Starting phenix.real_space_refine on Mon May 26 17:48:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xx4_38745/05_2025/8xx4_38745.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xx4_38745/05_2025/8xx4_38745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xx4_38745/05_2025/8xx4_38745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xx4_38745/05_2025/8xx4_38745.map" model { file = "/net/cci-nas-00/data/ceres_data/8xx4_38745/05_2025/8xx4_38745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xx4_38745/05_2025/8xx4_38745.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 43 5.49 5 Mg 1 5.21 5 S 164 5.16 5 C 18116 2.51 5 N 4951 2.21 5 O 5404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 28685 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 11091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1391, 11091 Classifications: {'peptide': 1391} Link IDs: {'PCIS': 2, 'PTRANS': 63, 'TRANS': 1325} Chain breaks: 6 Chain: "B" Number of atoms: 9255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1171, 9255 Classifications: {'peptide': 1171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1118} Chain breaks: 7 Chain: "C" Number of atoms: 2907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2907 Classifications: {'peptide': 358} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 338} 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: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "G" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 800 Classifications: {'peptide': 103} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 98} Chain: "H" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 569 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain breaks: 1 Chain: "P" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 190 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna3p': 8} Chain: "T" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 472 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "E" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 854 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "N" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 227 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} 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} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 450 SG CYS A 59 99.369 106.912 66.614 1.00 78.19 S ATOM 471 SG CYS A 62 96.703 109.169 67.898 1.00 61.50 S ATOM 531 SG CYS A 69 96.432 105.309 68.125 1.00 71.28 S ATOM 775 SG CYS A 99 92.498 93.060 22.447 1.00107.11 S ATOM 797 SG CYS A 102 92.503 96.792 21.594 1.00103.81 S ATOM 1049 SG CYS A 134 90.243 94.405 19.686 1.00110.87 S ATOM 1074 SG CYS A 137 94.119 94.251 19.360 1.00121.37 S ATOM 19865 SG CYS B1180 88.986 116.268 55.930 1.00 74.91 S ATOM 19890 SG CYS B1183 89.223 113.197 53.875 1.00 65.71 S ATOM 20006 SG CYS B1198 92.258 114.793 55.441 1.00 68.56 S ATOM 20028 SG CYS B1201 90.439 116.604 52.425 1.00 71.93 S ATOM 25597 SG CYS G 4 77.478 36.205 22.341 1.00126.71 S ATOM 25617 SG CYS G 7 80.086 37.735 24.507 1.00128.67 S ATOM 25751 SG CYS G 24 77.542 40.038 22.845 1.00126.50 S ATOM 25763 SG CYS G 26 80.143 38.331 20.703 1.00131.63 S ATOM 26133 SG CYS G 73 47.257 22.657 61.356 1.00 83.87 S ATOM 26154 SG CYS G 76 49.625 20.158 63.630 1.00 90.80 S ATOM 26311 SG CYS G 96 50.524 23.676 62.779 1.00 88.93 S ATOM 26328 SG CYS G 98 50.339 21.198 59.988 1.00 84.61 S ATOM 26417 SG CYS H 7 64.883 66.419 114.441 1.00 56.44 S ATOM 26441 SG CYS H 10 62.788 68.052 117.164 1.00 53.01 S ATOM 26798 SG CYS H 65 61.169 65.947 114.391 1.00 41.60 S ATOM 26804 SG CYS H 66 63.118 64.469 117.371 1.00 54.69 S Time building chain proxies: 16.84, per 1000 atoms: 0.59 Number of scatterers: 28685 At special positions: 0 Unit cell: (138.58, 147.6, 151.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 164 16.00 P 43 15.00 Mg 1 11.99 O 5404 8.00 N 4951 7.00 C 18116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 7.49 Conformation dependent library (CDL) restraints added in 3.6 seconds 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 99 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 102 " 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 4 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 7 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 26 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 24 " pdb=" ZN G 202 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 96 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 98 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 73 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 76 " pdb=" ZN H 101 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 10 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 7 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 66 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 65 " Number of angles added : 33 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6586 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 43 sheets defined 41.7% alpha, 17.1% beta 18 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 10.52 Creating SS restraints... 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 126 removed outlier: 4.296A pdb=" N LEU A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'A' and resid 188 through 195 removed outlier: 3.550A 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 238 Processing helix chain 'A' and resid 253 through 273 removed outlier: 3.680A pdb=" N ASP A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 303 removed outlier: 3.562A pdb=" N ARG A 302 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 303 " --> pdb=" O MET A 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 299 through 303' 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 450 through 455 removed outlier: 4.170A 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 Processing helix chain 'A' and resid 501 through 512 Processing helix chain 'A' and resid 524 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: 3.979A pdb=" N ASN A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 657 removed outlier: 3.507A pdb=" N LEU A 657 " --> pdb=" O ALA A 654 " (cutoff:3.500A) 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: 3.919A 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: 3.861A pdb=" N THR A 819 " --> pdb=" O LYS A 815 " (cutoff:3.500A) removed outlier: 4.363A 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 876 through 885 Processing helix chain 'A' and resid 891 through 918 removed outlier: 3.782A pdb=" N GLU A 895 " --> pdb=" O SER A 891 " (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 Processing helix chain 'A' and resid 995 through 1006 Processing helix chain 'A' and resid 1015 through 1032 Processing helix chain 'A' and resid 1040 through 1059 Proline residue: A1052 - end of helix removed outlier: 3.923A 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 1118 Processing helix chain 'A' and resid 1151 through 1162 Processing helix chain 'A' and resid 1181 through 1188 Processing helix chain 'A' and resid 1191 through 1203 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: 3.755A pdb=" N THR A1313 " --> pdb=" O ASP A1310 " (cutoff:3.500A) removed outlier: 4.075A 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 1327 Processing helix chain 'A' and resid 1327 through 1344 Processing helix chain 'A' and resid 1349 through 1361 removed outlier: 3.878A 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 helix chain 'B' and resid 22 through 38 removed outlier: 3.670A pdb=" N MET B 26 " --> pdb=" O THR B 22 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU B 27 " --> pdb=" O GLU B 23 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 61 removed outlier: 3.718A pdb=" N ILE B 44 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE B 55 " --> pdb=" O MET B 51 " (cutoff:3.500A) Proline residue: B 56 - end of helix Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 175 through 182 removed outlier: 3.519A pdb=" N ILE B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 279 removed outlier: 3.565A pdb=" N PHE B 279 " --> pdb=" O ILE B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 293 removed outlier: 3.674A pdb=" N VAL B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 314 removed outlier: 4.448A pdb=" N ASN B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 340 removed outlier: 3.875A pdb=" N ILE B 332 " --> pdb=" O ASN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 370 removed outlier: 3.589A pdb=" N ASP