASN : angle 1.60320 ( 9) link_BETA1-4 : bond 0.01657 ( 2) link_BETA1-4 : angle 2.84554 ( 6) hydrogen bonds : bond 0.04089 ( 520) hydrogen bonds : angle 4.68741 ( 1473) SS BOND : bond 0.00358 ( 3) SS BOND : angle 0.72532 ( 6) covalent geometry : bond 0.00349 (11383) covalent geometry : angle 0.54010 (15416) Misc. bond : bond 0.00099 ( 1) *********************** 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 156 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 1.429 Fit side-chains REVERT: A 172 GLU cc_start: 0.8076 (tp30) cc_final: 0.7573 (pt0) REVERT: A 271 ARG cc_start: 0.7907 (mpp-170) cc_final: 0.7359 (mpp-170) REVERT: A 526 GLN cc_start: 0.7495 (mm110) cc_final: 0.6926 (mm110) REVERT: A 604 SER cc_start: 0.8660 (OUTLIER) cc_final: 0.8300 (m) REVERT: A 635 THR cc_start: 0.7011 (OUTLIER) cc_final: 0.6803 (m) REVERT: A 640 GLN cc_start: 0.7649 (tp-100) cc_final: 0.7296 (mm-40) REVERT: A 644 ASP cc_start: 0.7669 (m-30) cc_final: 0.7093 (m-30) REVERT: A 752 ASP cc_start: 0.8709 (t70) cc_final: 0.8080 (t0) REVERT: A 843 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7751 (tm-30) REVERT: A 847 GLU cc_start: 0.7317 (tp30) cc_final: 0.6879 (tm-30) REVERT: A 848 GLN cc_start: 0.7538 (tp40) cc_final: 0.7248 (tp40) REVERT: A 916 MET cc_start: 0.6972 (mmt) cc_final: 0.6708 (mmp) REVERT: B 146 ASP cc_start: 0.7567 (t0) cc_final: 0.7202 (t0) REVERT: B 195 ILE cc_start: 0.7198 (mt) cc_final: 0.6977 (tt) REVERT: B 200 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7220 (ptpp) REVERT: B 201 LYS cc_start: 0.8140 (ptpt) cc_final: 0.7703 (ptmt) REVERT: B 244 ASP cc_start: 0.7955 (t0) cc_final: 0.7692 (t0) REVERT: B 246 ASP cc_start: 0.6814 (t0) cc_final: 0.6519 (t0) REVERT: B 261 MET cc_start: 0.8534 (mmm) cc_final: 0.8243 (mmm) REVERT: B 337 PHE cc_start: 0.7266 (m-80) cc_final: 0.6893 (t80) outliers start: 32 outliers final: 14 residues processed: 143 average time/residue: 1.0725 time to fit residues: 171.9568 Evaluate side-chains 127 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 1.327 ------------------------------------------------------------------------------- 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 276 THR 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 590 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 66 ILE 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 103 optimal weight: 0.1980 chunk 107 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 128 optimal weight: 0.4980 chunk 61 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 102 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A1179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.170030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.120338 restraints weight = 12048.186| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.93 r_work: 0.3287 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2042 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= 0.118 Angle : 0.520 9.575 15437 Z= 0.267 Chirality : 0.040 0.254 1727 Planarity : 0.004 0.059 1939 Dihedral : 6.860 93.168 1638 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.01 % Allowed : 13.45 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.23), residues: 1349 helix: 1.34 (0.21), residues: 632 sheet: 0.32 (0.36), residues: 206 loop : -1.06 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 669 HIS 0.002 0.001 HIS A 630 PHE 0.010 0.001 PHE A 239 TYR 0.010 0.001 TYR A1144 ARG 0.003 0.000 ARG A 841 Details of bonding type rmsd link_NAG-ASN : bond 0.00104 ( 3) link_NAG-ASN : angle 1.57006 ( 9) link_BETA1-4 : bond 0.01608 ( 2) link_BETA1-4 : angle 2.81424 ( 6) hydrogen bonds : bond 0.03683 ( 520) hydrogen bonds : angle 4.51292 ( 1473) SS BOND : bond 0.00571 ( 3) SS BOND : angle 1.53289 ( 6) covalent geometry : bond 0.00273 (11383) covalent geometry : angle 