Starting phenix.real_space_refine on Sun Sep 29 23:37:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0k_17335/09_2024/8p0k_17335_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0k_17335/09_2024/8p0k_17335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0k_17335/09_2024/8p0k_17335.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0k_17335/09_2024/8p0k_17335.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0k_17335/09_2024/8p0k_17335_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0k_17335/09_2024/8p0k_17335_neut.cif" } resolution = 2.64 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= -0.002 sd= 0.065 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: 8 Type Number sf(0) Gaussians Zn 4 6.06 5 P 75 5.49 5 Mg 1 5.21 5 S 165 5.16 5 C 24281 2.51 5 N 6394 2.21 5 O 7331 1.98 5 H 37892 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 76143 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 20617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1277, 20617 Classifications: {'peptide': 1277} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1233} Chain breaks: 1 Chain: "B" Number of atoms: 18659 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1155, 18634 Classifications: {'peptide': 1155} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1102} Conformer: "B" Number of residues, atoms: 1155, 18634 Classifications: {'peptide': 1155} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1102} bond proxies already assigned to first conformer: 18803 Chain: "C" Number of atoms: 4947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 4947 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 9, 'TRANS': 294} Chain: "E" Number of atoms: 3041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 3041 Classifications: {'peptide': 184} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 175} Chain: "F" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1736 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "G" Number of atoms: 2370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 2370 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 3, 'TRANS': 149} Chain breaks: 1 Chain: "H" Number of atoms: 6298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 6298 Classifications: {'peptide': 382} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 377} Chain: "I" Number of atoms: 4563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 4563 Classifications: {'peptide': 276} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 268} Chain breaks: 1 Chain: "J" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1017 Classifications: {'peptide': 61} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 58} Chain: "N" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 1236 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain breaks: 1 Chain: "O" Number of atoms: 8577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 8577 Classifications: {'peptide': 525} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 501} Chain: "S" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1916 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain: "T" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 1161 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain breaks: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "J" 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 714 SG CYS A 49 47.561 82.732 70.693 1.00156.56 S ATOM 760 SG CYS A 52 48.162 81.546 67.072 1.00157.53 S ATOM 862 SG CYS A 59 50.446 84.166 68.676 1.00130.88 S ATOM 1387 SG CYS A 90 29.649 128.179 77.540 1.00167.39 S ATOM 1432 SG CYS A 93 26.704 127.331 75.292 1.00158.82 S ATOM 2051 SG CYS A 130 27.658 130.922 75.899 1.00163.49 S ATOM 2125 SG CYS A 135 26.154 128.925 78.750 1.00194.79 S ATOM 38061 SG CYS B1087 42.074 93.163 57.924 1.00139.35 S ATOM 38100 SG CYS B1090 42.326 95.069 61.272 1.00103.51 S ATOM 38280 SG CYS B1103 41.331 91.698 61.325 1.00119.81 S ATOM 38333 SG CYS B1106 38.911 94.278 59.852 1.00125.33 S ATOM 62324 SG CYS J 7 121.780 90.466 75.495 1.00 58.45 S ATOM 62359 SG CYS J 10 124.156 89.103 72.490 1.00 27.86 S ATOM 62856 SG CYS J 39 123.534 92.761 73.288 1.00 68.63 S ATOM 62866 SG CYS J 40 125.598 90.382 75.485 1.00 51.05 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG B 206 " occ=0.26 ... (46 atoms not shown) pdb="HH22BARG B 206 " occ=0.74 Time building chain proxies: 30.58, per 1000 atoms: 0.40 Number of scatterers: 76143 At special positions: 0 Unit cell: (154.208, 194.621, 171.224, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 S 165 16.00 P 75 15.00 Mg 1 11.99 O 7331 8.00 N 6394 7.00 C 24281 6.00 H 37892 1.00 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: 14.85 Conformation dependent library (CDL) restraints added in 5.