Starting phenix.real_space_refine on Tue Aug 26 15:18:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xx5_38746/08_2025/8xx5_38746.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xx5_38746/08_2025/8xx5_38746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xx5_38746/08_2025/8xx5_38746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xx5_38746/08_2025/8xx5_38746.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xx5_38746/08_2025/8xx5_38746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xx5_38746/08_2025/8xx5_38746.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 7 6.06 5 Mg 1 5.21 5 S 213 5.16 5 C 24450 2.51 5 N 6531 2.21 5 O 7135 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38337 Number of models: 1 Model: "" Number of chains: 14 Chain: "B" Number of atoms: 9672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1222, 9672 Classifications: {'peptide': 1222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1168} Chain breaks: 2 Chain: "C" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2915 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 339} Chain: "D" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1669 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain: "F" Number of atoms: 2686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2686 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 13, 'TRANS': 320} Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 816 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "H" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 631 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 74} Chain: "I" Number of atoms: 7761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 952, 7761 Classifications: {'peptide': 952} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 907} Chain breaks: 6 Chain: "E" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 121} Chain breaks: 1 Chain: "A" Number of atoms: 11158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1404, 11158 Classifications: {'peptide': 1404} Link IDs: {'PCIS': 2, 'PTRANS': 63, 'TRANS': 1338} Chain breaks: 4 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9191 SG CYS B1180 96.925 56.865 68.891 1.00 39.67 S ATOM 9216 SG CYS B1183 96.146 58.234 72.347 1.00 38.47 S ATOM 9332 SG CYS B1198 99.513 58.520 70.990 1.00 49.51 S ATOM 9354 SG CYS B1201 98.037 54.886 71.875 1.00 60.19 S ATOM 16973 SG CYS G 4 64.165 94.296 138.941 1.00 72.57 S ATOM 16993 SG CYS G 7 67.695 94.778 137.470 1.00 79.97 S ATOM 17127 SG CYS G 24 65.638 91.839 136.390 1.00 84.16 S ATOM 17139 SG CYS G 26 66.981 91.981 139.939 1.00 83.49 S ATOM 17509 SG CYS G 73 34.785 126.596 109.237 1.00 60.83 S ATOM 17530 SG CYS G 76 36.432 129.993 109.883 1.00 65.05 S ATOM 17687 SG CYS G 96 38.497 127.238 108.569 1.00 54.88 S ATOM 17704 SG CYS G 98 37.130 127.035 112.172 1.00 55.06 S ATOM 17809 SG CYS H 7 71.092 130.379 48.381 1.00 36.20 S ATOM 17833 SG CYS H 10 69.975 130.714 44.722 1.00 44.04 S ATOM 18252 SG CYS H 65 67.460 130.413 47.593 1.00 35.19 S ATOM 18258 SG CYS H 66 69.598 133.608 46.847 1.00 41.47 S ATOM 21389 SG CYS I 451 112.602 82.904 41.551 1.00 80.37 S ATOM 21680 SG CYS I 496 111.194 86.175 42.891 1.00 76.59 S ATOM 21703 SG CYS I 499 108.802 83.512 41.352 1.00 69.70 S ATOM 27621 SG CYS A 59 106.817 71.943 68.455 1.00 34.62 S ATOM 27642 SG CYS A 62 104.667 70.764 65.600 1.00 37.60 S ATOM 27702 SG CYS A 69 103.543 73.773 67.741 1.00 36.37 S ATOM 27946 SG CYS A 99 90.939 54.177 108.874 1.00 67.59 S ATOM 27968 SG CYS A 102 91.712 50.719 107.412 1.00 72.52 S ATOM 28220 SG CYS A 134 88.726 51.102 109.583 1.00 88.40 S ATOM 28245 SG CYS A 137 92.297 51.528 111.076 1.00 92.64 S Time building chain proxies: 10.03, per 1000 atoms: 0.26 Number of scatterers: 38337 At special positions: 0 Unit cell: (147.6, 165.64, 171.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 7 29.99 S 213 16.00 Mg 1 11.99 O 7135 8.00 N 6531 7.00 C 24450 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS I 401 " - pdb=" SG CYS I 442 " distance=2.04 Simple disulfide: pdb=" SG CYS I 937 " - pdb=" SG CYS I 950 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.22 Conformation dependent library (CDL) restraints added in 2.0 seconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A 72 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 59 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 62 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 69 " pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 99 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 137 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 134 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1180 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1183 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1198 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1201 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 24 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 26 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 7 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 4 " pdb=" ZN G 202 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 76 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 96 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 73 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 98 " pdb=" ZN H 101 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 10 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 65 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 7 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 66 " pdb=" ZN I1301 " pdb="ZN ZN I1301 " - pdb=" ND1 HIS I 453 " pdb="ZN ZN I1301 " - pdb=" SG CYS I 496 " pdb="ZN ZN I1301 " - pdb=" SG CYS I 451 " pdb="ZN ZN I1301 " - pdb=" SG CYS I 499 " Number of angles added : 36 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9082 Finding SS restraints... Secondary structure from input PDB file: 203 helices and 48 sheets defined 45.6% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'B' and resid 12 through 16 removed outlier: 3.544A pdb=" N VAL B 16 " --> pdb=" O ILE B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 38 removed outlier: 3.938A pdb=" N PHE B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.950A pdb=" N ILE B 44 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 76 through 81 Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 175 through 182 Processing helix chain 'B' and resid 272 through 279 removed outlier: 3.615A pdb=" N PHE B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE B 279 " --> pdb=" O ILE B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 293 removed outlier: 3.875A pdb=" N VAL B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 315 removed outlier: 3.553A pdb=" N PHE B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 341 removed outlier: 3.558A pdb=" N ILE B 332 " --> pdb=" O ASN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 352 removed outlier: 3.577A pdb=" N SER B 352 " --> pdb=" O ALA B 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 349 through 352' Processing helix chain 'B' and resid 353 through 372 Processing helix chain 'B' and resid 373 through 377 Processing helix chain 'B' and resid 379 through 381 No H-bonds generated for 'chain 'B' and resid 379 through 381' Processing helix chain 'B' and resid 382 through 402 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 421 through 437 removed outlier: 3.697A pdb=" N ALA B 431 " --> pdb=" O LYS B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 452 Processing helix chain 'B' and resid 453 through 457 Processing helix chain 'B' and resid 460 through 473 removed outlier: 4.260A pdb=" N LEU B 470 " --> pdb=" O PHE B 466 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N SER B 471 " --> pdb=" O SER B 467 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN B 473 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 489 Processing helix chain 'B' and resid 513 through 522 Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 561 through 565 removed outlier: 4.097A pdb=" N LYS B 564 " --> pdb=" O THR B 561 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 565 " --> pdb=" O GLY B 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 561 through 565' Processing helix chain 'B' and resid 582 through 592 removed outlier: 3.938A pdb=" N LEU B 586 " --> pdb=" O GLU B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 602 No H-bonds generated for 'chain 'B' and resid 600 through 602' Processing helix chain 'B' and resid 603 through 610 Processing helix chain 'B' and resid 627 through 642 Processing helix chain 'B' and resid 679 through 697 Processing helix chain 'B' and resid 700 through 705 Processing helix chain 'B' and resid 715 through 724 Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 742 through 747 removed outlier: 3.674A pdb=" N GLU B 747 " --> pdb=" O PRO B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 761 Processing helix chain 'B' and resid 774 through 779 removed outlier: 3.538A pdb=" N ILE B 778 " --> pdb=" O PRO B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 786 Processing helix chain 'B' and resid 788 through 792 Processing helix chain 'B' and resid 793 through 805 removed outlier: 3.881A pdb=" N ARG B 805 " --> pdb=" O THR B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 818 Processing helix chain 'B' and resid 836 through 841 Processing helix chain 'B' and resid 869 through 874 Processing helix chain 'B' and resid 900 through 904 Processing helix chain 'B' and resid 1030 through 1033 Processing helix chain 'B' and resid 1038 through 1055 removed outlier: 3.799A pdb=" N MET B1042 " --> pdb=" O THR B1038 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B1050 " --> pdb=" O THR B1046 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B1053 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1077 Processing helix chain 'B' and resid 1114 through 1119 Processing helix chain 'B' and resid 1148 through 1158 Processing helix chain 'B' and resid 1163 through 1170 Processing helix chain 'B' and resid 1214 through 1226 Processing helix chain 'C' and resid 19 through 31 Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 89 through 99 removed outlier: 3.509A pdb=" N PHE C 99 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 230 through 258 removed outlier: 3.518A pdb=" N ILE C 253 " --> pdb=" O ARG C 249 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 302 removed outlier: 3.563A pdb=" N GLY C 291 " --> pdb=" O THR C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 358 Processing helix chain 'D' and resid 2 through 17 removed outlier: 4.392A pdb=" N TYR D 11 " --> pdb=" O PHE D 7 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU D 12 " --> pdb=" O THR D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 39 Processing helix chain 'D' and resid 62 through 66 removed outlier: 3.530A pdb=" N VAL D 65 " --> pdb=" O GLY D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 80 removed outlier: 3.606A pdb=" N MET D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 98 Processing helix chain 'D' and resid 99 through 113 removed outlier: 3.563A pdb=" N LEU D 103 " --> pdb=" O LYS D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 removed outlier: 3.516A pdb=" N LEU D 125 " --> pdb=" O PRO D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 133 Processing helix chain 'D' and resid 143 through 155 Processing helix chain 'D' and resid 157 through 161 removed outlier: 3.530A pdb=" N LEU D 161 " --> pdb=" O PRO D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 175 Processing helix chain 'F' and resid 15 through 20 Processing helix chain 'F' and resid 22 through 36 removed outlier: 3.575A pdb=" N HIS F 26 " --> pdb=" O ASN F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 99 removed outlier: 4.158A pdb=" N ASN F 98 " --> pdb=" O ASN F 95 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE F 99 " --> pdb=" O ASP F 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 95 through 99' Processing helix chain 'F' and resid 171 through 195 removed outlier: 3.936A pdb=" N LYS F 180 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU F 181 " --> pdb=" O ASN F 177 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER F 193 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS F 194 " --> pdb=" O GLU F 190 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS F 195 " --> pdb=" O SER F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 207 Processing helix chain 'F' and resid 239 through 247 Processing helix chain 'F' and resid 289 through 314 Processing helix chain 'F' and resid 316 through 323 removed outlier: 4.052A pdb=" N ILE F 320 " --> pdb=" O ASN F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 333 removed outlier: 3.831A pdb=" N LEU F 329 " --> pdb=" O ASN F 325 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE F 330 " --> pdb=" O ILE F 326 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU F 331 " --> pdb=" O TRP F 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 60 Processing helix chain 'G' and resid 61 through 63 No H-bonds generated for 'chain 'G' and resid 61 through 63' Processing helix chain 'H' and resid 13 through 16 Processing helix chain 'H' and resid 17 through 31 Processing helix chain 'H' and resid 37 through 44 Proline residue: H 42 - end of helix Processing helix chain 'H' and resid 51 through 58 Processing helix chain 'H' and