B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 370 " --> pdb=" O THR B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 377 Processing helix chain 'B' and resid 383 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: 3.504A pdb=" N THR B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 458 through 471 removed outlier: 3.725A pdb=" N ILE B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 470 " --> pdb=" O PHE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 487 Processing helix chain 'B' and resid 513 through 521 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.528A pdb=" N ASP B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 592 Processing helix chain 'B' and resid 603 through 610 removed outlier: 3.595A pdb=" N VAL B 608 " --> pdb=" O ASN B 604 " (cutoff:3.500A) 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: 3.690A 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 Processing helix chain 'B' and resid 782 through 786 removed outlier: 3.526A pdb=" N SER B 786 " --> pdb=" O ALA B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 792 Processing helix chain 'B' and resid 793 through 804 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 1030 through 1033 Processing helix chain 'B' and resid 1038 through 1055 removed outlier: 3.704A pdb=" N MET B1042 " --> pdb=" O THR B1038 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B1050 " --> pdb=" O THR B1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1078 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 1169 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: 3.568A pdb=" N PHE C 99 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 130 No H-bonds generated for 'chain 'C' and resid 128 through 130' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 230 through 259 removed outlier: 3.672A pdb=" N ILE C 253 " --> pdb=" O ARG C 249 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 302 Processing helix chain 'C' and resid 328 through 359 Processing helix chain 'D' and resid 2 through 17 removed outlier: 4.484A pdb=" N TYR D 11 " --> pdb=" O PHE D 7 " (cutoff:3.500A) removed outlier: 4.351A 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: 3.698A pdb=" N VAL D 65 " --> pdb=" O GLY D 62 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS D 66 " --> pdb=" O LYS D 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 66' Processing helix chain 'D' and resid 67 through 79 Processing helix chain 'D' and resid 93 through 98 Processing helix chain 'D' and resid 99 through 113 Processing helix chain 'D' and resid 122 through 126 removed outlier: 3.522A 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 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 35 Processing helix chain 'G' and resid 33 through 36 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 removed outlier: 3.546A pdb=" N THR H 16 " --> pdb=" O PRO H 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 13 through 16' Processing helix chain 'H' and resid 17 through 33 Processing helix chain 'H' and resid 51 through 59 Processing helix chain 'H' and resid 63 through 73 removed outlier: 3.609A pdb=" N THR H 73 " --> pdb=" O HIS H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 80 removed outlier: 3.582A pdb=" N TYR H 79 " --> pdb=" O ASP H 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 61 through 65 Processing helix chain 'E' and resid 72 through 90 Processing helix chain 'E' and resid 101 through 112 Processing helix chain 'E' and resid 137 through 141 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 removed outlier: 6.327A pdb=" N GLY A 4 " --> pdb=" O MET B1209 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASP B1211 " --> pdb=" O GLY A 4 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ALA A 6 " --> pdb=" O ASP B1211 " (cutoff:3.500A) removed outlier: 11.050A pdb=" N ARG B1213 " --> pdb=" O ALA A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1404 through 1406 Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA4, first strand: chain 'A' and resid 74 through 83 removed outlier: 6.220A pdb=" N LYS A 199 " --> pdb=" O MET A 78 " (cutoff:3.500A) removed outlier: 10.717A pdb=" N ALA A 80 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 10.167A pdb=" N VAL A 197 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 146 removed outlier: 4.395A pdb=" N PHE A 154 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 317 through 318 Processing sheet with id=AA7, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 7.363A pdb=" N PHE A 444 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR A 326 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N MET A 446 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N CYS A 328 " --> pdb=" O MET A 446 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 349 through 353 removed outlier: 3.856A pdb=" N ARG A 378 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ASP A 408 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N CYS A 376 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER A 386 " --> pdb=" O LYS A 381 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 514 through 515 Processing sheet with id=AB1, first strand: chain 'A' and resid 521 through 523 Processing sheet with id=AB2, first strand: chain 'A' and resid 567 through 569 removed outlier: 3.613A pdb=" N GLU A 600 " --> pdb=" O GLN A 592 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ARG A 594 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 753 through 754 Processing sheet with id=AB4, first strand: chain 'A' and resid 836 through 838 removed outlier: 6.425A pdb=" N VAL A 844 " --> pdb=" O VAL A 851 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 866 through 869 Processing sheet with id=AB6, first strand: chain 'A' and resid 1268 through 1278 removed outlier: 6.505A pdb=" N ARG A1275 " --> pdb=" O ASP A1288 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASP A1288 " --> pdb=" O ARG A1275 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ARG A1277 " --> pdb=" O ARG A1286 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ARG A1286 " --> pdb=" O ARG A1277 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A1094 " --> pdb=" O THR A1295 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB8, first strand: chain 'A' and resid 1206 through 1210 removed outlier: 6.367A pdb=" N CYS A1175 " --> pdb=" O LEU A1131 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU A1131 " --> pdb=" O CYS A1175 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG A1177 " --> pdb=" O TRP A1129 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TRP A1129 " --> pdb=" O ARG A1177 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLU A1179 " --> pdb=" O LEU A1127 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1428 through 1431 removed outlier: 6.850A pdb=" N ILE E 132 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL E 125 " --> pdb=" O GLN E 130 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN E 130 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE B1239 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ILE E 59 " --> pdb=" O PHE B1239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 65 through 69 removed outlier: 3.675A pdb=" N VAL B 65 " --> pdb=" O PHE B 89 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA B 131 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL B 94 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASN B 129 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE B 96 " --> pdb=" O PRO B 127 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 65 through 69 removed outlier: 3.675A pdb=" N VAL B 65 " --> pdb=" O PHE B 89 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA B 131 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL B 94 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASN B 129 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE B 96 " --> pdb=" O PRO B 127 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 158 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU B 130 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLN B 156 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AC4, first strand: chain 'B' and resid 193 through 195 Processing sheet with id=AC5, first strand: chain 'B' and resid 416 through 420 removed outlier: 3.738A pdb=" N LEU B 204 " --> pdb=" O THR B 523 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 213 through 216 Processing sheet with id=AC7, first strand: chain 'B' and resid 492 through 495 Processing