0.51508 (15416) Misc. bond : bond 0.00080 ( 1) *********************** 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 163 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 1.165 Fit side-chains REVERT: A 274 LYS cc_start: 0.8358 (ttpt) cc_final: 0.7909 (ttpt) REVERT: A 526 GLN cc_start: 0.7554 (mm110) cc_final: 0.6935 (mm110) REVERT: A 629 LEU cc_start: 0.5948 (OUTLIER) cc_final: 0.5676 (mm) REVERT: A 635 THR cc_start: 0.7030 (OUTLIER) cc_final: 0.6775 (m) REVERT: A 640 GLN cc_start: 0.7659 (tp-100) cc_final: 0.7376 (mm-40) REVERT: A 644 ASP cc_start: 0.7690 (m-30) cc_final: 0.7115 (m-30) REVERT: A 700 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7790 (tp) REVERT: A 752 ASP cc_start: 0.8722 (t70) cc_final: 0.8075 (t0) REVERT: A 843 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7778 (tm-30) REVERT: A 847 GLU cc_start: 0.7200 (tp30) cc_final: 0.6763 (tm-30) REVERT: A 848 GLN cc_start: 0.7546 (tp40) cc_final: 0.7282 (tp40) REVERT: A 916 MET cc_start: 0.6912 (mmt) cc_final: 0.6659 (mmp) REVERT: B 42 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8397 (mm-40) REVERT: B 146 ASP cc_start: 0.7573 (t0) cc_final: 0.7057 (p0) REVERT: B 200 LYS cc_start: 0.7690 (mtpp) cc_final: 0.7264 (ptpp) REVERT: B 201 LYS cc_start: 0.8141 (ptpt) cc_final: 0.7708 (ptmt) REVERT: B 244 ASP cc_start: 0.7988 (t0) cc_final: 0.7743 (t0) REVERT: B 261 MET cc_start: 0.8537 (mmm) cc_final: 0.8255 (mmm) REVERT: B 337 PHE cc_start: 0.7290 (m-80) cc_final: 0.6944 (t80) outliers start: 36 outliers final: 16 residues processed: 148 average time/residue: 1.0429 time to fit residues: 170.3639 Evaluate side-chains 136 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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 276 THR 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 590 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 635 THR 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 76 ARG Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 237 LEU 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 61 optimal weight: 0.8980 chunk 92 optimal weight: 0.3980 chunk 47 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN ** A 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.168014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.117694 restraints weight = 12230.271| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.96 r_work: 0.3255 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11392 Z= 0.155 Angle : 0.549 9.588 15437 Z= 0.281 Chirality : 0.041 0.250 1727 Planarity : 0.004 0.058 1939 Dihedral : 6.830 93.090 1638 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.01 % Allowed : 14.54 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.23), residues: 1349 helix: 1.29 (0.21), residues: 633 sheet: 0.31 (0.36), residues: 205 loop : -1.12 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 669 HIS 0.003 0.001 HIS A 417 PHE 0.013 0.001 PHE A 466 TYR 0.014 0.001 TYR A 92 ARG 0.003 0.000 ARG A 412 Details of bonding type rmsd link_NAG-ASN : bond 0.00069 ( 3) link_NAG-ASN : angle 1.59448 ( 9) link_BETA1-4 : bond 0.01623 ( 2) link_BETA1-4 : angle 2.98534 ( 6) hydrogen bonds : bond 0.03930 ( 520) hydrogen bonds : angle 4.50303 ( 1473) SS BOND : bond 0.00140 ( 3) SS BOND : angle 1.49002 ( 6) covalent geometry : bond 0.00373 (11383) covalent geometry : angle 0.54447 (15416) Misc. bond : bond 0.00139 ( 1) *********************** 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 153 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 1.289 Fit side-chains REVERT: A 271 ARG cc_start: 0.7875 (mpp-170) cc_final: 0.7437 (mpp-170) REVERT: A 526 GLN cc_start: 0.7573 (mm110) cc_final: 0.7017 (mm110) REVERT: A 635 THR cc_start: 0.7021 (OUTLIER) cc_final: 0.6803 (m) REVERT: A 640 GLN cc_start: 0.7697 (tp-100) cc_final: 0.7406 (mm-40) REVERT: A 644 ASP cc_start: 0.7655 (m-30) cc_final: 0.7085 (m-30) REVERT: A 700 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7856 (tp) REVERT: A 752 ASP cc_start: 0.8753 (t70) cc_final: 0.8112 (t0) REVERT: A 843 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7793 (tm-30) REVERT: A 847 GLU cc_start: 0.7281 (tp30) cc_final: 0.6813 (tm-30) REVERT: A 848 GLN cc_start: 0.7613 (tp40) cc_final: 0.7340 (tp40) REVERT: A 916 MET cc_start: 0.6960 (mmt) cc_final: 0.6719 (mmp) REVERT: B 42 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8519 (mm-40) REVERT: B 146 ASP cc_start: 0.7599 (t0) cc_final: 0.7104 (p0) REVERT: B 200 LYS cc_start: 0.7706 (mtpp) cc_final: 0.7289 (ptpp) REVERT: B 201 LYS cc_start: 0.8179 (ptpt) cc_final: 0.7759 (ptmt) REVERT: B 337 PHE cc_start: 0.7388 (m-80) cc_final: 0.7045 (t80) outliers start: 36 outliers final: 18 residues processed: 138 average time/residue: 1.0664 time to fit residues: 161.9766 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 : 1.271 ------------------------------------------------------------------------------- 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 276 THR 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 538 MET Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 700 LEU 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 165 ASP 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 94 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.167899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.117822 restraints weight = 12198.579| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.92 r_work: 0.3257 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11392 Z= 0.157 Angle : 0.547 9.579 15437 Z= 0.279 Chirality : 0.041 0.249 1727 Planarity : 0.004 0.057 1939 Dihedral : 6.806 93.226 1638 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.17 % Allowed : 14.70 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.23), residues: 1349 helix: 1.29 (0.21), residues: 634 sheet: 0.32 (0.36), residues: 205 loop : -1.14 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 669 HIS 0.003 0.001 HIS A 939 PHE 0.018 0.001 PHE A 666 TYR 0.015 0.001 TYR A1144 ARG 0.005 0.000 ARG A 841 Details of bonding type rmsd link_NAG-ASN : bond 0.00054 ( 3) link_NAG-ASN : angle 1.56109 ( 9) link_BETA1-4 : bond 0.01547 ( 2) link_BETA1-4 : angle 2.97883 ( 6) hydrogen bonds : bond 0.03901 ( 520) hydrogen bonds : angle 4.48829 ( 1473) SS BOND : bond 0.00171 ( 3) SS BOND : angle 1.31644 ( 6) covalent geometry : bond 0.00381 (11383) covalent geometry : angle 0.54209 (15416) Misc. bond : bond 0.00153 ( 1) *********************** 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 150 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 1.221 Fit side-chains REVERT: A 271 ARG cc_start: 0.7863 (mpp-170) cc_final: 0.7631 (mpp-170) REVERT: A 274 LYS cc_start: 0.8487 (ttpm) cc_final: 0.8202 (ttpt) REVERT: A 526 GLN cc_start: 0.7539 (mm110) cc_final: 0.6943 (mm110) REVERT: A 635 THR cc_start: 0.6960 (OUTLIER) cc_final: 0.6744 (m) REVERT: A 640 GLN cc_start: 0.7656 (tp-100) cc_final: 0.7381 (mm-40) REVERT: A 644 ASP cc_start: 0.7604 (m-30) cc_final: 0.7043 (m-30) REVERT: A 700 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7836 (tp) REVERT: A 752 ASP cc_start: 0.8747 (t70) cc_final: 0.8100 (t0) REVERT: A 843 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7760 (tm-30) REVERT: A 847 GLU cc_start: 0.7297 (tp30) cc_final: 0.6804 (tm-30) REVERT: A 848 GLN cc_start: 0.7599 (tp40) cc_final: 0.7336 (tp40) REVERT: A 916 MET cc_start: 0.6910 (mmt) cc_final: 0.6670 (mmp) REVERT: B 42 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8515 (mm-40) REVERT: B 146 ASP cc_start: 0.7602 (t0) cc_final: 0.7090 (p0) REVERT: B 200 LYS cc_start: 0.7692 (mtpp) cc_final: 0.7260 (ptpp) REVERT: B 