resid 63 through 73 removed outlier: 3.578A pdb=" N THR H 73 " --> pdb=" O HIS H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 79 Processing helix chain 'I' and resid 79 through 84 Processing helix chain 'I' and resid 138 through 149 removed outlier: 3.708A pdb=" N PHE I 142 " --> pdb=" O SER I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 163 Processing helix chain 'I' and resid 167 through 174 Processing helix chain 'I' and resid 175 through 177 No H-bonds generated for 'chain 'I' and resid 175 through 177' Processing helix chain 'I' and resid 192 through 211 Processing helix chain 'I' and resid 212 through 235 removed outlier: 3.705A pdb=" N ASP I 235 " --> pdb=" O LEU I 231 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 267 removed outlier: 3.859A pdb=" N THR I 267 " --> pdb=" O LYS I 263 " (cutoff:3.500A) Processing helix chain 'I' and resid 279 through 289 removed outlier: 3.589A pdb=" N ALA I 289 " --> pdb=" O ASP I 285 " (cutoff:3.500A) Processing helix chain 'I' and resid 291 through 296 removed outlier: 3.767A pdb=" N VAL I 294 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 300 through 341 removed outlier: 3.635A pdb=" N GLN I 305 " --> pdb=" O GLN I 301 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS I 306 " --> pdb=" O LYS I 302 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU I 339 " --> pdb=" O PHE I 335 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU I 340 " --> pdb=" O LYS I 336 " (cutoff:3.500A) Processing helix chain 'I' and resid 343 through 356 removed outlier: 3.771A pdb=" N MET I 356 " --> pdb=" O GLU I 352 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 369 Processing helix chain 'I' and resid 377 through 398 removed outlier: 3.574A pdb=" N LEU I 387 " --> pdb=" O THR I 383 " (cutoff:3.500A) Processing helix chain 'I' and resid 402 through 412 removed outlier: 3.755A pdb=" N LEU I 406 " --> pdb=" O ALA I 402 " (cutoff:3.500A) Processing helix chain 'I' and resid 415 through 429 removed outlier: 3.727A pdb=" N LEU I 420 " --> pdb=" O TYR I 416 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS I 421 " --> pdb=" O ALA I 417 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU I 429 " --> pdb=" O SER I 425 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 463 removed outlier: 3.665A pdb=" N ASP I 455 " --> pdb=" O CYS I 451 " (cutoff:3.500A) Processing helix chain 'I' and resid 466 through 474 Processing helix chain 'I' and resid 511 through 515 removed outlier: 3.780A pdb=" N VAL I 515 " --> pdb=" O THR I 512 " (cutoff:3.500A) Processing helix chain 'I' and resid 674 through 683 removed outlier: 3.806A pdb=" N LEU I 683 " --> pdb=" O THR I 679 " (cutoff:3.500A) Processing helix chain 'I' and resid 684 through 698 Processing helix chain 'I' and resid 707 through 720 Processing helix chain 'I' and resid 722 through 729 removed outlier: 3.596A pdb=" N SER I 728 " --> pdb=" O ALA I 724 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN I 729 " --> pdb=" O GLU I 725 " (cutoff:3.500A) Processing helix chain 'I' and resid 732 through 736 removed outlier: 3.942A pdb=" N LYS I 735 " --> pdb=" O PHE I 732 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE I 736 " --> pdb=" O TYR I 733 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 732 through 736' Processing helix chain 'I' and resid 773 through 791 Processing helix chain 'I' and resid 795 through 817 Processing helix chain 'I' and resid 845 through 849 Processing helix chain 'I' and resid 879 through 881 No H-bonds generated for 'chain 'I' and resid 879 through 881' Processing helix chain 'I' and resid 882 through 887 Processing helix chain 'I' and resid 904 through 911 removed outlier: 4.543A pdb=" N GLY I 909 " --> pdb=" O HIS I 906 " (cutoff:3.500A) Processing helix chain 'I' and resid 912 through 933 Processing helix chain 'I' and resid 965 through 973 Processing helix chain 'I' and resid 974 through 986 removed outlier: 3.586A pdb=" N LYS I 978 " --> pdb=" O TYR I 974 " (cutoff:3.500A) Processing helix chain 'I' and resid 1016 through 1028 removed outlier: 4.160A pdb=" N ILE I1020 " --> pdb=" O ASP I1016 " (cutoff:3.500A) Processing helix chain 'I' and resid 1030 through 1036 removed outlier: 3.930A pdb=" N ILE I1034 " --> pdb=" O SER I1030 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU I1035 " --> pdb=" O PRO I1031 " (cutoff:3.500A) Processing helix chain 'I' and resid 1044 through 1050 Processing helix chain 'I' and resid 1063 through 1085 removed outlier: 3.838A pdb=" N MET I1067 " --> pdb=" O ASP I1063 " (cutoff:3.500A) Processing helix chain 'I' and resid 1093 through 1098 Processing helix chain 'I' and resid 1104 through 1115 removed outlier: 4.168A pdb=" N GLU I1112 " --> pdb=" O LYS I1108 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS I1113 " --> pdb=" O GLU I1109 " (cutoff:3.500A) Processing helix chain 'I' and resid 1121 through 1133 Processing helix chain 'I' and resid 1133 through 1154 Processing helix chain 'I' and resid 1158 through 1182 removed outlier: 4.223A pdb=" N ASN I1163 " --> pdb=" O SER I1159 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ILE I1164 " --> pdb=" O TRP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1190 through 1194 removed outlier: 3.995A pdb=" N PHE I1194 " --> pdb=" O PHE I1191 " (cutoff:3.500A) Processing helix chain 'I' and resid 1209 through 1213 Processing helix chain 'I' and resid 1239 through 1247 removed outlier: 3.788A pdb=" N LEU I1243 " --> pdb=" O LEU I1240 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ASP I1244 " --> pdb=" O ASP I1241 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.632A pdb=" N ARG E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 90 removed outlier: 3.573A pdb=" N ILE E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 112 Processing helix chain 'E' and resid 137 through 141 removed outlier: 3.554A pdb=" N MET E 141 " --> pdb=" O PRO E 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 25 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 166 through 175 Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'A' and resid 188 through 195 removed outlier: 3.942A pdb=" N HIS A 192 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Proline residue: A 193 - end of helix Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 226 through 240 removed outlier: 3.588A pdb=" N ILE A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 273 Processing helix chain 'A' and resid 299 through 303 removed outlier: 3.555A pdb=" N LEU A 303 " --> pdb=" O MET A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 342 through 346 Processing helix chain 'A' and resid 358 through 369 Proline residue: A 364 - end of helix Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 450 through 455 removed outlier: 4.189A pdb=" N TYR A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.567A pdb=" N PHE A 487 " --> pdb=" O ARG A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 512 Processing helix chain 'A' and resid 523 through 530 Processing helix chain 'A' and resid 552 through 561 Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 615 through 625 Processing helix chain 'A' and resid 625 through 648 removed outlier: 3.843A pdb=" N ASN A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 657 Processing helix chain 'A' and resid 659 through 686 Processing helix chain 'A' and resid 696 through 709 Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 715 through 722 removed outlier: 3.926A pdb=" N ILE A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 781 through 785 Processing helix chain 'A' and resid 797 through 834 removed outlier: 3.774A pdb=" N THR A 819 " --> pdb=" O LYS A 815 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 858 Processing helix chain 'A' and resid 861 through 865 removed outlier: 4.157A pdb=" N LEU A 865 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 885 Processing helix chain 'A' and resid 891 through 918 removed outlier: 3.896A pdb=" N GLU A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 945 Processing helix chain 'A' and resid 953 through 970 Processing helix chain 'A' and resid 971 through 976 Processing helix chain 'A' and resid 977 through 984 Processing helix chain 'A' and resid 988 through 995 removed outlier: 3.504A pdb=" N ALA A 995 " --> pdb=" O LEU A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1006 Processing helix chain 'A' and resid 1015 through 1033 Processing helix chain 'A' and resid 1040 through 1059 Proline residue: A1052 - end of helix removed outlier: 4.153A pdb=" N GLN A1055 " --> pdb=" O GLU A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1063 Processing helix chain 'A' and resid 1074 through 1082 Processing helix chain 'A' and resid 1085 through 1089 Processing helix chain 'A' and resid 1106 through 1117 Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 5.367A pdb=" N SER A1150 " --> pdb=" O ASP A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1162 Processing helix chain 'A' and resid 1163 through 1166 removed outlier: 4.040A pdb=" N GLN A1166 " --> pdb=" O PRO A1163 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1163 through 1166' Processing helix chain 'A' and resid 1181 through 1188 Processing helix chain 'A' and resid 1191 through 1201 Processing helix chain 'A' and resid 1229 through 1233 Processing helix chain 'A' and resid 1242 through 1256 Processing helix chain 'A' and resid 1299 through 1306 Processing helix chain 'A' and resid 1310 through 1314 removed outlier: 3.551A pdb=" N THR A1313 " --> pdb=" O ASP A1310 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A1314 " --> pdb=" O PRO A1311 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1310 through 1314' Processing helix chain 'A' and resid 1318 through 1326 Processing helix chain 'A' and resid 1327 through 1344 Processing helix chain 'A' and resid 1349 through 1361 removed outlier: 3.753A pdb=" N LEU A1353 " --> pdb=" O ASN A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1378 Processing helix chain 'A' and resid 1381 through 1389 Processing helix chain 'A' and resid 1390 through 1402 Processing helix chain 'A' and resid 1410 through 1416 Processing helix chain 'A' and resid 1422 through 1426 Processing helix chain 'A' and resid 1432 through 1440 Processing sheet with id=AA1, first strand: chain 'B' and resid 145 through 161 removed outlier: 8.736A pdb=" N GLU B 146 " --> pdb=" O TYR B 140 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N TYR B 140 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N LYS B 148 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ALA B 138 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ALA B 150 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU B 136 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE B 152 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N VAL B 134 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ALA B 132 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N GLN B 156 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU B 130 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER B 158 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE B 96 " --> pdb=" O PRO B 127 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN B 129 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL B 94 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA B 131 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER B 84 " --> pdb=" O HIS B 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AA3, first strand: chain 'B' and resid 193 through 195 Processing sheet with id=AA4, first strand: chain 'B' and resid 416 through 420 Processing sheet with id=AA5, first strand: chain 'B' and resid 213 through 216 Processing sheet with id=AA6, first strand: chain 'B' and resid 498 through 501 Processing sheet with id=AA7, first strand: chain 'B' and resid 576 through 577 Processing sheet with id=AA8, first strand: chain 'B' and resid 710 through 712 Processing sheet with id=AA9, first strand: chain 'B' and resid 596 through 598 removed outlier: 5.494A pdb=" N TRP B 621 " --> pdb=" O ILE B 617 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE B 617 " --> pdb=" O TRP B 621 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY B 623 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 823 through 826 removed outlier: 6.055A pdb=" N ARG B 985 " --> pdb=" O VAL B 965 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N VAL B 965 " --> pdb=" O ARG B 985 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N GLU B 987 " --> pdb=" O ALA B 963 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N ALA B 963 " --> pdb=" O GLU B 987 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 834 through 835 Processing sheet with id=AB3, first strand: chain 'B' and resid 1085 through 1086 removed outlier: 6.175A pdb=" N VAL B 865 " --> pdb=" O ALA B1006 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B1008 " --> pdb=" O VAL B 865 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE B1102 " --> pdb=" O TYR B 853 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 895 through 896 removed outlier: 3.517A pdb=" N ILE B 951 " --> pdb=" O ALA B 938 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 932 through 933 removed outlier: 4.102A pdb=" N VAL B 955 " --> pdb=" O ILE B 933 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1017 through 1018 Processing sheet with