sheet with id=AC8, first strand: chain 'B' and resid 576 through 577 Processing sheet with id=AC9, first strand: chain 'B' and resid 710 through 712 removed outlier: 3.511A pdb=" N LEU B 674 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 596 through 598 removed outlier: 6.796A pdb=" N VAL B 615 " --> pdb=" O ILE B 622 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N CYS B 624 " --> pdb=" O ALA B 613 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ALA B 613 " --> pdb=" O CYS B 624 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 823 through 826 removed outlier: 6.047A pdb=" N ARG B 985 " --> pdb=" O VAL B 965 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N VAL B 965 " --> pdb=" O ARG B 985 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N GLU B 987 " --> pdb=" O ALA B 963 " (cutoff:3.500A) removed outlier: 9.178A pdb=" N ALA B 963 " --> pdb=" O GLU B 987 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 834 through 835 Processing sheet with id=AD4, first strand: chain 'B' and resid 1085 through 1086 removed outlier: 6.011A pdb=" N VAL B 865 " --> pdb=" O ALA B1006 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B1008 " --> pdb=" O VAL B 865 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE B1102 " --> pdb=" O TYR B 853 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 895 through 896 Processing sheet with id=AD6, first strand: chain 'B' and resid 932 through 933 removed outlier: 3.723A pdb=" N VAL B 955 " --> pdb=" O ILE B 933 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1017 through 1018 Processing sheet with id=AD8, first strand: chain 'B' and resid 1188 through 1190 Processing sheet with id=AD9, first strand: chain 'C' and resid 5 through 12 removed outlier: 4.327A pdb=" N ASN C 7 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL C 39 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA C 225 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N CYS C 222 " --> pdb=" O LYS C 181 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LYS C 181 " --> pdb=" O CYS C 222 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 68 through 73 removed outlier: 4.813A pdb=" N ILE C 159 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N SER C 115 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLU C 161 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU C 113 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL C 110 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 123 through 126 Processing sheet with id=AE3, first strand: chain 'C' and resid 267 through 269 Processing sheet with id=AE4, first strand: chain 'D' and resid 20 through 21 removed outlier: 6.293A pdb=" N ILE D 52 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ILE D 89 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N SER D 54 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE D 91 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE D 56 " --> pdb=" O ILE D 91 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 138 through 142 removed outlier: 3.863A pdb=" N LYS D 138 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE D 181 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N MET D 162 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N THR D 201 " --> pdb=" O MET D 162 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE D 164 " --> pdb=" O THR D 201 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 3 through 10 removed outlier: 6.057A pdb=" N SER F 75 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N VAL F 51 " --> pdb=" O SER F 75 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL F 77 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR F 49 " --> pdb=" O VAL F 77 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 67 through 69 removed outlier: 4.207A pdb=" N CYS G 67 " --> pdb=" O GLN G 83 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU G 94 " --> pdb=" O SER G 102 " (cutoff:3.500A) 1219 hydrogen bonds defined for protein. 3336 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 14.84 Time building geometry restraints manager: 8.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9104 1.34 - 1.46: 5513 1.46 - 1.58: 14353 1.58 - 1.70: 85 1.70 - 1.82: 269 Bond restraints: 29324 Sorted by residual: bond pdb=" CB PRO B 12 " pdb=" CG PRO B 12 " ideal model delta sigma weight residual 1.492 1.616 -0.124 5.00e-02 4.00e+02 6.17e+00 bond pdb=" C ARG A 419 " pdb=" N GLN A 420 " ideal model delta sigma weight residual 1.331 1.292 0.039 2.07e-02 2.33e+03 3.54e+00 bond pdb=" CB PRO B 440 " pdb=" CG PRO B 440 " ideal model delta sigma weight residual 1.492 1.585 -0.093 5.00e-02 4.00e+02 3.44e+00 bond pdb=" CG PRO B 12 " pdb=" CD PRO B 12 " ideal model delta sigma weight residual 1.503 1.563 -0.060 3.40e-02 8.65e+02 3.12e+00 bond pdb=" CB GLU A 476 " pdb=" CG GLU A 476 " ideal model delta sigma weight residual 1.520 1.469 0.051 3.00e-02 1.11e+03 2.91e+00 ... (remaining 29319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 39504 2.62 - 5.23: 332 5.23 - 7.85: 17 7.85 - 10.46: 8 10.46 - 13.08: 3 Bond angle restraints: 39864 Sorted by residual: angle pdb=" CA PRO B 440 " pdb=" N PRO B 440 " pdb=" CD PRO B 440 " ideal model delta sigma weight residual 112.00 101.47 10.53 1.40e+00 5.10e-01 5.66e+01 angle pdb=" CA PRO B 12 " pdb=" N PRO B 12 " pdb=" CD PRO B 12 " ideal model delta sigma weight residual 112.00 103.85 8.15 1.40e+00 5.10e-01 3.39e+01 angle pdb=" N ILE A1074 " pdb=" CA ILE A1074 " pdb=" C ILE A1074 " ideal model delta sigma weight residual 112.17 107.00 5.17 9.50e-01 1.11e+00 2.96e+01 angle pdb=" C SER B 488 " pdb=" CA SER B 488 " pdb=" CB SER B 488 " ideal model delta sigma weight residual 117.23 110.11 7.12 1.36e+00 5.41e-01 2.74e+01 angle pdb=" CA SER B 488 " pdb=" C SER B 488 " pdb=" N GLY B 489 " ideal model delta sigma weight residual 119.98 116.63 3.35 8.50e-01 1.38e+00 1.55e+01 ... (remaining 39859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.68: 14943 18.68 - 37.36: 1986 37.36 - 56.04: 632 56.04 - 74.71: 143 74.71 - 93.39: 43 Dihedral angle restraints: 17747 sinusoidal: 7564 harmonic: 10183 Sorted by residual: dihedral pdb=" CA ARG A1228 " pdb=" C ARG A1228 " pdb=" N GLU A1229 " pdb=" CA GLU A1229 " ideal model delta harmonic sigma weight residual 180.00 155.41 24.59 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA THR B1163 " pdb=" C THR B1163 " pdb=" N ILE B1164 " pdb=" CA ILE B1164 " ideal model delta harmonic sigma weight residual 180.00 158.53 21.47 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA THR B 904 " pdb=" C THR B 904 " pdb=" N LYS B 905 " pdb=" CA LYS B 905 " ideal model delta harmonic sigma weight residual 180.00 159.40 20.60 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 17744 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 3078 0.041 - 0.082: 1057 0.082 - 0.123: 353 0.123 - 0.164: 46 0.164 - 0.204: 2 Chirality restraints: 4536 Sorted by residual: chirality pdb=" CB VAL A1103 " pdb=" CA VAL A1103 " pdb=" CG1 VAL A1103 " pdb=" CG2 VAL A1103 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA PRO B 12 " pdb=" N PRO B 12 " pdb=" C PRO B 12 " pdb=" CB PRO B 12 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.83e-01 chirality pdb=" CA TYR F 69 " pdb=" N TYR F 69 " pdb=" C TYR F 69 " pdb=" CB TYR F 69 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.52e-01 ... (remaining 4533 not shown) Planarity restraints: 4975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 439 " 0.091 5.00e-02 4.00e+02 1.30e-01 2.71e+01 pdb=" N PRO B 440 " -0.225 5.00e-02 4.00e+02 pdb=" CA PRO B 440 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO B 440 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1100 " -0.074 5.00e-02 4.00e+02 1.11e-01 1.98e+01 pdb=" N PRO A1101 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO A1101 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A1101 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 235 " -0.071 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO B 236 " 0.183 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.056 5.00e-02 4.00e+02 ... (remaining 4972 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 202 2.50 - 3.10: 20383 3.10 - 3.70: 46364 3.70 - 4.30: 71473 4.30 - 4.90: 116191 Nonbonded interactions: 254613 Sorted by model distance: nonbonded pdb=" OD1 ASP A 459 " pdb="MG MG A1503 " model vdw 1.899 2.170 nonbonded pdb=" O3' A P 30 " pdb="MG MG A1503 " model vdw 1.949 2.170 nonbonded pdb=" OD1 ASP A 461 " pdb="MG MG A1503 " model vdw 1.983 2.170 nonbonded pdb=" OD1 ASP A 457 " pdb="MG MG A1503 " model vdw 2.004 2.170 nonbonded pdb=" OG1 THR G 14 " pdb=" O ILE G 21 " model vdw 2.110 3.040 ... (remaining 254608 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: 5.