201 LYS cc_start: 0.8132 (ptpt) cc_final: 0.7696 (ptmt) REVERT: B 337 PHE cc_start: 0.7370 (m-80) cc_final: 0.7044 (t80) outliers start: 38 outliers final: 20 residues processed: 134 average time/residue: 1.0245 time to fit residues: 151.7460 Evaluate side-chains 135 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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 276 THR 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 538 MET Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 635 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 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 125 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 0.1980 chunk 88 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 59 optimal weight: 0.0060 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3981 r_free = 0.3981 target = 0.169376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.115142 restraints weight = 12165.197| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.07 r_work: 0.3271 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11392 Z= 0.122 Angle : 0.526 9.576 15437 Z= 0.270 Chirality : 0.041 0.250 1727 Planarity : 0.004 0.056 1939 Dihedral : 6.613 92.939 1638 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.34 % Allowed : 15.54 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.23), residues: 1349 helix: 1.41 (0.21), residues: 635 sheet: 0.42 (0.37), residues: 199 loop : -1.07 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 669 HIS 0.002 0.001 HIS A 417 PHE 0.025 0.001 PHE A 666 TYR 0.012 0.001 TYR A 339 ARG 0.003 0.000 ARG A 841 Details of bonding type rmsd link_NAG-ASN : bond 0.00063 ( 3) link_NAG-ASN : angle 1.50782 ( 9) link_BETA1-4 : bond 0.01589 ( 2) link_BETA1-4 : angle 2.84201 ( 6) hydrogen bonds : bond 0.03618 ( 520) hydrogen bonds : angle 4.38379 ( 1473) SS BOND : bond 0.00250 ( 3) SS BOND : angle 1.28781 ( 6) covalent geometry : bond 0.00287 (11383) covalent geometry : angle 0.52172 (15416) Misc. bond : bond 0.00122 ( 1) *********************** 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 144 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 1.447 Fit side-chains REVERT: A 172 GLU cc_start: 0.7830 (tp30) cc_final: 0.7275 (pt0) REVERT: A 271 ARG cc_start: 0.7896 (mpp-170) cc_final: 0.7659 (mpp-170) REVERT: A 274 LYS cc_start: 0.8442 (ttpm) cc_final: 0.8133 (ttpt) REVERT: A 526 GLN cc_start: 0.7485 (mm110) cc_final: 0.6903 (mm110) REVERT: A 635 THR cc_start: 0.6844 (OUTLIER) cc_final: 0.6615 (m) REVERT: A 640 GLN cc_start: 0.7616 (tp-100) cc_final: 0.7323 (mm-40) REVERT: A 644 ASP cc_start: 0.7564 (m-30) cc_final: 0.6997 (m-30) REVERT: A 700 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7920 (tp) REVERT: A 752 ASP cc_start: 0.8743 (t70) cc_final: 0.8090 (t0) REVERT: A 843 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7710 (tm-30) REVERT: A 847 GLU cc_start: 0.7247 (tp30) cc_final: 0.6697 (tm-30) REVERT: A 848 GLN cc_start: 0.7531 (tp40) cc_final: 0.7272 (tp40) REVERT: A 916 MET cc_start: 0.6828 (mmt) cc_final: 0.6568 (mmp) REVERT: B 42 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8405 (mm-40) REVERT: B 146 ASP cc_start: 0.7599 (t0) cc_final: 0.7167 (p0) REVERT: B 200 LYS cc_start: 0.7629 (mtpp) cc_final: 0.7187 (ptpp) REVERT: B 201 LYS cc_start: 0.8085 (ptpt) cc_final: 0.7633 (ptmt) REVERT: B 337 PHE cc_start: 0.7326 (m-80) cc_final: 0.7017 (t80) outliers start: 28 outliers final: 19 residues processed: 129 average time/residue: 1.0587 time to fit residues: 151.4926 Evaluate side-chains 139 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 276 THR 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 590 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 700 LEU 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 165 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 