id=AB7, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 6.023A pdb=" N VAL A 338 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU A 436 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TYR A 340 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE A 444 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR A 326 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N MET A 446 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N CYS A 328 " --> pdb=" O MET A 446 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1146 through 1147 Processing sheet with id=AB9, first strand: chain 'B' and resid 1174 through 1179 Processing sheet with id=AC1, first strand: chain 'B' and resid 1188 through 1190 Processing sheet with id=AC2, first strand: chain 'B' and resid 1228 through 1232 Processing sheet with id=AC3, first strand: chain 'B' and resid 1238 through 1239 removed outlier: 6.526A pdb=" N THR E 56 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL E 133 " --> pdb=" O THR E 56 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL E 58 " --> pdb=" O VAL E 133 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ILE E 135 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLN E 130 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL E 125 " --> pdb=" O GLN E 130 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE E 132 " --> pdb=" O ILE E 123 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 5 through 12 removed outlier: 5.157A pdb=" N PHE C 5 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LYS C 48 " --> pdb=" O PHE C 5 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASN C 7 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N VAL C 39 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA C 225 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N CYS C 222 " --> pdb=" O LYS C 181 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LYS C 181 " --> pdb=" O CYS C 222 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 68 through 73 removed outlier: 5.137A pdb=" N ILE C 159 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N SER C 115 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N GLU C 161 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU C 113 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL C 110 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 123 through 126 Processing sheet with id=AC7, first strand: chain 'C' and resid 267 through 271 Processing sheet with id=AC8, first strand: chain 'D' and resid 20 through 21 removed outlier: 3.738A pdb=" N GLU D 87 " --> pdb=" O ILE D 52 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 138 through 142 removed outlier: 3.723A pdb=" N LYS D 138 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N PHE D 181 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N MET D 162 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N THR D 201 " --> pdb=" O MET D 162 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE D 164 " --> pdb=" O THR D 201 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 2 through 10 removed outlier: 6.211A pdb=" N SER F 75 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N VAL F 51 " --> pdb=" O SER F 75 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL F 77 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR F 49 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N SER F 79 " --> pdb=" O ASN F 47 " (cutoff:3.500A) removed outlier: 9.864A pdb=" N ASN F 47 " --> pdb=" O SER F 79 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 86 through 91 removed outlier: 4.630A pdb=" N ALA F 89 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL F 130 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 237 through 238 removed outlier: 3.520A pdb=" N ALA F 258 " --> pdb=" O TYR F 271 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL F 163 " --> pdb=" O ILE F 285 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N CYS F 287 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N HIS F 165 " --> pdb=" O CYS F 287 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 38 through 43 removed outlier: 3.953A pdb=" N SER G 40 " --> pdb=" O LEU A1131 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A1128 " --> pdb=" O GLU A1179 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N TRP A1174 " --> pdb=" O LEU A1227 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 67 through 69 removed outlier: 4.115A pdb=" N CYS G 67 " --> pdb=" O GLN G 83 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 100 through 101 removed outlier: 6.380A pdb=" N ILE I 91 " --> pdb=" O TYR I 128 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU I 130 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL I 89 " --> pdb=" O LEU I 130 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLU I 108 " --> pdb=" O VAL I 88 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 100 through 101 Processing sheet with id=AD8, first strand: chain 'I' and resid 493 through 495 removed outlier: 4.053A pdb=" N ALA I 504 " --> pdb=" O TYR I 494 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 875 through 878 removed outlier: 6.746A pdb=" N ILE I 861 " --> pdb=" O LEU I 896 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU I 896 " --> pdb=" O ILE I 861 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL I 863 " --> pdb=" O ALA I 894 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 35 through 36 removed outlier: 3.530A pdb=" N LEU A 39 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 76 through 83 removed outlier: 10.669A pdb=" N ALA A 80 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA A 200 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 143 through 146 removed outlier: 4.413A pdb=" N PHE A 154 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 349 through 353 removed outlier: 3.895A pdb=" N ARG A 378 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASP A 408 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N CYS A 376 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 514 through 515 Processing sheet with id=AE6, first strand: chain 'A' and resid 521 through 522 Processing sheet with id=AE7, first strand: chain 'A' and resid 567 through 569 removed outlier: 6.676A pdb=" N GLN A 592 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 753 through 754 Processing sheet with id=AE9, first strand: chain 'A' and resid 836 through 838 removed outlier: 6.560A pdb=" N VAL A 844 " --> pdb=" O VAL A 851 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 866 through 869 Processing sheet with id=AF2, first strand: chain 'A' and resid 1267 through 1278 removed outlier: 3.821A pdb=" N ASN A1267 " --> pdb=" O ASN A1296 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A1290 " --> pdb=" O LEU A1273 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ARG A1275 " --> pdb=" O ASP A1288 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ASP A1288 " --> pdb=" O ARG A1275 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ARG A1277 " --> pdb=" O ARG A1286 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ARG A1286 " --> pdb=" O ARG A1277 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 1120 through 1121 1703 hydrogen bonds defined for protein. 4698 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: 9.91 Time building geometry restraints manager: 5.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12549 1.34 - 1.46: 8556 1.46 - 1.58: 17646 1.58 - 1.71: 1 1.71 - 1.83: 347 Bond restraints: 39099 Sorted by residual: bond pdb=" CB PRO F 236 " pdb=" CG PRO F 236 " ideal model delta sigma weight residual 1.492 1.586 -0.094 5.00e-02 4.00e+02 3.54e+00 bond pdb=" CG GLU A 476 " pdb=" CD GLU A 476 " ideal model delta sigma weight residual 1.516 1.474 0.042 2.50e-02 1.60e+03 2.80e+00 bond pdb=" C LEU A 971 " pdb=" N PRO A 972 " ideal model delta sigma weight residual 1.336 1.353 -0.017 1.08e-02 8.57e+03 2.52e+00 bond pdb=" CB GLU A 476 " pdb=" CG GLU A 476 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.48e+00 bond pdb=" CB GLU A1193 " pdb=" CG GLU A1193 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.93e+00 ... (remaining 39094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 52633 2.94 - 5.88: 258 5.88 - 8.82: 17 8.82 - 11.75: 4 11.75 - 14.69: 2 Bond angle restraints: 52914 Sorted by residual: angle pdb=" N TYR I 78 " pdb=" CA TYR I 78 " pdb=" C TYR I 78 " ideal model delta sigma weight residual 114.56 106.58 7.98 1.27e+00 6.20e-01 3.95e+01 angle pdb=" N ILE A 226 " pdb=" CA ILE A 226 " pdb=" C ILE A 226 " ideal model delta sigma weight residual 113.71 108.11 5.60 9.50e-01 1.11e+00 3.47e+01 angle pdb=" CA TYR I 78 " pdb=" CB TYR I 78 " pdb=" CG TYR I 78 " ideal model delta sigma weight residual 113.90 123.08 -9.18 1.80e+00 3.09e-01 2.60e+01 angle pdb=" C MET D 192 " pdb=" N HIS D 193 " pdb=" CA HIS D 193 " ideal model delta sigma weight residual 121.54 130.88 -9.34 1.91e+00 2.74e-01 2.39e+01 angle pdb=" C TYR I 78 " pdb=" CA TYR I 78 " pdb=" CB TYR I 78 " ideal model delta sigma weight residual 109.13 116.31 -7.18 1.56e+00 4.11e-01 2.12e+01 ... (remaining 52909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 20058 18.00 - 36.00: 2670 36.00 - 54.00: 858 54.00 - 72.00: 185 72.00 - 90.00: 77 Dihedral angle restraints: 23848 sinusoidal: 9802 harmonic: 14046 Sorted by residual: dihedral pdb=" CA LYS I 952 " pdb=" C LYS I 952 " pdb=" N CYS I 953 " pdb=" CA CYS I 953 " ideal model delta harmonic sigma weight residual 180.00 145.79 34.21 0 5.00e+00 4.00e-02 4.68e+01 dihedral pdb=" CA ILE I 353 " pdb=" C ILE I 353 " pdb=" N LEU I 354 " pdb=" CA LEU I 354 " ideal model delta harmonic sigma weight residual 180.00 151.76 28.24 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA ILE A 252 " pdb=" C ILE A 252 " pdb=" N PRO A 253 " pdb=" CA PRO A 253 " ideal model delta harmonic sigma weight residual -180.00 -157.79 -22.21 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 23845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 5213 0.065 - 0.130: 747 0.130 - 0.196: 16 0.196 - 0.261: 1 0.261 - 0.326: 2 Chirality restraints: 5979 Sorted by residual: chirality pdb=" CB ILE I 342 " pdb=" CA ILE I 342 " pdb=" CG1 ILE I 342 " pdb=" CG2 ILE I 342 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CB ILE I 75 " pdb=" CA ILE I 75 " pdb=" CG1 ILE I 75 " pdb=" CG2 ILE I 75 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CG LEU F 234 " pdb=" CB LEU F 234 " pdb=" CD1 LEU F 234 " pdb=" CD2 LEU F 234 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 5976 not shown) Planarity restraints: 6804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 235 " 0.085 5.00e-02 4.00e+02 1.25e-01 2.52e+01 pdb=" N PRO F 236 " -0.217 5.00e-02 4.00e+02 pdb=" CA PRO F 236 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO F 236 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU I 68 " -0.073 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO I 69 " 0.189 5.00e-02 4.00e+02 pdb=" CA PRO I 69 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO I 69 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN I 966 " -0.047 5.00e-02 4.00e+02 6.98e-02 7.79e+00 pdb=" N PRO I 967 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO I 967 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO I 967 " -0.039 5.00e-02 4.00e+02 ... (remaining 6801 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 348 2.56 - 3.15: 30502 3.15 - 3.73: 64338 3.73 - 4.32: 93068 4.32 - 4.90: 150276 Nonbonded interactions: 338532 Sorted by model distance: nonbonded pdb=" OD1 ASP A 457 " pdb="MG MG A1503 " model vdw 1.981 2.170 nonbonded pdb=" OD1 ASP A 459 " pdb="MG MG A1503 " model vdw 1.984 2.170 nonbonded pdb=" OD1 ASP A 461 " pdb="MG MG A1503 " model vdw 2.039 2.170 nonbonded pdb=" OG SER B 123 " pdb=" OE2 GLU B 483 " model vdw 2.168 3.040 nonbonded pdb=" O ARG B 970 " pdb=" OG1 THR I 679 " model vdw 2.169 3.040 ... (remaining 338527 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 9.