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.350 Check model and map are aligned: 0.240 Set scattering table: 0.310 Process input model: 80.360 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.110 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: 0.020 Load rotamer database and sin/cos tables:11.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 29348 Z= 0.224 Angle : 0.627 13.777 39897 Z= 0.328 Chirality : 0.046 0.204 4536 Planarity : 0.005 0.130 4975 Dihedral : 19.163 93.392 11161 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.94 % Favored : 94.77 % Rotamer: Outliers : 2.39 % Allowed : 27.69 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.14), residues: 3444 helix: 0.76 (0.14), residues: 1287 sheet: -0.43 (0.23), residues: 503 loop : -0.41 (0.16), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 466 HIS 0.005 0.001 HIS A1203 PHE 0.027 0.002 PHE B 304 TYR 0.021 0.002 TYR F 69 ARG 0.011 0.000 ARG A1228 Details of bonding type rmsd hydrogen bonds : bond 0.16219 ( 1256) hydrogen bonds : angle 6.81554 ( 3430) metal coordination : bond 0.00834 ( 24) metal coordination : angle 4.38373 ( 33) covalent geometry : bond 0.00542 (29324) covalent geometry : angle 0.61492 (39864) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 364 time to evaluate : 3.056 Fit side-chains revert: symmetry clash REVERT: A 126 SER cc_start: 0.8285 (t) cc_final: 0.8077 (m) REVERT: A 954 GLU cc_start: 0.7032 (tt0) cc_final: 0.6763 (tm-30) REVERT: A 1179 GLU cc_start: 0.7247 (tt0) cc_final: 0.6684 (mt-10) REVERT: A 1346 LYS cc_start: 0.7607 (tptp) cc_final: 0.7343 (tppt) REVERT: B 721 ASP cc_start: 0.8132 (m-30) cc_final: 0.7805 (m-30) REVERT: D 72 ARG cc_start: 0.7867 (ttp-110) cc_final: 0.7656 (ttp-110) outliers start: 74 outliers final: 67 residues processed: 426 average time/residue: 1.2580 time to fit residues: 636.2514 Evaluate side-chains 425 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 358 time to evaluate : 3.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1160 GLU Chi-restraints excluded: chain A residue 1211 SER Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1262 ILE Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1318 SER Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1402 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 558 SER Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 766 THR Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1198 CYS Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 146 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 294 optimal weight: 4.9990 chunk 264 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 178 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 273 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 166 optimal weight: 0.5980 chunk 203 optimal weight: 7.9990 chunk 316 optimal weight: 0.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 77 GLN ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN A 721 ASN A1100 ASN A1161 ASN B 95 ASN ** B 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 HIS ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 HIS G 36 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.129718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.095386 restraints weight = 35400.569| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.70 r_work: 0.3042 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29348 Z= 0.169 Angle : 0.587 15.207 39897 Z= 0.305 Chirality : 0.045 0.184 4536 Planarity : 0.005 0.074 4975 Dihedral : 11.877 92.628 4357 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.73 % Favored : 95.01 % Rotamer: Outliers : 3.91 % Allowed : 24.62 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.14), residues: 3444 helix: 0.83 (0.14), residues: 1310 sheet: -0.34 (0.23), residues: 496 loop : -0.34 (0.16), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 466 HIS 0.005 0.001 HIS B1033 PHE 0.025 0.001 PHE A 918 TYR 0.020 0.001 TYR F 69 ARG 0.007 0.000 ARG B 417 Details of bonding type rmsd hydrogen bonds : bond 0.04504 ( 1256) hydrogen bonds : angle 5.44132 ( 3430) metal coordination : bond 0.00809 ( 24) metal coordination : angle 4.36147 ( 33) covalent geometry : bond 0.00391 (29324) covalent geometry : angle 0.57326 (39864) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 409 time to evaluate : 3.245 Fit side-chains revert: symmetry clash REVERT: A 65 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7893 (mt0) REVERT: A 185 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7738 (mm) REVERT: A 258 ARG cc_start: 0.6354 (ttm-80) cc_final: 0.6007 (mtp85) REVERT: A 417 PHE cc_start: 0.9483 (OUTLIER) cc_final: 0.9199 (t80) REVERT: A 519 LYS cc_start: 0.8833 (mtpp) cc_final: 0.8418 (tttm) REVERT: A 574 TYR cc_start: 0.8844 (t80) cc_final: 0.8625 (t80) REVERT: A 597 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8256 (mp0) REVERT: A 900 ARG cc_start: 0.7921 (tpt170) cc_final: 0.7707 (tpt170) REVERT: A 954 GLU cc_start: 0.7047 (tt0) cc_final: 0.6814 (tm-30) REVERT: A 1179 GLU cc_start: 0.7722 (tt0) cc_final: 0.7134 (tt0) REVERT: A 1245 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.7102 (tttm) REVERT: B 95 ASN cc_start: 0.7109 (t0) cc_final: 0.6562 (p0) REVERT: B 250 TYR cc_start: 0.8274 (t80) cc_final: 0.7988 (t80) REVERT: B 319 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7627 (pt) REVERT: B 434 ASN cc_start: 0.7635 (m-40) cc_final: 0.7227 (m110) REVERT: B 682 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8254 (mtpm) REVERT: B 721 ASP cc_start: 0.8169 (m-30) cc_final: 0.7758 (m-30) REVERT: B 1088 MET cc_start: 0.9220 (ttm) cc_final: 0.9008 (ttt) REVERT: C 233 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7865 (tt0) REVERT: C 338 LYS cc_start: 0.7950 (ttpt) cc_final: 0.7659 (ttmm) REVERT: D 64 TYR cc_start: 0.8452 (m-80) cc_final: 0.8124 (m-80) REVERT: D 101 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7775 (p0) REVERT: G 89 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7471 (pm20) REVERT: E 64 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8528 (mt-10) outliers start: 121 outliers final: 51 residues processed: 486 average time/residue: 1.3288 time to fit residues: 763.9992 Evaluate side-chains 436 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 374 time to evaluate : 3.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1211 SER Chi-restraints excluded: chain A residue 1245 LYS Chi-restraints excluded: chain A residue 1262 ILE Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1318 SER Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 1046 THR Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 126 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 172 optimal weight: 0.6980 chunk 304 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 187 optimal weight: 0.4980 chunk 319 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 174 optimal weight: 0.7980 chunk 245 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1375 ASN B 57 GLN B 334 GLN B 461 ASN ** B 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 ASN B1039 ASN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.130466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.096210 restraints weight = 35548.267| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.71 r_work: 0.3050 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29348 Z= 0.150 Angle : 0.557 15.204 39897 Z= 0.288 Chirality : 0.044 0.211 4536 Planarity : 0.004 0.064 4975 Dihedral : 11.463 91.724 4308 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.73 % Favored : 95.01 % Rotamer: Outliers : 3.68 % Allowed : 24.65 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.14), residues: 3444 helix: 0.96 (0.14), residues: 1309 sheet: -0.35 (0.23), residues: 490 loop : -0.33 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 466 HIS 0.006 0.001 HIS D 193 PHE 0.025 0.001 PHE A 918 TYR 0.019 0.001 TYR F 69 ARG 0.006 0.000 ARG B 417 Details of bonding type rmsd hydrogen bonds : bond 0.04085 ( 1256) hydrogen bonds : angle 5.23359 ( 3430) metal coordination : bond 0.00743 ( 24) metal coordination : angle 4.22034 ( 33) covalent geometry : bond 0.00347 (29324) covalent geometry : angle 0.54427 (39864) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 397 time to evaluate : 3.318 Fit side-chains REVERT: A 65 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7875 (mt0) REVERT: A 109 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6890 (mp) REVERT: A 185 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7697 (mm) REVERT: A 258 ARG cc_start: 0.6311 (ttm-80) cc_final: 0.6046 (ttt-90) REVERT: A 372 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7535 (tt0) REVERT: A 574 TYR cc_start: 0.8881 (t80) cc_final: 0.8666 (t80) REVERT: A 900 ARG cc_start: 0.7894 (tpt170) cc_final: 0.7605 (tpt170) REVERT: A 954 GLU cc_start: 0.7040 (tt0) cc_final: 0.6812 (tm-30) REVERT: A 1179 GLU cc_start: 0.7712 (tt0) cc_final: 0.7277 (tt0) REVERT: A 1288 ASP cc_start: 0.7860 (m-30) cc_final: 0.7210 (p0) REVERT: B 95 ASN cc_start: 0.7108 (t0) cc_final: 0.6633 (p0) REVERT: B 205 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8253 (tt) REVERT: B 250 TYR cc_start: 0.8277 (t80) cc_final: 0.7964 (t80) REVERT: B 319 ILE cc_start: 0.8187 (mt) cc_final: 0.7637 (pt) REVERT: B 334 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.7011 (mm-40) REVERT: B 434 ASN cc_start: 0.7664 (m-40) cc_final: 0.7281 (m110) REVERT: B 682 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8258 (mtpm) REVERT: B 721 ASP cc_start: 0.8180 (m-30) cc_final: 0.7798 (m-30) REVERT: B 1042 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.7918 (mmm) REVERT: C 233 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: C 338 LYS cc_start: 0.7975 (ttpt) cc_final: 0.7687 (ttmm) REVERT: D 64 TYR cc_start: 0.8514 (m-80) cc_final: 0.8160 (m-80) REVERT: D 101 ASN cc_start: 0.8035 (OUTLIER) cc_final: 0.7726 (p0) REVERT: G 89 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7467 (pm20) REVERT: E 64 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8461 (mt-10) outliers start: 114 outliers final: 53 residues processed: 470 average time/residue: 1.3090 time to fit residues: 730.1482 Evaluate side-chains 441 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 376 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1211 SER Chi-restraints excluded: chain A residue 1262 ILE Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 956 MET Chi-restraints excluded: chain B residue 978 ILE Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1037 MET Chi-restraints excluded: chain B residue 1042 MET Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 126 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 269 optimal weight: 0.0970 chunk 78 optimal weight: 8.9990 chunk 290 optimal weight: 0.5980 chunk 53 optimal weight: 0.1980 chunk 157 optimal weight: 9.9990 chunk 218 optimal weight: 4.9990 chunk 185 optimal weight: 8.9990 chunk 214 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 overall best weight: 1.1580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 33 ASN ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN A1161 ASN A1375 ASN B 18 ASN B 57 GLN ** B 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1134 GLN C 31 GLN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.130833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.096508 restraints weight = 35668.218| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.72 r_work: 0.3057 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29348 Z= 0.144 Angle : 0.546 14.945 39897 Z= 0.282 Chirality : 0.044 0.208 4536 Planarity : 0.004 0.060 4975 Dihedral : 11.257 90.653 4294 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.85 % Favored : 94.92 % Rotamer: Outliers : 3.84 % Allowed : 24.52 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3444 helix: 1.02 (0.14), residues: 1311 sheet: -0.38 (0.23), residues: 492 loop : -0.32 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 466 HIS 0.007 0.001 HIS D 193 PHE 0.024 0.001 PHE A 918 TYR 0.018 0.001 TYR F 69 ARG 0.007 0.000 ARG A1228 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 1256) hydrogen bonds : angle 5.12883 ( 3430) metal coordination : bond 0.00716 ( 24) metal coordination : angle 4.07321 ( 33) covalent geometry : bond 0.00332 (29324) covalent geometry : angle 0.53352 (39864) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 409 time to evaluate : 3.355 Fit side-chains REVERT: A 77 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8113 (mm-40) REVERT: A 109 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6888 (mp) REVERT: A 185 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7663 (mm) REVERT: A 258 ARG cc_start: 0.6289 (ttm-80) cc_final: 0.6032 (ttt-90) REVERT: A 372 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7510 (tt0) REVERT: A 574 TYR cc_start: 0.8866 (t80) cc_final: 0.8651 (t80) REVERT: A 597 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8083 (mp0) REVERT: A 1155 MET cc_start: 0.6711 (mtp) cc_final: 0.6256 (mtm) REVERT: A 1179 GLU cc_start: 0.7758 (tt0) cc_final: 0.7246 (tt0) REVERT: A 1245 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.7179 (tttm) REVERT: A 1288 ASP cc_start: 0.7869 (m-30) cc_final: 0.7160 (p0) REVERT: B 95 ASN cc_start: 0.7092 (t0) cc_final: 0.6653 (p0) REVERT: B 205 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8238 (tt) REVERT: B 250 TYR cc_start: 0.8287 (t80) cc_final: 0.8020 (t80) REVERT: B 278 MET cc_start: 0.8595 (mtp) cc_final: 0.8389 (mtp) REVERT: B 319 ILE cc_start: 0.8201 (mt) cc_final: 0.7651 (pt) REVERT: B 434 ASN cc_start: 0.7648 (m-40) cc_final: 0.7263 (m110) REVERT: B 682 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8258 (mtpm) REVERT: B 721 ASP cc_start: 0.8153 (m-30) cc_final: 0.7785 (m-30) REVERT: B 842 VAL cc_start: 0.9136 (OUTLIER) cc_final: 0.8868 (m) REVERT: B 928 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7716 (ptmt) REVERT: B 1042 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.7928 (mmm) REVERT: C 233 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: C 338 LYS cc_start: 0.8010 (ttpt) cc_final: 0.7724 (ttmm) REVERT: D 64 TYR cc_start: 0.8501 (m-80) cc_final: 0.8083 (m-80) REVERT: D 101 ASN cc_start: 0.8013 (OUTLIER) cc_final: 0.7690 (p0) REVERT: G 89 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7455 (pm20) REVERT: E 64 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8564 (mt-10) outliers start: 119 outliers final: 56 residues processed: 490 average time/residue: 1.2918 time to fit residues: 750.7065 Evaluate side-chains 446 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 376 time to evaluate : 3.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1147 ASP Chi-restraints excluded: chain A residue 1245 LYS Chi-restraints excluded: chain A residue 1262 ILE Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 928 LYS Chi-restraints excluded: chain B residue 956 MET Chi-restraints excluded: chain B residue 978 ILE Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1037 MET Chi-restraints excluded: chain B residue 1042 MET Chi-restraints excluded: chain B residue 1046 THR Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 126 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 128 optimal weight: 5.9990 chunk 198 optimal weight: 5.9990 chunk 282 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 136 optimal weight: 0.2980 chunk 168 optimal weight: 9.9990 chunk 224 optimal weight: 9.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 33 ASN ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN A 264 GLN ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1161 ASN A1375 ASN B 57 GLN B 459 GLN ** B 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.127878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.093423 restraints weight = 35593.533| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.70 r_work: 0.3008 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 29348 Z= 0.270 Angle : 0.631 14.937 39897 Z= 0.324 Chirality : 0.048 0.225 4536 Planarity : 0.005 0.061 4975 Dihedral : 11.325 88.401 4289 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.11 % Favored : 94.66 % Rotamer: Outliers : 4.39 % Allowed : 24.23 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3444 helix: 0.82 (0.14), residues: 1308 sheet: -0.45 (0.23), residues: 495 loop : -0.37 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 466 HIS 0.006 0.001 HIS D 193 PHE 0.026 0.002 PHE A 918 TYR 0.023 0.002 TYR F 69 ARG 0.008 0.001 ARG B 417 Details of bonding type rmsd hydrogen bonds : bond 0.04536 ( 1256) hydrogen bonds : angle 5.30295 ( 3430) metal coordination : bond 0.00877 ( 24) metal coordination : angle 4.31969 ( 33) covalent geometry : bond 0.00650 (29324) covalent geometry : angle 0.61849 (39864) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 