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1302 " pdb="ZN ZN A1302 " - pdb=" NE2 HIS A 62 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 59 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 52 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 49 " pdb=" ZN A1303 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 90 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 93 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 135 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1090 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1103 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1087 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1106 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 39 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 40 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " Number of angles added : 21 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8680 Finding SS restraints... Secondary structure from input PDB file: 183 helices and 46 sheets defined 43.6% alpha, 15.7% beta 22 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 28.63 Creating SS restraints... Processing helix chain 'A' and resid 13 through 19 Processing helix chain 'A' and resid 38 through 42 Processing helix chain 'A' and resid 78 through 87 Processing helix chain 'A' and resid 107 through 112 removed outlier: 6.684A pdb=" N SER A 112 " --> pdb=" O LYS A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 125 removed outlier: 4.303A pdb=" N ARG A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 172 removed outlier: 3.733A pdb=" N ILE A 172 " --> pdb=" O LYS A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 176 through 181 Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.738A pdb=" N ILE A 202 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 234 Processing helix chain 'A' and resid 236 through 249 removed outlier: 3.699A pdb=" N ILE A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 253 Processing helix chain 'A' and resid 261 through 267 removed outlier: 3.997A pdb=" N ILE A 265 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 304 through 311 Processing helix chain 'A' and resid 321 through 331 Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 428 through 438 Processing helix chain 'A' and resid 459 through 471 removed outlier: 3.919A pdb=" N VAL A 463 " --> pdb=" O GLN A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 485 through 488 removed outlier: 4.182A pdb=" N ARG A 488 " --> pdb=" O LYS A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 485 through 488' Processing helix chain 'A' and resid 499 through 508 Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.800A pdb=" N VAL A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 550 through 573 Processing helix chain 'A' and resid 585 through 615 Processing helix chain 'A' and resid 622 through 656 Processing helix chain 'A' and resid 659 through 668 Processing helix chain 'A' and resid 672 through 681 Processing helix chain 'A' and resid 696 through 700 removed outlier: 3.611A pdb=" N ARG A 700 " --> pdb=" O VAL A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'A' and resid 727 through 764 removed outlier: 3.559A pdb=" N VAL A 737 " --> pdb=" O PHE A 733 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL A 746 " --> pdb=" O SER A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 821 Processing helix chain 'A' and resid 841 through 846 removed outlier: 3.727A pdb=" N VAL A 844 " --> pdb=" O ASN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 877 Processing helix chain 'A' and resid 882 through 893 removed outlier: 3.591A pdb=" N GLU A 886 " --> pdb=" O ILE A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 919 Processing helix chain 'A' and resid 925 through 944 Processing helix chain 'A' and resid 952 through 957 Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 985 through 996 Processing helix chain 'A' and resid 1001 through 1004 Processing helix chain 'A' and resid 1024 through 1030 Processing helix chain 'A' and resid 1033 through 1048 removed outlier: 3.609A pdb=" N PHE A1044 " --> pdb=" O MET A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1093 removed outlier: 3.613A pdb=" N ASN A1081 " --> pdb=" O PRO A1077 " (cutoff:3.500A) Proline residue: A1090 - end of helix Processing helix chain 'A' and resid 1130 through 1136 removed outlier: 4.006A pdb=" N SER A1135 " --> pdb=" O GLU A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1154 Processing helix chain 'A' and resid 1155 through 1172 removed outlier: 4.049A pdb=" N TYR A1171 " --> pdb=" O MET A1167 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLY A1172 " --> pdb=" O LEU A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1177 No H-bonds generated for 'chain 'A' and resid 1175 through 1177' Processing helix chain 'A' and resid 1178 through 1190 Processing helix chain 'A' and resid 1207 through 1215 Processing helix chain 'A' and resid 1218 through 1227 Processing helix chain 'A' and resid 1234 through 1241 Processing helix chain 'A' and resid 1247 through 1252 removed outlier: 3.691A pdb=" N TYR A1252 " --> pdb=" O THR A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1282 removed outlier: 4.649A pdb=" N ASP A1270 " --> pdb=" O ARG A1266 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS A1271 " --> pdb=" O LYS A1267 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 19 Processing helix chain 'B' and resid 28 through 44 removed outlier: 4.568A pdb=" N PHE B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N GLN B 34 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 