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 45.670 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 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 : 0.003 0.094 39129 Z= 0.135 Angle : 0.577 14.692 52954 Z= 0.308 Chirality : 0.043 0.326 5979 Planarity : 0.004 0.125 6804 Dihedral : 18.784 90.000 14760 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.55 % Allowed : 4.61 % Favored : 94.84 % Rotamer: Outliers : 3.09 % Allowed : 27.88 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.12), residues: 4746 helix: 1.12 (0.12), residues: 1844 sheet: -0.16 (0.21), residues: 601 loop : -0.36 (0.14), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I1098 TYR 0.023 0.001 TYR I 958 PHE 0.021 0.001 PHE I 260 TRP 0.012 0.001 TRP A 466 HIS 0.011 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00306 (39099) covalent geometry : angle 0.57026 (52914) SS BOND : bond 0.00461 ( 2) SS BOND : angle 1.38414 ( 4) hydrogen bonds : bond 0.17054 ( 1701) hydrogen bonds : angle 6.60363 ( 4698) metal coordination : bond 0.00770 ( 28) metal coordination : angle 3.26800 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 4268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 466 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 40 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7647 (pp) REVERT: F 187 MET cc_start: 0.6884 (OUTLIER) cc_final: 0.6465 (mtm) REVERT: F 231 MET cc_start: 0.6035 (tpt) cc_final: 0.5376 (mtt) REVERT: F 290 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7382 (tm-30) REVERT: I 319 GLN cc_start: 0.6848 (mm-40) cc_final: 0.6440 (mm110) REVERT: I 357 GLU cc_start: 0.6494 (pt0) cc_final: 0.5787 (pp20) REVERT: I 368 GLN cc_start: 0.6825 (mp-120) cc_final: 0.6535 (pm20) REVERT: I 419 LEU cc_start: 0.5851 (OUTLIER) cc_final: 0.5555 (mt) outliers start: 132 outliers final: 105 residues processed: 585 average time/residue: 0.7162 time to fit residues: 510.6131 Evaluate side-chains 553 residues out of total 4268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 445 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 949 LYS Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 985 ARG Chi-restraints excluded: chain B residue 1035 SER Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1113 LYS Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain B residue 1172 SER Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 187 MET Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 237 CYS Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain I residue 78 TYR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 161 SER Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 272 SER Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 277 SER Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 335 PHE Chi-restraints excluded: chain I residue 342 ILE Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 419 LEU Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 775 THR Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 901 CYS Chi-restraints excluded: chain I residue 908 VAL Chi-restraints excluded: chain I residue 934 GLU Chi-restraints excluded: chain I residue 1034 ILE Chi-restraints excluded: chain I residue 1096 VAL Chi-restraints excluded: chain I residue 1114 VAL Chi-restraints excluded: chain I residue 1156 LYS Chi-restraints excluded: chain I residue 1161 VAL Chi-restraints excluded: chain I residue 1199 VAL Chi-restraints excluded: chain I residue 1215 SER Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1402 SER Chi-restraints excluded: chain A residue 1419 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 432 optimal weight: 0.8980 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 0.8980 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.0470 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 470 optimal weight: 0.6980 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 ASN ** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN C 345 GLN F 238 ASN F 325 ASN G 36 ASN I 195 ASN I 388 ASN ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 794 ASN ** I 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 ASN A 228 ASN A 532 GLN ** A1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1181 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.144062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.109722 restraints weight = 48035.718| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.76 r_work: 0.3285 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.0703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 39129 Z= 0.144 Angle : 0.569 14.213 52954 Z= 0.300 Chirality : 0.044 0.214 5979 Planarity : 0.004 0.082 6804 Dihedral : 7.250 88.749 5380 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.64 % Favored : 94.86 % Rotamer: Outliers : 4.29 % Allowed : 24.77 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.12), residues: 4746 helix: 1.19 (0.12), residues: 1896 sheet: -0.27 (0.21), residues: 613 loop : -0.33 (0.14), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 417 TYR 0.031 0.001 TYR I 78 PHE 0.019 0.001 PHE A 918 TRP 0.015 0.001 TRP A 466 HIS 0.009 0.001 HIS I 453 Details of bonding type rmsd covalent geometry : bond 0.00318 (39099) covalent geometry : angle 0.56172 (52914) SS BOND : bond 0.00643 ( 2) SS BOND : angle 1.70961 ( 4) hydrogen bonds : bond 0.04547 ( 1701) hydrogen bonds : angle 5.24991 ( 4698) metal coordination : bond 0.00871 ( 28) metal coordination : angle 3.46322 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 4268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 487 time to evaluate : 1.812 Fit side-chains revert: symmetry clash REVERT: B 40 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7381 (pp) REVERT: B 90 ASN cc_start: 0.8420 (p0) cc_final: 0.8207 (p0) REVERT: B 450 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7767 (tmtp) REVERT: B 540 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.8039 (p0) REVERT: B 563 GLU cc_start: 0.8397 (pm20) cc_final: 0.8189 (pt0) REVERT: B 630 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: B 972 HIS cc_start: 0.6252 (OUTLIER) cc_final: 0.5736 (p90) REVERT: F 290 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7456 (tm-30) REVERT: I 303 PHE cc_start: 0.5634 (OUTLIER) cc_final: 0.3965 (p90) REVERT: I 319 GLN cc_start: 0.6885 (mm-40) cc_final: 0.6640 (mm-40) REVERT: I 380 GLU cc_start: 0.7602 (mm-30) cc_final: 0.6831 (mp0) REVERT: I 979 ASP cc_start: 0.7604 (m-30) cc_final: 0.7387 (m-30) REVERT: I 1019 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7707 (mmmm) REVERT: I 1022 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7142 (mttm) REVERT: A 12 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.7660 (tm-30) REVERT: A 171 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8293 (ttt180) REVERT: A 551 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.7912 (p0) REVERT: A 752 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8833 (mp) REVERT: A 900 ARG cc_start: 0.8346 (tpt170) cc_final: 0.7998 (tpt170) REVERT: A 1152 VAL cc_start: 0.5185 (OUTLIER) cc_final: 0.4931 (m) REVERT: A 1306 ASP cc_start: 0.7360 (t0) cc_final: 0.7133 (t0) REVERT: A 1428 ASP cc_start: 0.8411 (p0) cc_final: 0.8104 (p0) outliers start: 183 outliers final: 75 residues processed: 623 average time/residue: 0.7299 time to fit residues: 551.6772 Evaluate side-chains 531 residues out of total 4268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 443 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 450 LYS Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 630 GLU Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 949 LYS Chi-restraints excluded: chain B residue 972 HIS Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1119 ARG Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 145 MET Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 173 MET Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 268 MET Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 303 PHE Chi-restraints excluded: chain I residue 335 PHE Chi-restraints excluded: chain I residue 342 ILE Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 450 LEU Chi-restraints excluded: chain I residue 453 HIS Chi-restraints excluded: chain I residue 511 ARG Chi-restraints excluded: chain I residue 517 ILE Chi-restraints excluded: chain I residue 678 LEU Chi-restraints excluded: chain I residue 775 THR Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 908 VAL Chi-restraints excluded: chain I residue 1019 LYS Chi-restraints excluded: chain I residue 1022 LYS Chi-restraints excluded: chain I residue 1156 LYS Chi-restraints excluded: chain I residue 1161 VAL Chi-restraints excluded: chain I residue 1199 VAL Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1419 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 141 optimal weight: 0.9980 chunk 469 optimal weight: 0.9980 chunk 268 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 282 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 ASN ** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1031 HIS ** B1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN C 345 GLN I 309 GLN I 388 ASN ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 794 ASN ** I 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 ASN A 33 ASN A 159 GLN A 228 ASN ** A1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN A1078 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.141866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.106931 restraints weight = 47740.529| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.78 r_work: 0.3248 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 39129 Z= 0.200 Angle : 0.599 13.788 52954 Z= 0.314 Chirality : 0.046 0.239 5979 Planarity : 0.004 0.070 6804 Dihedral : 6.533 81.018 5281 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.78 % Favored : 94.71 % Rotamer: Outliers : 4.87 % Allowed : 23.92 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.12), residues: 4746 helix: 1.13 (0.12), residues: 1892 sheet: -0.38 (0.20), residues: 612 loop : -0.38 (0.14), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1277 TYR 0.031 0.002 TYR I 973 PHE 0.021 0.002 PHE A 918 TRP 0.012 0.002 TRP B 200 HIS 0.008 0.001 HIS B1033 Details of bonding type rmsd covalent geometry : bond 0.00463 (39099) covalent geometry : angle 0.59055 (52914) SS BOND : bond 0.00656 ( 2) SS BOND : angle 2.05428 ( 4) hydrogen bonds : bond 0.04544 ( 1701) hydrogen bonds : angle 5.12653 ( 4698) metal coordination : bond 0.01360 ( 28) metal coordination : angle 3.90586 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 4268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 474 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 40 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7489 (pp) REVERT: B 90 ASN cc_start: 0.8417 (p0) cc_final: 0.8213 (p0) REVERT: B 563 GLU cc_start: 0.8415 (pm20) cc_final: 0.8212 (pt0) REVERT: B 630 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: B 699 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7660 (ttmt) REVERT: B 972 HIS cc_start: 0.6228 (OUTLIER) cc_final: 0.5641 (p90) REVERT: C 121 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: C 275 GLU cc_start: 0.6525 (OUTLIER) cc_final: 0.6308 (tm-30) REVERT: D 1 MET cc_start: 0.5835 (OUTLIER) cc_final: 0.5562 (tpt) REVERT: D 144 GLN cc_start: 0.8312 (mm-40) cc_final: 0.8032 (mm-40) REVERT: F 234 LEU cc_start: 0.3925 (OUTLIER) cc_final: 0.3527 (mp) REVERT: F 244 TYR cc_start: 0.6701 (m-80) cc_final: 0.6427 (m-80) REVERT: F 290 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7502 (tm-30) REVERT: F 328 MET cc_start: 0.5832 (OUTLIER) cc_final: 0.5617 (pmm) REVERT: I 303 PHE cc_start: 0.5706 (OUTLIER) cc_final: 0.4020 (p90) REVERT: I 311 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6791 (tt0) REVERT: I 319 GLN cc_start: 0.7002 (mm-40) cc_final: 0.6728 (mm110) REVERT: I 326 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6502 (mp0) REVERT: I 357 GLU cc_start: 0.6712 (pt0) cc_final: 0.5963 (pp20) REVERT: I 376 LYS cc_start: 0.3400 (mptt) cc_final: 0.3116 (mmtt) REVERT: I 380 GLU cc_start: 0.7503 (mm-30) cc_final: 0.6686 (mp0) REVERT: I 448 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.6557 (mttp) REVERT: I 798 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7507 (mt-10) REVERT: I 1019 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7704 (mmmm) REVERT: I 1022 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7116 (mttm) REVERT: I 1097 GLU cc_start: 0.7490 (tp30) cc_final: 0.7261 (tp30) REVERT: A 1 MET cc_start: 0.6548 (OUTLIER) cc_final: 0.6206 (ptm) REVERT: A 12 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7628 (tm-30) REVERT: A 171 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8338 (ttt180) REVERT: A 551 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.7948 (p0) REVERT: A 752 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8898 (mp) REVERT: A 900 ARG cc_start: 0.8393 (tpt170) cc_final: 0.8028 (tpt170) REVERT: A 1027 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8511 (ttp80) REVERT: A 1306 ASP cc_start: 0.7391 (t0) cc_final: 0.6978 (t0) REVERT: A 1428 ASP cc_start: 0.8461 (p0) cc_final: 0.8194 (p0) outliers start: 208 outliers final: 86 residues processed: 628 average time/residue: 0.7923 time to fit residues: 606.8995 Evaluate side-chains 554 residues out of total 4268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 447 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 630 GLU Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain B residue 949 LYS Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 972 HIS Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1119 ARG Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 145 MET Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 173 MET Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 303 PHE Chi-restraints excluded: chain I residue 311 GLU Chi-restraints excluded: chain I residue 326 GLU Chi-restraints excluded: chain I residue 335 PHE Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 448 LYS Chi-restraints excluded: chain I residue 450 LEU Chi-restraints excluded: chain I residue 453 HIS Chi-restraints excluded: chain I residue 511 ARG Chi-restraints excluded: chain I residue 517 ILE Chi-restraints excluded: chain I residue 678 LEU Chi-restraints excluded: chain I residue 775 THR Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 908 VAL Chi-restraints excluded: chain I residue 1019 LYS Chi-restraints excluded: chain I residue 1022 LYS Chi-restraints excluded: chain I residue 1156 LYS Chi-restraints excluded: chain I residue 1161 VAL Chi-restraints excluded: chain I residue 1199 VAL Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 96 LYS Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 1027 ARG Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1419 