89 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3947 r_free = 0.3947 target = 0.166201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.115238 restraints weight = 12202.545| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.99 r_work: 0.3241 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11392 Z= 0.202 Angle : 0.586 9.583 15437 Z= 0.299 Chirality : 0.043 0.248 1727 Planarity : 0.004 0.057 1939 Dihedral : 6.805 92.271 1638 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.92 % Allowed : 16.46 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.23), residues: 1349 helix: 1.21 (0.21), residues: 636 sheet: 0.26 (0.37), residues: 205 loop : -1.15 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 669 HIS 0.003 0.001 HIS A 417 PHE 0.027 0.002 PHE A 666 TYR 0.015 0.002 TYR A1144 ARG 0.005 0.000 ARG A 412 Details of bonding type rmsd link_NAG-ASN : bond 0.00149 ( 3) link_NAG-ASN : angle 1.61997 ( 9) link_BETA1-4 : bond 0.01512 ( 2) link_BETA1-4 : angle 3.01026 ( 6) hydrogen bonds : bond 0.04149 ( 520) hydrogen bonds : angle 4.50779 ( 1473) SS BOND : bond 0.00176 ( 3) SS BOND : angle 1.30230 ( 6) covalent geometry : bond 0.00493 (11383) covalent geometry : angle 0.58173 (15416) Misc. bond : bond 0.00203 ( 1) *********************** 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 149 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 1.286 Fit side-chains REVERT: A 172 GLU cc_start: 0.7892 (tp30) cc_final: 0.7411 (pt0) REVERT: A 271 ARG cc_start: 0.8013 (mpp-170) cc_final: 0.7461 (mpp-170) REVERT: A 526 GLN cc_start: 0.7604 (mm110) cc_final: 0.6988 (mm110) REVERT: A 635 THR cc_start: 0.6925 (OUTLIER) cc_final: 0.6714 (m) REVERT: A 640 GLN cc_start: 0.7745 (tp-100) cc_final: 0.7466 (mm-40) REVERT: A 644 ASP cc_start: 0.7654 (m-30) cc_final: 0.7097 (m-30) REVERT: A 700 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7984 (tp) REVERT: A 752 ASP cc_start: 0.8763 (t70) cc_final: 0.8111 (t0) REVERT: A 847 GLU cc_start: 0.7261 (tp30) cc_final: 0.6745 (tm-30) REVERT: A 848 GLN cc_start: 0.7686 (tp40) cc_final: 0.7418 (tp40) REVERT: B 42 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8467 (mm-40) REVERT: B 146 ASP cc_start: 0.7729 (t0) cc_final: 0.7322 (p0) REVERT: B 200 LYS cc_start: 0.7744 (mtpp) cc_final: 0.7320 (ptpp) REVERT: B 201 LYS cc_start: 0.8200 (ptpt) cc_final: 0.7666 (ptmt) REVERT: B 244 ASP cc_start: 0.8180 (t0) cc_final: 0.7973 (t0) REVERT: B 337 PHE cc_start: 0.7424 (m-80) cc_final: 0.7111 (t80) outliers start: 23 outliers final: 16 residues processed: 137 average time/residue: 1.4853 time to fit residues: 226.5787 Evaluate side-chains 135 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 1.674 ------------------------------------------------------------------------------- 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 276 THR 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 590 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 700 LEU 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 7 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 105 optimal weight: 0.0040 chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3953 r_free = 0.3953 target = 0.166777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.112374 restraints weight = 12155.701| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.06 r_work: 0.3235 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11392 Z= 0.174 Angle : 0.574 9.585 15437 Z= 0.295 Chirality : 0.042 0.248 1727 Planarity : 0.004 0.057 1939 Dihedral : 6.813 92.774 1638 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.34 % Allowed : 16.