384 time to evaluate : 3.515 Fit side-chains revert: symmetry clash REVERT: A 65 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7831 (tt0) REVERT: A 77 GLN cc_start: 0.8434 (mm-40) cc_final: 0.8177 (mm-40) REVERT: A 109 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6914 (mp) REVERT: A 130 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6639 (tp30) REVERT: A 185 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7723 (mm) REVERT: A 225 ASP cc_start: 0.6555 (OUTLIER) cc_final: 0.6295 (t70) REVERT: A 383 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7575 (pp) REVERT: A 1100 ASN cc_start: 0.7719 (t0) cc_final: 0.7498 (t0) REVERT: A 1179 GLU cc_start: 0.7855 (tt0) cc_final: 0.7415 (tt0) REVERT: A 1245 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.7150 (tttm) REVERT: B 95 ASN cc_start: 0.7169 (t0) cc_final: 0.6761 (p0) REVERT: B 122 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8324 (mt) REVERT: B 278 MET cc_start: 0.8644 (mtp) cc_final: 0.8381 (mtp) REVERT: B 319 ILE cc_start: 0.8218 (mt) cc_final: 0.7660 (pt) REVERT: B 434 ASN cc_start: 0.7722 (m-40) cc_final: 0.7348 (m110) REVERT: B 681 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: B 682 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8242 (mtpm) REVERT: B 721 ASP cc_start: 0.8177 (m-30) cc_final: 0.7768 (m-30) REVERT: B 928 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7698 (ptmt) REVERT: C 233 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7882 (tt0) REVERT: C 338 LYS cc_start: 0.8063 (ttpt) cc_final: 0.7776 (ttmm) REVERT: D 101 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7771 (p0) REVERT: D 145 GLU cc_start: 0.7936 (mp0) cc_final: 0.7621 (mp0) REVERT: D 168 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8525 (t70) REVERT: G 54 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7740 (ttpp) REVERT: G 89 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7538 (pm20) REVERT: E 64 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8494 (mt-10) outliers start: 136 outliers final: 62 residues processed: 473 average time/residue: 1.3346 time to fit residues: 749.0181 Evaluate side-chains 456 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 377 time to evaluate : 3.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1147 ASP Chi-restraints excluded: chain A residue 1160 GLU Chi-restraints excluded: chain A residue 1245 LYS Chi-restraints excluded: chain A residue 1262 ILE Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 928 LYS Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain B residue 978 ILE Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1046 THR Chi-restraints excluded: chain B residue 1198 CYS Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 126 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 243 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 237 optimal weight: 0.9980 chunk 332 optimal weight: 0.0270 chunk 86 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 197 optimal weight: 5.9990 chunk 295 optimal weight: 5.9990 chunk 250 optimal weight: 0.7980 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 33 ASN ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN A 264 GLN A1161 ASN B 18 ASN ** B 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.131695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.097549 restraints weight = 35383.808| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.71 r_work: 0.3073 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29348 Z= 0.122 Angle : 0.547 15.528 39897 Z= 0.281 Chirality : 0.044 0.217 4536 Planarity : 0.004 0.059 4975 Dihedral : 11.109 88.436 4289 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.65 % Favored : 95.12 % Rotamer: Outliers : 3.07 % Allowed : 25.82 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.15), residues: 3444 helix: 1.03 (0.14), residues: 1308 sheet: -0.37 (0.23), residues: 501 loop : -0.33 (0.16), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 466 HIS 0.009 0.001 HIS D 193 PHE 0.025 0.001 PHE A 918 TYR 0.016 0.001 TYR F 69 ARG 0.007 0.000 ARG B 609 Details of bonding type rmsd hydrogen bonds : bond 0.03623 ( 1256) hydrogen bonds : angle 5.03273 ( 3430) metal coordination : bond 0.00714 ( 24) metal coordination : angle 3.90633 ( 33) covalent geometry : bond 0.00275 (29324) covalent geometry : angle 0.53540 (39864) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 403 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.8391 (mm-40) cc_final: 0.8170 (mm-40) REVERT: A 109 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6933 (mp) REVERT: A 185 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7675 (mm) REVERT: A 225 ASP cc_start: 0.6307 (OUTLIER) cc_final: 0.6059 (t70) REVERT: A 258 ARG cc_start: 0.6240 (mtm-85) cc_final: 0.6010 (ttt-90) REVERT: A 383 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7510 (pp) REVERT: A 900 ARG cc_start: 0.7812 (tpt170) cc_final: 0.7454 (tpt170) REVERT: A 1179 GLU cc_start: 0.7815 (tt0) cc_final: 0.7359 (tt0) REVERT: B 95 ASN cc_start: 0.7082 (t0) cc_final: 0.6692 (p0) REVERT: B 97 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7768 (mm-30) REVERT: B 122 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8295 (mt) REVERT: B 227 ILE cc_start: 0.8281 (mt) cc_final: 0.8016 (mt) REVERT: B 319 ILE cc_start: 0.8126 (mt) cc_final: 0.7606 (pt) REVERT: B 494 MET cc_start: 0.5350 (tmm) cc_final: 0.4610 (tpt) REVERT: B 682 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8255 (mtpm) REVERT: B 721 ASP cc_start: 0.8161 (m-30) cc_final: 0.7791 (m-30) REVERT: B 842 VAL cc_start: 0.9094 (OUTLIER) cc_final: 0.8853 (m) REVERT: B 928 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7726 (ptmt) REVERT: C 28 LYS cc_start: 0.7478 (pttt) cc_final: 0.6936 (tmtm) REVERT: C 105 LYS cc_start: 0.8381 (mppt) cc_final: 0.8089 (mptt) REVERT: C 233 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7873 (tt0) REVERT: C 338 LYS cc_start: 0.7974 (ttpt) cc_final: 0.7675 (ttmm) REVERT: D 101 ASN cc_start: 0.8096 (OUTLIER) cc_final: 0.7742 (p0) REVERT: G 89 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7452 (pm20) REVERT: E 64 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8553 (mt-10) REVERT: E 100 SER cc_start: 0.9074 (p) cc_final: 0.8692 (t) outliers start: 95 outliers final: 46 residues processed: 466 average time/residue: 1.3150 time to fit residues: 724.3787 Evaluate side-chains 441 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 383 time to evaluate : 3.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1155 MET Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1160 GLU Chi-restraints excluded: chain A residue 1262 ILE Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 928 LYS Chi-restraints excluded: chain B residue 978 ILE Chi-restraints excluded: chain B residue 1046 THR Chi-restraints excluded: chain B residue 1088 MET Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 64 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 342 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 325 optimal weight: 2.9990 chunk 315 optimal weight: 8.9990 chunk 326 optimal weight: 0.9980 chunk 314 optimal weight: 0.0040 chunk 311 optimal weight: 1.9990 chunk 146 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 209 optimal weight: 0.9980 chunk 172 optimal weight: 6.