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 231 optimal weight: 5.9990 chunk 451 optimal weight: 7.9990 chunk 211 optimal weight: 3.9990 chunk 383 optimal weight: 0.8980 chunk 241 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 329 optimal weight: 3.9990 chunk 283 optimal weight: 0.7980 chunk 280 optimal weight: 3.9990 chunk 111 optimal weight: 0.4980 chunk 436 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN B 507 GLN B 528 ASN ** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN ** B1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN C 345 GLN F 325 ASN ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 729 GLN I 794 ASN ** I 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 ASN A 133 GLN A 228 ASN A1018 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.143225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.108623 restraints weight = 47771.875| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.77 r_work: 0.3277 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 39129 Z= 0.144 Angle : 0.554 14.477 52954 Z= 0.290 Chirality : 0.044 0.204 5979 Planarity : 0.004 0.063 6804 Dihedral : 6.294 81.200 5273 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.55 % Favored : 94.96 % Rotamer: Outliers : 4.52 % Allowed : 24.23 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.12), residues: 4746 helix: 1.21 (0.12), residues: 1894 sheet: -0.41 (0.20), residues: 612 loop : -0.36 (0.14), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 92 TYR 0.030 0.001 TYR I 973 PHE 0.018 0.001 PHE A 918 TRP 0.014 0.001 TRP A 466 HIS 0.008 0.001 HIS I 453 Details of bonding type rmsd covalent geometry : bond 0.00326 (39099) covalent geometry : angle 0.54610 (52914) SS BOND : bond 0.00644 ( 2) SS BOND : angle 1.74685 ( 4) hydrogen bonds : bond 0.03945 ( 1701) hydrogen bonds : angle 5.00258 ( 4698) metal coordination : bond 0.00862 ( 28) metal coordination : angle 3.63451 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 4268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 479 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 40 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7385 (pp) REVERT: B 90 ASN cc_start: 0.8399 (p0) cc_final: 0.8188 (p0) REVERT: B 321 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: B 514 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8327 (mt) REVERT: B 540 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8142 (p0) REVERT: B 563 GLU cc_start: 0.8372 (pm20) cc_final: 0.8161 (pt0) REVERT: B 630 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: B 699 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7630 (ttmt) REVERT: B 972 HIS cc_start: 0.6102 (OUTLIER) cc_final: 0.5553 (p90) REVERT: C 121 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7737 (mp0) REVERT: D 1 MET cc_start: 0.5802 (OUTLIER) cc_final: 0.5523 (tpt) REVERT: D 44 ASN cc_start: 0.8156 (m110) cc_final: 0.7628 (m-40) REVERT: D 46 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6920 (tp30) REVERT: F 125 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.6015 (tt0) REVERT: F 200 ILE cc_start: 0.5458 (OUTLIER) cc_final: 0.4977 (mt) REVERT: F 234 LEU cc_start: 0.4057 (OUTLIER) cc_final: 0.3659 (mp) REVERT: F 290 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7421 (tm-30) REVERT: F 332 GLN cc_start: 0.5479 (OUTLIER) cc_final: 0.4845 (pp30) REVERT: G 38 LEU cc_start: 0.7097 (tp) cc_final: 0.6838 (tm) REVERT: I 95 LYS cc_start: 0.5040 (OUTLIER) cc_final: 0.4345 (ptmm) REVERT: I 224 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6811 (mm-30) REVERT: I 303 PHE cc_start: 0.5655 (OUTLIER) cc_final: 0.4073 (p90) REVERT: I 311 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6720 (tt0) REVERT: I 326 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6494 (mp0) REVERT: I 365 SER cc_start: 0.8068 (m) cc_final: 0.7733 (t) REVERT: I 376 LYS cc_start: 0.3482 (mptt) cc_final: 0.3267 (mmtt) REVERT: I 380 GLU cc_start: 0.7516 (mm-30) cc_final: 0.6687 (mp0) REVERT: I 425 SER cc_start: 0.6294 (OUTLIER) cc_final: 0.6061 (m) REVERT: I 438 ASN cc_start: 0.6638 (m110) cc_final: 0.6224 (p0) REVERT: I 448 LYS cc_start: 0.6851 (OUTLIER) cc_final: 0.6579 (mttp) REVERT: I 682 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7956 (mm) REVERT: I 798 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7459 (mt-10) REVERT: I 1019 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7711 (mmmm) REVERT: I 1022 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7059 (mttm) REVERT: I 1097 GLU cc_start: 0.7448 (tp30) cc_final: 0.7167 (tp30) REVERT: A 12 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: A 171 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8289 (ttt180) REVERT: A 551 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.7903 (p0) REVERT: A 752 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8840 (mp) REVERT: A 900 ARG cc_start: 0.8390 (tpt170) cc_final: 0.7955 (tpt170) REVERT: A 1027 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8413 (ttp80) REVERT: A 1306 ASP cc_start: 0.7374 (t0) cc_final: 0.7030 (t0) REVERT: A 1343 MET cc_start: 0.8259 (mmp) cc_final: 0.8048 (mmp) outliers start: 193 outliers final: 82 residues processed: 632 average time/residue: 0.7605 time to fit residues: 583.1865 Evaluate side-chains 547 residues out of total 4268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 437 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 630 GLU Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 949 LYS Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain B residue 972 HIS Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1119 ARG Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 332 GLN Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 173 MET Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 303 PHE Chi-restraints excluded: chain I residue 311 GLU Chi-restraints excluded: chain I residue 326 GLU Chi-restraints excluded: chain I residue 335 PHE Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 425 SER Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 448 LYS Chi-restraints excluded: chain I residue 453 HIS Chi-restraints excluded: chain I residue 511 ARG Chi-restraints excluded: chain I residue 517 ILE Chi-restraints excluded: chain I residue 678 LEU Chi-restraints excluded: chain I residue 682 LEU Chi-restraints excluded: chain I residue 707 THR Chi-restraints excluded: chain I residue 775 THR Chi-restraints excluded: chain I residue 908 VAL Chi-restraints excluded: chain I residue 1019 LYS Chi-restraints excluded: chain I residue 1022 LYS Chi-restraints excluded: chain I residue 1156 LYS Chi-restraints excluded: chain I residue 1161 VAL Chi-restraints excluded: chain I residue 1173 LEU Chi-restraints excluded: chain I residue 1199 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 1027 ARG Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1419 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 424 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 422 optimal weight: 0.7980 chunk 391 optimal weight: 5.9990 chunk 393 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 188 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 344 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 ASN ** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN ** B1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN C 345 GLN D 157 GLN G 36 ASN ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 794 ASN ** I 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 ASN A 133 GLN A 228 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.143584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.108286 restraints weight = 47651.282| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.71 r_work: 0.3291 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 39129 Z= 0.147 Angle : 0.557 14.454 52954 Z= 0.291 Chirality : 0.044 0.229 5979 Planarity : 0.004 0.056 6804 Dihedral : 6.158 82.461 5264 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.78 % Favored : 94.75 % Rotamer: Outliers : 4.33 % Allowed : 24.74 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.12), residues: 4746 helix: 1.23 (0.12), residues: 1896 sheet: -0.48 (0.20), residues: 622 loop : -0.34 (0.14), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 92 TYR 0.020 0.001 TYR I 973 PHE 0.018 0.001 PHE A 918 TRP 0.014 0.001 TRP A 466 HIS 0.008 0.001 HIS I 453 Details of bonding type rmsd covalent geometry : bond 0.00335 (39099) covalent geometry : angle 0.54862 (52914) SS BOND : bond 0.00337 ( 2) SS BOND : angle 2.33012 ( 4) hydrogen bonds : bond 0.03880 ( 1701) hydrogen bonds : angle 4.96275 ( 4698) metal coordination : bond 0.00894 ( 28) metal coordination : angle 3.66957 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 4268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 459 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 ILE cc_start: 0.7690 (OUTLIER) cc_final: 0.7322 (pp) REVERT: B 90 ASN cc_start: 0.8404 (p0) cc_final: 0.8201 (p0) REVERT: B 321 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7803 (tt0) REVERT: B 514 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8334 (mt) REVERT: B 630 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7646 (tm-30) REVERT: B 699 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7612 (ttmt) REVERT: B 972 HIS cc_start: 0.6126 (OUTLIER) cc_final: 0.5585 (p90) REVERT: C 121 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: D 1 MET cc_start: 0.5790 (OUTLIER) cc_final: 0.5534 (tpt) REVERT: D 44 ASN cc_start: 0.8142 (m110) cc_final: 0.7613 (m-40) REVERT: D 168 ASP cc_start: 0.8731 (t70) cc_final: 0.8329 (t70) REVERT: D 189 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: F 125 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.6021 (tt0) REVERT: F 146 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7239 (mp10) REVERT: F 200 ILE cc_start: 0.5441 (OUTLIER) cc_final: 0.5027 (mt) REVERT: F 231 MET cc_start: 0.5639 (tpt) cc_final: 0.4795 (mtt) REVERT: F 234 LEU cc_start: 0.4112 (OUTLIER) cc_final: 0.3886 (mp) REVERT: F 278 PHE cc_start: 0.7194 (OUTLIER) cc_final: 0.6751 (m-80) REVERT: F 290 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7429 (tm-30) REVERT: F 332 GLN cc_start: 0.5496 (OUTLIER) cc_final: 0.4896 (pp30) REVERT: G 38 LEU cc_start: 0.7081 (tp) cc_final: 0.6841 (tm) REVERT: I 95 LYS cc_start: 0.5030 (OUTLIER) cc_final: 0.4352 (ptmm) REVERT: I 179 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: I 224 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6777 (mm-30) REVERT: I 303 PHE cc_start: 0.5678 (OUTLIER) cc_final: 0.4161 (p90) REVERT: I 305 GLN cc_start: 0.6854 (pp30) cc_final: 0.6239 (pp30) REVERT: I 311 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6679 (tt0) REVERT: I 326 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6667 (mp0) REVERT: I 357 GLU cc_start: 0.6741 (pt0) cc_final: 0.5911 (pp20) REVERT: I 365 SER cc_start: 0.8078 (m) cc_final: 0.7726 (t) REVERT: I 380 GLU cc_start: 0.7504 (mm-30) cc_final: 0.6661 (mp0) REVERT: I 425 SER cc_start: 0.6231 (OUTLIER) cc_final: 0.5994 (m) REVERT: I 448 LYS cc_start: 0.6835 (OUTLIER) cc_final: 0.6574 (mttp) REVERT: I 491 ILE cc_start: 0.6398 (OUTLIER) cc_final: 0.5952 (tp) REVERT: I 682 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7946 (mm) REVERT: I 798 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7492 (mt-10) REVERT: I 915 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7086 (tmtm) REVERT: I 969 LEU cc_start: 0.7373 (pp) cc_final: 0.6840 (tm) REVERT: I 1019 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7749 (mmmm) REVERT: I 1022 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7125 (mttm) REVERT: I 1097 GLU cc_start: 0.7519 (tp30) cc_final: 0.7256 (tp30) REVERT: A 12 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.7584 (tm-30) REVERT: A 171 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8270 (ttt180) REVERT: A 752 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8857 (mp) REVERT: A 900 ARG cc_start: 0.8421 (tpt170) cc_final: 0.7940 (tpt170) REVERT: A 1027 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8443 (ttp80) REVERT: A 1253 LYS cc_start: 0.7977 (ttpt) cc_final: 0.7574 (ttmm) REVERT: A 1306 ASP cc_start: 0.7368 (t0) cc_final: 0.6968 (t0) REVERT: A 1307 ASP cc_start: 0.8006 (m-30) cc_final: 0.7784 (t70) REVERT: A 1324 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6449 (tp30) REVERT: A 1343 MET cc_start: 0.8253 (mmp) cc_final: 0.8044 (mmp) outliers start: 185 outliers final: 88 residues processed: 607 average time/residue: 0.7950 time to fit residues: 585.2893 Evaluate side-chains 558 residues out of total 4268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 437 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 630 GLU Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 949 LYS Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 972 HIS Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1119 ARG Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain F residue 332 GLN Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 173 MET Chi-restraints excluded: chain I residue 179 GLU Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 303 PHE Chi-restraints excluded: chain I residue 311 GLU Chi-restraints excluded: chain I residue 326 GLU Chi-restraints excluded: chain I residue 335 PHE Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 425 SER Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 448 LYS Chi-restraints excluded: chain I residue 450 LEU Chi-restraints excluded: chain I residue 453 HIS Chi-restraints excluded: chain I residue 491 ILE Chi-restraints excluded: chain I residue 511 ARG Chi-restraints excluded: chain I residue 517 ILE Chi-restraints excluded: chain I residue 678 LEU Chi-restraints excluded: chain I residue 682 LEU Chi-restraints excluded: chain I residue 707 THR Chi-restraints excluded: chain I residue 775 THR Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain I residue 908 VAL Chi-restraints excluded: chain I residue 915 LYS Chi-restraints excluded: chain I residue 952 LYS Chi-restraints excluded: chain I residue 1019 LYS Chi-restraints excluded: chain I residue 1022 LYS Chi-restraints excluded: chain I residue 1161 VAL Chi-restraints excluded: chain I residue 1173 LEU Chi-restraints excluded: chain I residue 1199 VAL Chi-restraints excluded: chain I residue 1240 LEU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 96 LYS Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 1027 ARG Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1324 GLU Chi-restraints excluded: chain A residue 1419 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 405 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 367 optimal weight: 5.9990 chunk 448 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 432 optimal weight: 2.9990 chunk 299 optimal weight: 0.0060 overall best weight: 2.