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.23), residues: 1349 helix: 1.20 (0.21), residues: 636 sheet: 0.22 (0.37), residues: 205 loop : -1.11 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 669 HIS 0.003 0.001 HIS A 939 PHE 0.020 0.002 PHE A 666 TYR 0.018 0.002 TYR A1144 ARG 0.005 0.000 ARG A 849 Details of bonding type rmsd link_NAG-ASN : bond 0.00062 ( 3) link_NAG-ASN : angle 1.54855 ( 9) link_BETA1-4 : bond 0.01437 ( 2) link_BETA1-4 : angle 2.87099 ( 6) hydrogen bonds : bond 0.03978 ( 520) hydrogen bonds : angle 4.48039 ( 1473) SS BOND : bond 0.00190 ( 3) SS BOND : angle 1.30124 ( 6) covalent geometry : bond 0.00422 (11383) covalent geometry : angle 0.56942 (15416) Misc. bond : bond 0.00210 ( 1) ********************** 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 148 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 1.280 Fit side-chains REVERT: A 142 TYR cc_start: 0.6079 (p90) cc_final: 0.5754 (p90) REVERT: A 172 GLU cc_start: 0.7938 (tp30) cc_final: 0.7328 (pt0) REVERT: A 274 LYS cc_start: 0.8492 (ttpm) cc_final: 0.8173 (ttpt) REVERT: A 526 GLN cc_start: 0.7493 (mm110) cc_final: 0.6865 (mm110) REVERT: A 635 THR cc_start: 0.6689 (OUTLIER) cc_final: 0.6453 (m) REVERT: A 640 GLN cc_start: 0.7613 (tp-100) cc_final: 0.7319 (mm-40) REVERT: A 644 ASP cc_start: 0.7537 (m-30) cc_final: 0.6979 (m-30) REVERT: A 700 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7954 (tp) REVERT: A 752 ASP cc_start: 0.8746 (t70) cc_final: 0.8090 (t0) REVERT: A 847 GLU cc_start: 0.7186 (tp30) cc_final: 0.6661 (tm-30) REVERT: A 916 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7153 (mmt) REVERT: B 42 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8418 (mm-40) REVERT: B 59 LEU cc_start: 0.8202 (tt) cc_final: 0.7868 (tp) REVERT: B 146 ASP cc_start: 0.7701 (t0) cc_final: 0.7224 (p0) REVERT: B 200 LYS cc_start: 0.7678 (mtpp) cc_final: 0.7204 (ptpp) REVERT: B 201 LYS cc_start: 0.8106 (ptpt) cc_final: 0.7556 (ptmt) REVERT: B 337 PHE cc_start: 0.7327 (m-80) cc_final: 0.7033 (t80) outliers start: 28 outliers final: 18 residues processed: 129 average time/residue: 1.3534 time to fit residues: 193.3934 Evaluate side-chains 137 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.161 ------------------------------------------------------------------------------- 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 276 THR 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 590 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 635 THR 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 76 ARG 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 7 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3957 r_free = 0.3957 target = 0.167050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.116460 restraints weight = 12072.149| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.99 r_work: 0.3259 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11392 Z= 0.158 Angle : 0.563 9.593 15437 Z= 0.288 Chirality : 0.042 0.248 1727 Planarity : 0.004 0.056 1939 Dihedral : 6.793 92.201 1638 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.09 % Allowed : 17.13 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.23), residues: 1349 helix: 1.23 (0.21), residues: 636 sheet: 0.19 (0.37), residues: 204 loop : -1.11 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 669 HIS 0.003 0.001 HIS A 939 PHE 0.027 0.002 PHE A 239 TYR 0.017 0.001 TYR A1144 ARG 0.003 0.000 ARG A 412 Details of bonding type rmsd link_NAG-ASN : bond 0.00047 ( 3) link_NAG-ASN : angle 1.54519 ( 9) link_BETA1-4 : bond 0.01459 ( 2) link_BETA1-4 : angle 2.80810 ( 6) hydrogen bonds : bond 0.03904 ( 520) hydrogen bonds : angle 4.45022 ( 1473) SS BOND : bond 0.00188 ( 3) SS BOND : angle 1.26713 ( 6) covalent geometry : bond 0.00381 (11383) covalent geometry : angle 0.55911 (15416) Misc. bond : bond 0.00212 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9830.38 seconds wall clock time: 179 minutes 0.57 seconds (10740.57 seconds total)