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN A 264 GLN A1161 ASN A1173 ASN B 57 GLN ** B 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 ASN C 31 GLN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** 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 = 0.3597 r_free = 0.3597 target = 0.131550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.097387 restraints weight = 35278.765| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.72 r_work: 0.3057 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29348 Z= 0.133 Angle : 0.550 15.354 39897 Z= 0.282 Chirality : 0.044 0.199 4536 Planarity : 0.004 0.057 4975 Dihedral : 10.949 87.398 4283 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.88 % Favored : 94.89 % Rotamer: Outliers : 2.88 % Allowed : 25.95 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 3444 helix: 1.10 (0.14), residues: 1312 sheet: -0.31 (0.23), residues: 495 loop : -0.31 (0.16), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 466 HIS 0.009 0.001 HIS D 193 PHE 0.024 0.001 PHE A 918 TYR 0.018 0.001 TYR F 69 ARG 0.008 0.000 ARG A1228 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 1256) hydrogen bonds : angle 4.98840 ( 3430) metal coordination : bond 0.00697 ( 24) metal coordination : angle 3.86850 ( 33) covalent geometry : bond 0.00309 (29324) covalent geometry : angle 0.53924 (39864) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 393 time to evaluate : 3.128 Fit side-chains REVERT: A 77 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8142 (mm-40) REVERT: A 109 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6919 (mp) REVERT: A 162 ILE cc_start: 0.7944 (mt) cc_final: 0.7733 (mm) REVERT: A 185 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7646 (mm) REVERT: A 225 ASP cc_start: 0.6339 (OUTLIER) cc_final: 0.6057 (t70) REVERT: A 258 ARG cc_start: 0.6234 (mtm-85) cc_final: 0.6007 (ttt-90) REVERT: A 383 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7498 (pp) REVERT: A 441 ILE cc_start: 0.8754 (mt) cc_final: 0.8465 (mm) REVERT: A 900 ARG cc_start: 0.7818 (tpt170) cc_final: 0.7329 (tpt170) REVERT: A 1179 GLU cc_start: 0.7796 (tt0) cc_final: 0.7369 (tt0) REVERT: B 95 ASN cc_start: 0.7078 (t0) cc_final: 0.6730 (p0) REVERT: B 97 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7773 (mm-30) REVERT: B 122 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8269 (mt) REVERT: B 227 ILE cc_start: 0.8276 (mt) cc_final: 0.7999 (mt) REVERT: B 319 ILE cc_start: 0.8174 (mt) cc_final: 0.7641 (pt) REVERT: B 434 ASN cc_start: 0.7706 (m-40) cc_final: 0.7354 (m110) REVERT: B 494 MET cc_start: 0.5351 (tmm) cc_final: 0.4630 (tpt) REVERT: B 682 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8259 (mtpm) REVERT: B 721 ASP cc_start: 0.8131 (m-30) cc_final: 0.7758 (m-30) REVERT: B 842 VAL cc_start: 0.9106 (OUTLIER) cc_final: 0.8846 (m) REVERT: B 928 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7786 (ptmt) REVERT: B 1042 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.7654 (mmm) REVERT: C 9 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7121 (mp0) REVERT: C 28 LYS cc_start: 0.7453 (pttt) cc_final: 0.6914 (tmtm) REVERT: C 233 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: C 338 LYS cc_start: 0.7998 (ttpt) cc_final: 0.7700 (ttmm) REVERT: D 101 ASN cc_start: 0.8080 (OUTLIER) cc_final: 0.7715 (p0) REVERT: G 89 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7458 (pm20) REVERT: E 64 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8554 (mt-10) outliers start: 89 outliers final: 50 residues processed: 456 average time/residue: 1.2745 time to fit residues: 689.3970 Evaluate side-chains 441 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 379 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1262 ILE Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 410 ARG Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 845 ASN Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 928 LYS Chi-restraints excluded: chain B residue 1042 MET Chi-restraints excluded: chain B residue 1088 MET Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain E residue 56 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 230 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 210 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 33 ASN ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN A 264 GLN A1161 ASN A1173 ASN B 57 GLN ** B 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 972 HIS B1002 ASN ** B1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.129031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.094594 restraints weight = 35578.088| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.71 r_work: 0.3011 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 29348 Z= 0.225 Angle : 0.610 15.693 39897 Z= 0.313 Chirality : 0.047 0.227 4536 Planarity : 0.005 0.057 4975 Dihedral : 11.054 87.027 4282 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.02 % Favored : 94.74 % Rotamer: Outliers : 3.49 % Allowed : 25.75 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.14), residues: 3444 helix: 0.93 (0.14), residues: 1310 sheet: -0.40 (0.23), residues: 494 loop : -0.33 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 466 HIS 0.006 0.001 HIS D 193 PHE 0.025 0.002 PHE A 918 TYR 0.023 0.002 TYR F 69 ARG 0.010 0.000 ARG A1228 Details of bonding type rmsd hydrogen bonds : bond 0.04213 ( 1256) hydrogen bonds : angle 5.16454 ( 3430) metal coordination : bond 0.00782 ( 24) metal coordination : angle 4.11032 ( 33) covalent geometry : bond 0.00539 (29324) covalent geometry : angle 0.59828 (39864) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 389 time to evaluate : 3.741 Fit side-chains revert: symmetry clash REVERT: A 77 GLN cc_start: 0.8438 (mm-40) cc_final: 0.8209 (mm-40) REVERT: A 109 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7021 (mp) REVERT: A 128 GLN cc_start: 0.6206 (pm20) cc_final: 0.5682 (tt0) REVERT: A 162 ILE cc_start: 0.7937 (mt) cc_final: 0.7731 (mm) REVERT: A 185 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7751 (mm) REVERT: A 225 ASP cc_start: 0.6503 (OUTLIER) cc_final: 0.6190 (t70) REVERT: A 258 ARG cc_start: 0.6223 (mtm-85) cc_final: 0.6016 (ttt-90) REVERT: A 441 ILE cc_start: 0.8807 (mt) cc_final: 0.8512 (mm) REVERT: A 900 ARG cc_start: 0.7849 (tpt170) cc_final: 0.7540 (tpt170) REVERT: A 1164 LEU cc_start: 0.6541 (OUTLIER) cc_final: 0.6269 (tm) REVERT: A 1179 GLU cc_start: 0.7847 (tt0) cc_final: 0.7438 (tt0) REVERT: A 1274 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8769 (mtp) REVERT: B 95 ASN cc_start: 0.7120 (t0) cc_final: 0.6775 (p0) REVERT: B 122 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8301 (mt) REVERT: B 319 ILE cc_start: 0.8196 (mt) cc_final: 0.7661 (pt) REVERT: B 434 ASN cc_start: 0.7734 (m-40) cc_final: 0.7396 (m110) REVERT: B 494 MET cc_start: 0.5348 (tmm) cc_final: 0.4618 (tpt) REVERT: B 609 ARG cc_start: 0.7899 (mpt-90) cc_final: 0.7568 (mpt-90) REVERT: B 681 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: B 682 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8259 (mtpm) REVERT: B 721 ASP cc_start: 0.8147 (m-30) cc_final: 0.7737 (m-30) REVERT: B 928 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7730 (ptmt) REVERT: C 9 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: C 233 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7861 (tt0) REVERT: C 338 LYS cc_start: 0.8053 (ttpt) cc_final: 0.7758 (ttmm) REVERT: D 101 ASN cc_start: 0.8026 (OUTLIER) cc_final: 0.7678 (p0) REVERT: G 89 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7518 (pm20) outliers start: 108 outliers final: 55 residues processed: 463 average time/residue: 1.3272 time to fit residues: 726.7123 Evaluate side-chains 453 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 385 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 1160 GLU Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1190 ILE Chi-restraints excluded: chain A residue 1262 ILE Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 928 LYS Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1088 MET Chi-restraints excluded: chain B residue 1198 CYS Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 125 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 122 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 271 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 113 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 324 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 314 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 33 ASN ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN A 264 GLN A1161 ASN A1173 ASN B 18 ASN B 57 GLN ** B 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 972 HIS ** B1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.131426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.097215 restraints weight = 35300.855| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.72 r_work: 0.3070 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29348 Z= 0.134 Angle : 0.568 16.050 39897 Z= 0.290 Chirality : 0.044 0.252 4536 Planarity : 0.004 0.058 4975 Dihedral : 10.946 86.440 4282 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.56 % Favored : 95.21 % Rotamer: Outliers : 2.58 % Allowed : 26.62 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3444 helix: 1.07 (0.14), residues: 1311 sheet: -0.36 (0.23), residues: 496 loop : -0.28 (0.16), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 466 HIS 0.009 0.001 HIS D 193 PHE 0.031 0.001 PHE B 304 TYR 0.018 0.001 TYR F 69 ARG 0.013 0.000 ARG A1228 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 1256) hydrogen bonds : angle 5.00396 ( 3430) metal coordination : bond 0.00703 ( 24) metal coordination : angle 