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN B 528 ASN ** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN ** B1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN C 345 GLN D 157 GLN I 368 GLN I 399 ASN ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1249 GLN A 19 ASN A 133 GLN A 228 ASN A 334 HIS A 532 GLN A1181 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.140907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.105549 restraints weight = 47846.343| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.71 r_work: 0.3243 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 39129 Z= 0.227 Angle : 0.618 13.816 52954 Z= 0.323 Chirality : 0.047 0.223 5979 Planarity : 0.005 0.057 6804 Dihedral : 6.297 84.366 5259 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.04 % Favored : 94.48 % Rotamer: Outliers : 4.78 % Allowed : 24.11 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.12), residues: 4746 helix: 1.07 (0.12), residues: 1894 sheet: -0.44 (0.20), residues: 603 loop : -0.41 (0.14), residues: 2249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 92 TYR 0.031 0.002 TYR I 973 PHE 0.021 0.002 PHE F 44 TRP 0.018 0.002 TRP I 439 HIS 0.009 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00530 (39099) covalent geometry : angle 0.60833 (52914) SS BOND : bond 0.01038 ( 2) SS BOND : angle 4.05251 ( 4) hydrogen bonds : bond 0.04428 ( 1701) hydrogen bonds : angle 5.07615 ( 4698) metal coordination : bond 0.01347 ( 28) metal coordination : angle 4.04463 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 4268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 449 time to evaluate : 1.650 Fit side-chains revert: symmetry clash REVERT: B 40 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7492 (pp) REVERT: B 90 ASN cc_start: 0.8437 (p0) cc_final: 0.8227 (p0) REVERT: B 321 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7776 (tt0) REVERT: B 334 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7889 (tm-30) REVERT: B 630 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7651 (tm-30) REVERT: B 918 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.7903 (t0) REVERT: B 972 HIS cc_start: 0.6243 (OUTLIER) cc_final: 0.5664 (p90) REVERT: C 121 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: C 318 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8308 (pt0) REVERT: D 1 MET cc_start: 0.5874 (OUTLIER) cc_final: 0.5642 (tpt) REVERT: D 109 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7909 (mp10) REVERT: D 144 GLN cc_start: 0.8333 (mm-40) cc_final: 0.8046 (mm-40) REVERT: D 189 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: F 146 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7188 (mp10) REVERT: F 200 ILE cc_start: 0.5399 (OUTLIER) cc_final: 0.4915 (mt) REVERT: F 231 MET cc_start: 0.5780 (tpt) cc_final: 0.4889 (mtt) REVERT: F 234 LEU cc_start: 0.4196 (OUTLIER) cc_final: 0.3966 (mp) REVERT: F 254 LEU cc_start: 0.7507 (mt) cc_final: 0.7259 (mt) REVERT: F 278 PHE cc_start: 0.7170 (OUTLIER) cc_final: 0.6692 (m-80) REVERT: F 290 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7479 (tm-30) REVERT: G 38 LEU cc_start: 0.7112 (tp) cc_final: 0.6863 (tm) REVERT: I 95 LYS cc_start: 0.5034 (OUTLIER) cc_final: 0.4371 (ptmm) REVERT: I 303 PHE cc_start: 0.5899 (OUTLIER) cc_final: 0.4343 (p90) REVERT: I 311 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6763 (tt0) REVERT: I 326 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6459 (mp0) REVERT: I 330 GLN cc_start: 0.7107 (OUTLIER) cc_final: 0.6477 (tt0) REVERT: I 365 SER cc_start: 0.8115 (m) cc_final: 0.7775 (t) REVERT: I 414 LEU cc_start: 0.6132 (OUTLIER) cc_final: 0.5671 (pp) REVERT: I 421 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6994 (ptmm) REVERT: I 448 LYS cc_start: 0.6766 (OUTLIER) cc_final: 0.6496 (mttp) REVERT: I 491 ILE cc_start: 0.6414 (OUTLIER) cc_final: 0.6001 (tp) REVERT: I 682 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7943 (mm) REVERT: I 798 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7571 (mt-10) REVERT: I 915 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7067 (tmtm) REVERT: I 960 ILE cc_start: 0.5933 (OUTLIER) cc_final: 0.5492 (mp) REVERT: I 1019 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7716 (mmmm) REVERT: I 1022 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7091 (mttm) REVERT: I 1097 GLU cc_start: 0.7440 (tp30) cc_final: 0.7191 (tp30) REVERT: A 1 MET cc_start: 0.6601 (OUTLIER) cc_final: 0.6295 (ptm) REVERT: A 12 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.7589 (tm-30) REVERT: A 171 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8341 (ttt180) REVERT: A 551 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.7942 (p0) REVERT: A 752 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8912 (mp) REVERT: A 900 ARG cc_start: 0.8403 (tpt170) cc_final: 0.7917 (tpt170) REVERT: A 1027 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8596 (ttp80) REVERT: A 1200 ARG cc_start: 0.7052 (mtt180) cc_final: 0.6847 (mtt-85) REVERT: A 1306 ASP cc_start: 0.7431 (t0) cc_final: 0.7125 (t0) outliers start: 204 outliers final: 96 residues processed: 610 average time/residue: 0.8057 time to fit residues: 596.8855 Evaluate side-chains 568 residues out of total 4268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 437 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 630 GLU Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 949 LYS Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 972 HIS Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1119 ARG Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 317 GLN Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 109 GLN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 173 MET Chi-restraints excluded: chain I residue 179 GLU Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 303 PHE Chi-restraints excluded: chain I residue 311 GLU Chi-restraints excluded: chain I residue 326 GLU Chi-restraints excluded: chain I residue 330 GLN Chi-restraints excluded: chain I residue 335 PHE Chi-restraints excluded: chain I residue 345 VAL Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 414 LEU Chi-restraints excluded: chain I residue 421 LYS Chi-restraints excluded: chain I residue 425 SER Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 448 LYS Chi-restraints excluded: chain I residue 453 HIS Chi-restraints excluded: chain I residue 491 ILE Chi-restraints excluded: chain I residue 511 ARG Chi-restraints excluded: chain I residue 517 ILE Chi-restraints excluded: chain I residue 678 LEU Chi-restraints excluded: chain I residue 682 LEU Chi-restraints excluded: chain I residue 707 THR Chi-restraints excluded: chain I residue 775 THR Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain I residue 908 VAL Chi-restraints excluded: chain I residue 915 LYS Chi-restraints excluded: chain I residue 960 ILE Chi-restraints excluded: chain I residue 1019 LYS Chi-restraints excluded: chain I residue 1022 LYS Chi-restraints excluded: chain I residue 1161 VAL Chi-restraints excluded: chain I residue 1173 LEU Chi-restraints excluded: chain I residue 1199 VAL Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 96 LYS Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 1027 ARG Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1419 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 222 optimal weight: 4.9990 chunk 379 optimal weight: 0.9980 chunk 295 optimal weight: 0.0980 chunk 411 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 329 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 chunk 422 optimal weight: 0.9980 chunk 407 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 ASN ** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN ** B1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN C 345 GLN D 157 GLN ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 729 GLN I 794 ASN ** I 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 ASN A 228 ASN A 265 GLN ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 GLN A1393 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.143953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.108981 restraints weight = 47680.978| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.72 r_work: 0.3293 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 39129 Z= 0.129 Angle : 0.556 14.654 52954 Z= 0.290 Chirality : 0.044 0.217 5979 Planarity : 0.004 0.055 6804 Dihedral : 6.038 83.628 5259 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.68 % Favored : 94.86 % Rotamer: Outliers : 3.75 % Allowed : 25.12 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.12), residues: 4746 helix: 1.24 (0.12), residues: 1890 sheet: -0.53 (0.20), residues: 621 loop : -0.33 (0.14), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 92 TYR 0.021 0.001 TYR I 958 PHE 0.018 0.001 PHE A 918 TRP 0.015 0.001 TRP A 466 HIS 0.008 0.001 HIS I 453 Details of bonding type rmsd covalent geometry : bond 0.00288 (39099) covalent geometry : angle 0.54839 (52914) SS BOND : bond 0.00521 ( 2) SS BOND : angle 3.05034 ( 4) hydrogen bonds : bond 0.03674 ( 1701) hydrogen bonds : angle 4.90887 ( 4698) metal coordination : bond 0.00722 ( 28) metal coordination : angle 3.53090 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 4268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 467 time to evaluate : 1.610 Fit side-chains revert: symmetry clash REVERT: B 40 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7283 (pp) REVERT: B 90 ASN cc_start: 0.8408 (p0) cc_final: 0.8182 (p0) REVERT: B 321 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7748 (tt0) REVERT: B 334 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7896 (tm-30) REVERT: B 514 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8365 (mt) REVERT: B 605 LYS cc_start: 0.8107 (tmtt) cc_final: 0.7906 (tmmt) REVERT: B 630 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7611 (tm-30) REVERT: B 972 HIS cc_start: 0.6095 (OUTLIER) cc_final: 0.5560 (p90) REVERT: C 121 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7742 (mp0) REVERT: C 311 GLN cc_start: 0.8437 (pt0) cc_final: 0.7967 (pm20) REVERT: D 1 MET cc_start: 0.5880 (OUTLIER) cc_final: 0.5502 (tpt) REVERT: D 44 ASN cc_start: 0.8174 (m110) cc_final: 0.7757 (m-40) REVERT: D 54 SER cc_start: 0.8944 (m) cc_final: 0.8625 (t) REVERT: D 168 ASP cc_start: 0.8640 (t70) cc_final: 0.8274 (t70) REVERT: D 189 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: F 146 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7195 (mp10) REVERT: F 195 LYS cc_start: 0.5367 (OUTLIER) cc_final: 0.5120 (mmtt) REVERT: F 200 ILE cc_start: 0.5395 (OUTLIER) cc_final: 0.5061 (mt) REVERT: F 231 MET cc_start: 0.5738 (tpt) cc_final: 0.4864 (mtt) REVERT: F 234 LEU cc_start: 0.4555 (OUTLIER) cc_final: 0.4018 (mp) REVERT: F 290 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7453 (tm-30) REVERT: F 332 GLN cc_start: 0.5483 (OUTLIER) cc_final: 0.4898 (pp30) REVERT: G 38 LEU cc_start: 0.7079 (tp) cc_final: 0.6816 (tm) REVERT: G 104 ARG cc_start: 0.5438 (OUTLIER) cc_final: 0.5193 (mtm-85) REVERT: I 95 LYS cc_start: 0.5027 (OUTLIER) cc_final: 0.4340 (ptmm) REVERT: I 301 GLN cc_start: 0.7532 (mp10) cc_final: 0.7093 (mm110) REVERT: I 305 GLN cc_start: 0.6786 (pp30) cc_final: 0.6203 (pp30) REVERT: I 311 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6734 (tt0) REVERT: I 326 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6277 (mp0) REVERT: I 352 GLU cc_start: 0.6823 (tm-30) cc_final: 0.6621 (pp20) REVERT: I 357 GLU cc_start: 0.6745 (pt0) cc_final: 0.5841 (pp20) REVERT: I 365 SER cc_start: 0.8063 (m) cc_final: 0.7573 (t) REVERT: I 369 GLU cc_start: 0.6137 (OUTLIER) cc_final: 0.5548 (mp0) REVERT: I 425 SER cc_start: 0.6258 (OUTLIER) cc_final: 0.6032 (m) REVERT: I 491 ILE cc_start: 0.6382 (OUTLIER) cc_final: 0.5934 (tp) REVERT: I 682 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7964 (mm) REVERT: I 798 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7471 (mt-10) REVERT: I 915 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7074 (tmtm) REVERT: I 960 ILE cc_start: 0.5894 (OUTLIER) cc_final: 0.5464 (mp) REVERT: I 1019 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7691 (mmmm) REVERT: I 1022 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7177 (mttm) REVERT: I 1097 GLU cc_start: 0.7390 (tp30) cc_final: 0.7153 (tp30) REVERT: A 171 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8267 (ttt180) REVERT: A 551 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7854 (p0) REVERT: A 752 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8798 (mp) REVERT: A 848 THR cc_start: 0.8785 (p) cc_final: 0.8536 (m) REVERT: A 900 ARG cc_start: 0.8396 (tpt170) cc_final: 0.7900 (tpt170) REVERT: A 1027 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8339 (ttp80) REVERT: A 1182 LYS cc_start: 0.5335 (tptt) cc_final: 0.5074 (tptt) REVERT: A 1253 LYS cc_start: 0.8007 (ttpt) cc_final: 0.7598 (ttmm) REVERT: A 1306 ASP cc_start: 0.7376 (t0) cc_final: 0.6994 (t0) outliers start: 160 outliers final: 83 residues processed: 595 average time/residue: 0.7947 time to fit residues: 573.1723 Evaluate side-chains 555 residues out of total 4268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 442 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 630 GLU Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 949 LYS Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain B residue 972 HIS Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1119 ARG Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 332 GLN Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain G residue 104 ARG Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 173 MET Chi-restraints excluded: chain I residue 179 GLU Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 311 GLU Chi-restraints excluded: chain I residue 326 GLU Chi-restraints excluded: chain I residue 335 PHE Chi-restraints excluded: chain I residue 345 VAL Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 369 GLU Chi-restraints excluded: chain I residue 425 SER Chi-restraints excluded: chain I residue 453 HIS Chi-restraints excluded: chain I residue 491 ILE Chi-restraints excluded: chain I residue 511 ARG Chi-restraints excluded: chain I residue 517 ILE Chi-restraints excluded: chain I residue 678 LEU Chi-restraints excluded: chain I residue 682 LEU Chi-restraints excluded: chain I residue 707 THR Chi-restraints excluded: chain I residue 775 THR Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain I residue 908 VAL Chi-restraints excluded: chain I residue 915 LYS Chi-restraints excluded: chain I residue 960 ILE Chi-restraints excluded: chain I residue 1019 LYS Chi-restraints excluded: chain I residue 1022 LYS Chi-restraints excluded: chain I residue 1161 VAL Chi-restraints excluded: chain I residue 1173 LEU Chi-restraints excluded: chain I residue 1199 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 1027 ARG Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1419 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 112 optimal weight: 5.9990 chunk 296 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 438 optimal weight: 0.8980 chunk 162 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 219 optimal weight: 8.9990 chunk 206 optimal weight: 4.9990 chunk 393 optimal weight: 4.9990 chunk 417 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 ASN ** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN ** B1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1227 ASN C 106 ASN C 345 GLN ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 368 GLN ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 ASN A 228 ASN A 532 GLN A 744 ASN A1393 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.139070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.103654 restraints weight = 48096.015| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.73 r_work: 0.3210 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 39129 Z= 0.304 Angle : 0.685 13.292 52954 Z= 0.357 Chirality : 0.050 0.232 5979 Planarity : 0.005 0.058 6804 Dihedral : 6.458 84.521 5258 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.35 % Favored : 94.14 % Rotamer: Outliers : 3.98 % Allowed : 24.88 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.12), residues: 4746 helix: 0.91 (0.12), residues: 1891 sheet: -0.50 (0.20), residues: 607 loop : -0.47 (0.14), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 92 TYR 0.028 0.002 TYR D 28 PHE 0.023 0.002 PHE A 487 TRP 0.018 0.002 TRP B 200 HIS 0.014 0.002 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00711 (39099) covalent geometry : angle 0.67525 (52914) SS BOND : bond 0.00583 ( 2) SS BOND : angle 3.51546 ( 4) hydrogen bonds : bond 0.04847 ( 1701) hydrogen bonds : angle 5.17098 ( 4698) metal coordination : bond 0.01747 ( 28) metal coordination : angle 4.38612 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 4268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 447 time to evaluate : 1.741 Fit side-chains revert: symmetry clash REVERT: B 40 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7649 (pp) REVERT: B 90 ASN cc_start: 0.8441 (p0) cc_final: 0.8237 (p0) REVERT: B 321 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7836 (tt0) REVERT: B 334 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.7870 (tm-30) REVERT: B 630 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7686 (tm-30) REVERT: B 731 ASP cc_start: 0.7751 (m-30) cc_final: 0.7496 (m-30) REVERT: B 972 HIS cc_start: 0.6306 (OUTLIER) cc_final: 0.5694 (p90) REVERT: B 1179 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8939 (mp) REVERT: C 27 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8239 (tptm) REVERT: C 121 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: D 1 MET cc_start: 0.6099 (OUTLIER) cc_final: 0.5763 (tpt) REVERT: D 46 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6597 (tp30) REVERT: D 54 SER cc_start: 0.8957 (m) cc_final: 0.8661 (t) REVERT: D 109 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7940 (mp10) REVERT: D 189 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: F 146 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7183 (mp10) REVERT: F 195 LYS cc_start: 0.5250 (OUTLIER) cc_final: 0.5034 (mmtt) REVERT: F 231 MET cc_start: 0.5870 (tpt) cc_final: 0.4946 (mtt) REVERT: F 234 LEU cc_start: 0.4548 (OUTLIER) cc_final: 0.3982 (mp) REVERT: F 278 PHE cc_start: 0.7206 (OUTLIER) cc_final: 0.6651 (m-80) REVERT: F 290 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7465 (tm-30) REVERT: G 23 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7076 (mmp80) REVERT: I 95 LYS cc_start: 0.5005 (OUTLIER) cc_final: 0.4341 (ptmm) REVERT: I 303 PHE cc_start: 0.5931 (OUTLIER) cc_final: 0.4362 (p90) REVERT: I 311 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6696 (tt0) REVERT: I 319 GLN cc_start: 0.7015 (mm-40) cc_final: 0.6786 (mm110) REVERT: I 326 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6253 (mp0) REVERT: I 357 GLU cc_start: 0.6650 (pt0) cc_final: 0.5781 (pp20) REVERT: I 365 SER cc_start: 0.8100 (m) cc_final: 0.7582 (t) REVERT: I 369 GLU cc_start: 0.6168 (OUTLIER) cc_final: 0.5498 (mp0) REVERT: I 491 ILE cc_start: 0.6459 (OUTLIER) cc_final: 0.6046 (tp) REVERT: I 798 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7555 (mt-10) REVERT: I 915 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7162 (tmtm) REVERT: I 960 ILE cc_start: 0.5939 (OUTLIER) cc_final: 0.5494 (mp) REVERT: I 986 MET cc_start: 0.5330 (OUTLIER) cc_final: 0.3430 (ptt) REVERT: I 1019 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7529 (mmpt) REVERT: I 1022 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7077 (mttm) REVERT: I 1097 GLU cc_start: 0.7425 (tp30) cc_final: 0.7205 (tp30) REVERT: E 97 LYS cc_start: 0.7927 (ttmp) cc_final: 0.7623 (ttmt) REVERT: A 171 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8346 (ttt180) REVERT: A 276 SER cc_start: 0.8501 (OUTLIER) cc_final: 0.8269 (t) REVERT: A 551 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.7998 (p0) REVERT: A 752 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.8959 (mp) REVERT: A 900 ARG cc_start: 0.8385 (tpt170) cc_final: 0.7888 (tpt170) REVERT: A 1027 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8745 (ttp80) REVERT: A 1306 ASP cc_start: 0.7440 (t0) cc_final: 0.7045 (t0) outliers start: 170 outliers final: 91 residues processed: 576 average time/residue: 0.8002 time to fit residues: 559.3276 Evaluate side-chains 563 residues out of total 4268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 439 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 630 GLU Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 949 LYS Chi-restraints excluded: chain B residue 972 HIS Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1179 ILE Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 109 GLN Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain G residue 23 ARG Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 173 MET Chi-restraints excluded: chain I residue 179 GLU Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 303 PHE Chi-restraints excluded: chain I residue 311 GLU Chi-restraints excluded: chain I residue 326 GLU Chi-restraints excluded: chain I residue 335 PHE Chi-restraints excluded: chain I residue 342 ILE Chi-restraints excluded: chain I residue 345 VAL Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 369 GLU Chi-restraints excluded: chain I residue 423 LEU Chi-restraints excluded: chain I residue 425 SER Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 453 HIS Chi-restraints excluded: chain I residue 491 ILE Chi-restraints excluded: chain I residue 511 ARG Chi-restraints excluded: chain I residue 517 ILE Chi-restraints excluded: chain I residue 707 THR Chi-restraints excluded: chain I residue 775 THR Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain I residue 908 VAL Chi-restraints excluded: chain I residue 915 LYS Chi-restraints excluded: chain I residue 934 GLU Chi-restraints excluded: chain I residue 960 ILE Chi-restraints excluded: chain I residue 986 MET Chi-restraints excluded: chain I residue 1019 LYS Chi-restraints excluded: chain I residue 1022 LYS Chi-restraints excluded: chain I residue 1161 VAL Chi-restraints excluded: chain I residue 1173 LEU Chi-restraints excluded: chain I residue 1199 VAL Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 1027 ARG Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1185 MET Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1419 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 450 optimal weight: 5.9990 chunk 325 optimal weight: 0.0000 chunk 307 optimal weight: 0.9980 chunk 442 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 353 optimal weight: 0.6980 chunk 250 optimal weight: 2.9990 chunk 418 optimal weight: 0.9990 chunk 179 optimal weight: 3.9990 chunk 156 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN B 111 ASN B 528 ASN ** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN ** B1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN I 368 GLN ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 ASN A 228 ASN ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 GLN A1181 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.142908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.107951 restraints weight = 48184.304| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.72 r_work: 0.3279 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 39129 Z= 0.135 Angle : 0.577 14.388 52954 Z= 0.300 Chirality : 0.044 0.210 5979 Planarity : 0.004 0.055 6804 Dihedral : 6.140 83.782 5258 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.70 % Favored : 94.80 % Rotamer: Outliers : 2.95 % Allowed : 25.91 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.12), residues: 4746 helix: 1.11 (0.12), residues: 1895 sheet: -0.53 (0.20), residues: 611 loop : -0.38 (0.14), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 92 TYR 0.018 0.001 TYR I 269 PHE 0.019 0.001 PHE A 918 TRP 0.015 0.001 TRP A 466 HIS 0.010 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00306 (39099) covalent geometry : angle 0.56879 (52914) SS BOND : bond 0.00520 ( 2) SS BOND : angle 2.55734 ( 4) hydrogen bonds : bond 0.03802 ( 1701) hydrogen bonds : angle 4.97278 ( 4698) metal coordination : bond 0.00744 ( 28) metal coordination : angle 3.69075 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 4268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 449 time to evaluate : 1.570 Fit side-chains revert: symmetry clash REVERT: B 40 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7368 (pp) REVERT: B 90 ASN cc_start: 0.8426 (p0) cc_final: 0.8200 (p0) REVERT: B 321 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7768 (tt0) REVERT: B 334 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.7905 (tm-30) REVERT: B 514 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8345 (mt) REVERT: B 630 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7620 (tm-30) REVERT: B 972 HIS cc_start: 0.6142 (OUTLIER) cc_final: 0.5591 (p90) REVERT: C 121 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: C 311 GLN cc_start: 0.8459 (pt0) cc_final: 0.7966 (pm20) REVERT: D 1 MET cc_start: 0.5925 (OUTLIER) cc_final: 0.5503 (tpt) REVERT: D 44 ASN cc_start: 0.8118 (m110) cc_final: 0.7744 (m-40) REVERT: D 54 SER cc_start: 0.8983 (m) cc_final: 0.8644 (t) REVERT: D 168 