3.84634 ( 33) covalent geometry : bond 0.00311 (29324) covalent geometry : angle 0.55764 (39864) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 386 time to evaluate : 3.127 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7152 (ttm) cc_final: 0.6506 (ttp) REVERT: A 109 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.6993 (mp) REVERT: A 128 GLN cc_start: 0.6231 (pm20) cc_final: 0.5732 (tt0) REVERT: A 185 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7640 (mm) REVERT: A 225 ASP cc_start: 0.6420 (OUTLIER) cc_final: 0.6105 (t70) REVERT: A 258 ARG cc_start: 0.6283 (ttm-80) cc_final: 0.5999 (mtp85) REVERT: A 441 ILE cc_start: 0.8763 (mt) cc_final: 0.8477 (mm) REVERT: A 900 ARG cc_start: 0.7791 (tpt170) cc_final: 0.7444 (tpt170) REVERT: A 1078 GLN cc_start: 0.8176 (mt0) cc_final: 0.7858 (mt0) REVERT: A 1179 GLU cc_start: 0.7800 (tt0) cc_final: 0.7379 (tt0) REVERT: B 122 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8273 (mt) REVERT: B 196 ARG cc_start: 0.8330 (mmm-85) cc_final: 0.8121 (mmm-85) REVERT: B 205 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8234 (tt) REVERT: B 227 ILE cc_start: 0.8313 (mt) cc_final: 0.8039 (mt) REVERT: B 319 ILE cc_start: 0.8171 (mt) cc_final: 0.7642 (pt) REVERT: B 434 ASN cc_start: 0.7723 (m-40) cc_final: 0.7376 (m110) REVERT: B 494 MET cc_start: 0.5224 (tmm) cc_final: 0.4658 (tpt) REVERT: B 609 ARG cc_start: 0.7899 (mpt-90) cc_final: 0.7604 (mpt-90) REVERT: B 682 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8250 (mtpp) REVERT: B 721 ASP cc_start: 0.8105 (m-30) cc_final: 0.7757 (m-30) REVERT: B 928 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7809 (ptmt) REVERT: C 9 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: C 28 LYS cc_start: 0.7510 (pttt) cc_final: 0.6979 (tmtm) REVERT: C 233 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7856 (tt0) REVERT: C 338 LYS cc_start: 0.7994 (ttpt) cc_final: 0.7698 (ttmm) REVERT: D 101 ASN cc_start: 0.8105 (OUTLIER) cc_final: 0.7753 (p0) REVERT: G 89 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7475 (pm20) REVERT: E 64 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8531 (mt-10) outliers start: 80 outliers final: 46 residues processed: 444 average time/residue: 1.3064 time to fit residues: 690.8242 Evaluate side-chains 439 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 382 time to evaluate : 4.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1262 ILE Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 928 LYS Chi-restraints excluded: chain B residue 1088 MET Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain E residue 56 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 330 optimal weight: 0.6980 chunk 247 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 319 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 185 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 327 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 245 GLN A 264 GLN A 721 ASN A1173 ASN B 57 GLN ** B 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 972 HIS ** B1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.130759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.096445 restraints weight = 35455.353| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.72 r_work: 0.3060 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29348 Z= 0.157 Angle : 0.583 15.952 39897 Z= 0.297 Chirality : 0.045 0.233 4536 Planarity : 0.004 0.058 4975 Dihedral : 10.916 85.960 4282 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.70 % Favored : 95.06 % Rotamer: Outliers : 2.29 % Allowed : 27.17 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 3444 helix: 1.05 (0.14), residues: 1306 sheet: -0.32 (0.23), residues: 493 loop : -0.29 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1154 HIS 0.008 0.001 HIS D 193 PHE 0.036 0.001 PHE B 304 TYR 0.020 0.001 TYR F 69 ARG 0.011 0.000 ARG A1228 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 1256) hydrogen bonds : angle 5.03249 ( 3430) metal coordination : bond 0.00692 ( 24) metal coordination : angle 3.86935 ( 33) covalent geometry : bond 0.00372 (29324) covalent geometry : angle 0.57295 (39864) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 383 time to evaluate : 3.208 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7167 (ttm) cc_final: 0.6522 (ttp) REVERT: A 109 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7017 (mp) REVERT: A 128 GLN cc_start: 0.6326 (pm20) cc_final: 0.5691 (tt0) REVERT: A 185 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7636 (mm) REVERT: A 225 ASP cc_start: 0.6404 (OUTLIER) cc_final: 0.6078 (t70) REVERT: A 441 ILE cc_start: 0.8769 (mt) cc_final: 0.8477 (mm) REVERT: A 900 ARG cc_start: 0.7803 (tpt170) cc_final: 0.7529 (tpt170) REVERT: A 1078 GLN cc_start: 0.8165 (mt0) cc_final: 0.7845 (mt0) REVERT: A 1179 GLU cc_start: 0.7803 (tt0) cc_final: 0.7374 (tt0) REVERT: A 1274 MET cc_start: 0.9005 (mtm) cc_final: 0.8756 (mtp) REVERT: B 20 GLU cc_start: 0.7385 (pm20) cc_final: 0.6978 (mp0) REVERT: B 122 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8288 (mt) REVERT: B 196 ARG cc_start: 0.8314 (mmm-85) cc_final: 0.8094 (mmm-85) REVERT: B 319 ILE cc_start: 0.8094 (mt) cc_final: 0.7604 (pt) REVERT: B 401 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7226 (mm) REVERT: B 434 ASN cc_start: 0.7723 (m-40) cc_final: 0.7397 (m110) REVERT: B 494 MET cc_start: 0.5207 (tmm) cc_final: 0.4658 (tpt) REVERT: B 609 ARG cc_start: 0.7869 (mpt-90) cc_final: 0.7577 (mpt-90) REVERT: B 682 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8276 (mtpm) REVERT: B 721 ASP cc_start: 0.8109 (m-30) cc_final: 0.7758 (m-30) REVERT: B 928 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7743 (ptmt) REVERT: C 9 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: C 28 LYS cc_start: 0.7478 (pttt) cc_final: 0.6974 (tmtm) REVERT: C 233 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: C 338 LYS cc_start: 0.7995 (ttpt) cc_final: 0.7699 (ttmm) REVERT: D 101 ASN cc_start: 0.8060 (OUTLIER) cc_final: 0.7723 (p0) REVERT: G 89 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7494 (pm20) REVERT: E 64 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8549 (mt-10) outliers start: 71 outliers final: 48 residues processed: 431 average time/residue: 1.3531 time to fit residues: 689.6139 Evaluate side-chains 433 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 374 time to evaluate : 3.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1262 ILE Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 928 LYS Chi-restraints excluded: chain B residue 1088 MET Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain E residue 56 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 73 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 149 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 255 optimal weight: 2.9990 chunk 284 optimal weight: 2.9990 chunk 283 optimal weight: 5.9990 chunk 196 optimal weight: 0.7980 chunk 345 optimal weight: 0.9980 chunk 331 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 245 GLN A 264 GLN A 721 ASN A1173 ASN B 57 GLN ** B 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 972 HIS ** B1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 ASN ** G 36 ASN ** 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 = 0.3602 r_free = 0.3602 target = 0.131969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.097824 restraints weight = 35468.892| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.72 r_work: 0.3077 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29348 Z= 0.131 Angle : 0.569 16.092 39897 Z= 0.289 Chirality : 0.044 0.222 4536 Planarity : 0.004 0.057 4975 Dihedral : 10.846 85.224 4282 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.59 % Favored : 95.18 % Rotamer: Outliers : 2.42 % Allowed : 27.17 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.15), residues: 3444 helix: 1.13 (0.14), residues: 1301 sheet: -0.30 (0.23), residues: 495 loop : -0.27 (0.16), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1154 HIS 0.009 0.001 HIS D 193 PHE 0.037 0.001 PHE B 304 TYR 0.017 0.001 TYR F 69 ARG 0.009 0.000 ARG A1228 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 1256) hydrogen bonds : angle 4.95354 ( 3430) metal coordination : bond 0.00677 ( 24) metal coordination : angle 3.75293 ( 33) covalent geometry : bond 0.00304 (29324) covalent geometry : angle 0.55871 (39864) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23239.11 seconds wall clock time: 400 minutes 52.92 seconds (24052.92 seconds total)