ASP cc_start: 0.8705 (t70) cc_final: 0.8289 (t70) REVERT: D 189 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: F 146 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7215 (mp10) REVERT: F 187 MET cc_start: 0.6804 (mpp) cc_final: 0.6432 (mtm) REVERT: F 195 LYS cc_start: 0.5320 (OUTLIER) cc_final: 0.5083 (mmtt) REVERT: F 200 ILE cc_start: 0.5343 (OUTLIER) cc_final: 0.4997 (mt) REVERT: F 231 MET cc_start: 0.5808 (tpt) cc_final: 0.4876 (mtt) REVERT: F 234 LEU cc_start: 0.4694 (OUTLIER) cc_final: 0.4207 (mp) REVERT: F 290 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7440 (tm-30) REVERT: G 38 LEU cc_start: 0.7245 (tp) cc_final: 0.6893 (tm) REVERT: G 71 LYS cc_start: 0.8351 (tttm) cc_final: 0.8022 (ttmm) REVERT: I 95 LYS cc_start: 0.4981 (OUTLIER) cc_final: 0.4288 (ptmm) REVERT: I 301 GLN cc_start: 0.7538 (mp10) cc_final: 0.7098 (mm110) REVERT: I 305 GLN cc_start: 0.6797 (pp30) cc_final: 0.6220 (pp30) REVERT: I 311 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6769 (tt0) REVERT: I 326 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6248 (mp0) REVERT: I 357 GLU cc_start: 0.6652 (pt0) cc_final: 0.5753 (pp20) REVERT: I 365 SER cc_start: 0.8036 (m) cc_final: 0.7523 (t) REVERT: I 369 GLU cc_start: 0.6078 (OUTLIER) cc_final: 0.5435 (mp0) REVERT: I 425 SER cc_start: 0.6268 (OUTLIER) cc_final: 0.6020 (m) REVERT: I 491 ILE cc_start: 0.6397 (OUTLIER) cc_final: 0.5950 (tp) REVERT: I 678 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7919 (mm) REVERT: I 798 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7481 (mt-10) REVERT: I 915 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7084 (tmtm) REVERT: I 960 ILE cc_start: 0.5899 (OUTLIER) cc_final: 0.5467 (mp) REVERT: I 986 MET cc_start: 0.5138 (OUTLIER) cc_final: 0.3277 (ptt) REVERT: I 1019 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7505 (mmpt) REVERT: I 1022 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7185 (mttm) REVERT: E 97 LYS cc_start: 0.7886 (ttmp) cc_final: 0.7581 (ttmt) REVERT: A 171 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8274 (ttt180) REVERT: A 551 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.7915 (p0) REVERT: A 752 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8816 (mp) REVERT: A 848 THR cc_start: 0.8812 (p) cc_final: 0.8559 (m) REVERT: A 900 ARG cc_start: 0.8377 (tpt170) cc_final: 0.7858 (tpt170) REVERT: A 946 THR cc_start: 0.6913 (OUTLIER) cc_final: 0.6645 (p) REVERT: A 1027 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8384 (ttp80) REVERT: A 1182 LYS cc_start: 0.5353 (tptt) cc_final: 0.4649 (mtmp) REVERT: A 1253 LYS cc_start: 0.7944 (ttpt) cc_final: 0.7518 (ttmm) REVERT: A 1306 ASP cc_start: 0.7474 (t0) cc_final: 0.7109 (t0) outliers start: 126 outliers final: 74 residues processed: 544 average time/residue: 0.7483 time to fit residues: 492.5638 Evaluate side-chains 539 residues out of total 4268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 435 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 630 GLU Chi-restraints excluded: chain B residue 949 LYS Chi-restraints excluded: chain B residue 972 HIS Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1129 ASP Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain G residue 10 CYS Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 173 MET Chi-restraints excluded: chain I residue 179 GLU Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 311 GLU Chi-restraints excluded: chain I residue 326 GLU Chi-restraints excluded: chain I residue 335 PHE Chi-restraints excluded: chain I residue 345 VAL Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 369 GLU Chi-restraints excluded: chain I residue 425 SER Chi-restraints excluded: chain I residue 453 HIS Chi-restraints excluded: chain I residue 491 ILE Chi-restraints excluded: chain I residue 511 ARG Chi-restraints excluded: chain I residue 517 ILE Chi-restraints excluded: chain I residue 678 LEU Chi-restraints excluded: chain I residue 707 THR Chi-restraints excluded: chain I residue 775 THR Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain I residue 908 VAL Chi-restraints excluded: chain I residue 915 LYS Chi-restraints excluded: chain I residue 960 ILE Chi-restraints excluded: chain I residue 986 MET Chi-restraints excluded: chain I residue 1019 LYS Chi-restraints excluded: chain I residue 1022 LYS Chi-restraints excluded: chain I residue 1161 VAL Chi-restraints excluded: chain I residue 1173 LEU Chi-restraints excluded: chain I residue 1199 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 1027 ARG Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1419 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 327 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 409 optimal weight: 0.7980 chunk 255 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 349 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 342 optimal weight: 1.9990 chunk 413 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN B 528 ASN ** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN ** B1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN C 345 GLN F 273 GLN ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 ASN A 228 ASN ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.143188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.108624 restraints weight = 47602.933| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.65 r_work: 0.3289 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 39129 Z= 0.149 Angle : 0.584 14.311 52954 Z= 0.303 Chirality : 0.044 0.210 5979 Planarity : 0.004 0.054 6804 Dihedral : 6.048 83.910 5258 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.91 % Favored : 94.58 % Rotamer: Outliers : 2.72 % Allowed : 26.24 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.12), residues: 4746 helix: 1.17 (0.12), residues: 1897 sheet: -0.52 (0.20), residues: 614 loop : -0.33 (0.14), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 92 TYR 0.035 0.002 TYR I 973 PHE 0.025 0.001 PHE I 260 TRP 0.014 0.001 TRP A 466 HIS 0.020 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00342 (39099) covalent geometry : angle 0.57570 (52914) SS BOND : bond 0.00525 ( 2) SS BOND : angle 2.38878 ( 4) hydrogen bonds : bond 0.03825 ( 1701) hydrogen bonds : angle 4.93205 ( 4698) metal coordination : bond 0.00856 ( 28) metal coordination : angle 3.71121 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 4268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 440 time to evaluate : 1.404 Fit side-chains revert: symmetry clash REVERT: B 40 ILE cc_start: 0.7676 (OUTLIER) cc_final: 0.7300 (pp) REVERT: B 90 ASN cc_start: 0.8447 (p0) cc_final: 0.8233 (p0) REVERT: B 321 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: B 334 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7909 (tm-30) REVERT: B 514 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8402 (mt) REVERT: B 630 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7631 (tm-30) REVERT: B 972 HIS cc_start: 0.6166 (OUTLIER) cc_final: 0.5630 (p90) REVERT: C 121 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: D 1 MET cc_start: 0.5968 (OUTLIER) cc_final: 0.5490 (tpt) REVERT: D 44 ASN cc_start: 0.8117 (m110) cc_final: 0.7769 (m-40) REVERT: D 54 SER cc_start: 0.8980 (m) cc_final: 0.8644 (t) REVERT: D 168 ASP cc_start: 0.8704 (t70) cc_final: 0.8302 (t70) REVERT: D 189 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: F 146 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7221 (mp10) REVERT: F 195 LYS cc_start: 0.5343 (OUTLIER) cc_final: 0.5096 (mmtt) REVERT: F 200 ILE cc_start: 0.5414 (OUTLIER) cc_final: 0.5141 (mt) REVERT: F 231 MET cc_start: 0.5750 (tpt) cc_final: 0.4846 (mtt) REVERT: F 290 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7432 (tm-30) REVERT: G 38 LEU cc_start: 0.7222 (tp) cc_final: 0.6866 (tm) REVERT: G 71 LYS cc_start: 0.8369 (tttm) cc_final: 0.8050 (ttmm) REVERT: I 95 LYS cc_start: 0.4958 (OUTLIER) cc_final: 0.4262 (ptmm) REVERT: I 301 GLN cc_start: 0.7533 (mp10) cc_final: 0.7092 (mm110) REVERT: I 305 GLN cc_start: 0.6795 (pp30) cc_final: 0.6232 (pp30) REVERT: I 311 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6768 (tt0) REVERT: I 326 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6301 (mp0) REVERT: I 352 GLU cc_start: 0.6907 (tm-30) cc_final: 0.6661 (pp20) REVERT: I 357 GLU cc_start: 0.6653 (pt0) cc_final: 0.5778 (pp20) REVERT: I 365 SER cc_start: 0.8064 (m) cc_final: 0.7531 (t) REVERT: I 369 GLU cc_start: 0.6135 (OUTLIER) cc_final: 0.5502 (mp0) REVERT: I 425 SER cc_start: 0.6332 (OUTLIER) cc_final: 0.6098 (m) REVERT: I 491 ILE cc_start: 0.6426 (OUTLIER) cc_final: 0.5965 (tp) REVERT: I 678 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7855 (mm) REVERT: I 798 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7503 (mt-10) REVERT: I 915 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7100 (tmtm) REVERT: I 960 ILE cc_start: 0.5919 (OUTLIER) cc_final: 0.5403 (mp) REVERT: I 986 MET cc_start: 0.5160 (OUTLIER) cc_final: 0.3274 (ptt) REVERT: I 1019 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7564 (mmpt) REVERT: I 1022 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7226 (mttm) REVERT: E 97 LYS cc_start: 0.7863 (ttmp) cc_final: 0.7462 (ttmt) REVERT: A 171 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8286 (ttt180) REVERT: A 752 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8869 (mp) REVERT: A 848 THR cc_start: 0.8797 (p) cc_final: 0.8563 (m) REVERT: A 900 ARG cc_start: 0.8392 (tpt170) cc_final: 0.7856 (tpt170) REVERT: A 946 THR cc_start: 0.6914 (OUTLIER) cc_final: 0.6651 (p) REVERT: A 1027 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8403 (ttp80) REVERT: A 1253 LYS cc_start: 0.8001 (ttpt) cc_final: 0.7582 (ttmm) REVERT: A 1306 ASP cc_start: 0.7417 (t0) cc_final: 0.7085 (t0) outliers start: 116 outliers final: 72 residues processed: 534 average time/residue: 0.6878 time to fit residues: 447.3240 Evaluate side-chains 527 residues out of total 4268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 427 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 630 GLU Chi-restraints excluded: chain B residue 949 LYS Chi-restraints excluded: chain B residue 972 HIS Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1129 ASP Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 173 MET Chi-restraints excluded: chain I residue 179 GLU Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 311 GLU Chi-restraints excluded: chain I residue 326 GLU Chi-restraints excluded: chain I residue 335 PHE Chi-restraints excluded: chain I residue 345 VAL Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 369 GLU Chi-restraints excluded: chain I residue 425 SER Chi-restraints excluded: chain I residue 453 HIS Chi-restraints excluded: chain I residue 491 ILE Chi-restraints excluded: chain I residue 511 ARG Chi-restraints excluded: chain I residue 517 ILE Chi-restraints excluded: chain I residue 678 LEU Chi-restraints excluded: chain I residue 707 THR Chi-restraints excluded: chain I residue 775 THR Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain I residue 908 VAL Chi-restraints excluded: chain I residue 915 LYS Chi-restraints excluded: chain I residue 934 GLU Chi-restraints excluded: chain I residue 960 ILE Chi-restraints excluded: chain I residue 986 MET Chi-restraints excluded: chain I residue 1019 LYS Chi-restraints excluded: chain I residue 1022 LYS Chi-restraints excluded: chain I residue 1161 VAL Chi-restraints excluded: chain I residue 1173 LEU Chi-restraints excluded: chain I residue 1199 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 1027 ARG Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1419 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 121 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 430 optimal weight: 0.7980 chunk 157 optimal weight: 6.9990 chunk 289 optimal weight: 3.9990 chunk 434 optimal weight: 0.8980 chunk 301 optimal weight: 0.6980 chunk 326 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 ASN ** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN C 345 GLN G 36 ASN ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 ASN A 228 ASN A 532 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.141575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.106260 restraints weight = 47833.672| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.70 r_work: 0.3260 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 39129 Z= 0.207 Angle : 0.627 13.819 52954 Z= 0.326 Chirality : 0.046 0.215 5979 Planarity : 0.005 0.055 6804 Dihedral : 6.188 84.573 5257 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.14 % Favored : 94.35 % Rotamer: Outliers : 2.91 % Allowed : 26.22 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.12), residues: 4746 helix: 1.06 (0.12), residues: 1896 sheet: -0.49 (0.20), residues: 604 loop : -0.39 (0.14), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 92 TYR 0.027 0.002 TYR D 28 PHE 0.020 0.002 PHE F 44 TRP 0.012 0.002 TRP B 200 HIS 0.014 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00484 (39099) covalent geometry : angle 0.61877 (52914) SS BOND : bond 0.00550 ( 2) SS BOND : angle 2.70673 ( 4) hydrogen bonds : bond 0.04246 ( 1701) hydrogen bonds : angle 5.03162 ( 4698) metal coordination : bond 0.01214 ( 28) metal coordination : angle 3.95238 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18301.57 seconds wall clock time: 311 minutes 45.57 seconds (18705.57 seconds total)