216 through 219 Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 244 through 253 Processing helix chain 'B' and resid 257 through 277 removed outlier: 3.565A pdb=" N LEU B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 299 Processing helix chain 'B' and resid 303 through 314 Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 323 through 344 removed outlier: 3.560A pdb=" N PHE B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 348 Processing helix chain 'B' and resid 353 through 357 Processing helix chain 'B' and resid 361 through 392 removed outlier: 3.622A pdb=" N PHE B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 403 Processing helix chain 'B' and resid 406 through 417 Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 463 through 467 Processing helix chain 'B' and resid 498 through 516 Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 544 through 558 Processing helix chain 'B' and resid 604 through 611 removed outlier: 3.995A pdb=" N GLU B 608 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER B 609 " --> pdb=" O PRO B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 614 No H-bonds generated for 'chain 'B' and resid 612 through 614' Processing helix chain 'B' and resid 615 through 623 Processing helix chain 'B' and resid 632 through 637 Processing helix chain 'B' and resid 643 through 649 Processing helix chain 'B' and resid 651 through 658 removed outlier: 3.671A pdb=" N GLN B 657 " --> pdb=" O ASP B 653 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 669 removed outlier: 3.693A pdb=" N ASP B 669 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 675 Processing helix chain 'B' and resid 678 through 682 Processing helix chain 'B' and resid 683 through 695 removed outlier: 3.843A pdb=" N LYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 731 removed outlier: 3.574A pdb=" N GLU B 729 " --> pdb=" O SER B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 767 Processing helix chain 'B' and resid 795 through 799 Processing helix chain 'B' and resid 898 through 902 Processing helix chain 'B' and resid 916 through 924 removed outlier: 4.254A pdb=" N ILE B 920 " --> pdb=" O ASN B 916 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 921 " --> pdb=" O SER B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 941 removed outlier: 4.010A pdb=" N LEU B 929 " --> pdb=" O THR B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 977 removed outlier: 3.603A pdb=" N TYR B 965 " --> pdb=" O SER B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 991 Processing helix chain 'B' and resid 1021 through 1025 Processing helix chain 'B' and resid 1054 through 1065 Processing helix chain 'B' and resid 1066 through 1075 Processing helix chain 'B' and resid 1077 through 1081 removed outlier: 3.754A pdb=" N TYR B1081 " --> pdb=" O GLU B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1109 Processing helix chain 'B' and resid 1121 through 1134 Processing helix chain 'C' and resid 14 through 29 Processing helix chain 'C' and resid 47 through 57 removed outlier: 4.030A pdb=" N HIS C 57 " --> pdb=" O THR C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 63 removed outlier: 5.341A pdb=" N MET C 61 " --> pdb=" O ILE C 58 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS C 62 " --> pdb=" O PRO C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 94 through 98 Processing helix chain 'C' and resid 116 through 122 Processing helix chain 'C' and resid 151 through 157 removed outlier: 3.736A pdb=" N LYS C 156 " --> pdb=" O ASP C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 176 Processing helix chain 'C' and resid 206 through 230 removed outlier: 3.836A pdb=" N CYS C 211 " --> pdb=" O ASP C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 249 Processing helix chain 'C' and resid 255 through 265 Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 283 through 304 Processing helix chain 'E' and resid 4 through 22 removed outlier: 3.801A pdb=" N TYR E 8 " --> pdb=" O TYR E 4 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU E 15 " --> pdb=" O LYS E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 34 removed outlier: 3.610A pdb=" N LEU E 32 " --> pdb=" O ASN E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 101 removed outlier: 3.641A pdb=" N TYR E 101 " --> pdb=" O ASN E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 98 through 101' Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 146 through 153 Processing helix chain 'F' and resid 62 through 75 removed outlier: 3.747A pdb=" N ARG F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 95 Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'F' and resid 112 through 123 Processing helix chain 'F' and resid 140 through 142 No H-bonds generated for 'chain 'F' and resid 140 through 142' Processing helix chain 'F' and resid 143 through 161 Processing helix chain 'G' and resid 15 through 19 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'H' and resid 2 through 12 Processing helix chain 'H' and resid 32 through 44 Processing helix chain 'H' and resid 46 through 51 Processing helix chain 'H' and resid 53 through 57 removed outlier: 3.760A pdb=" N ILE H 56 " --> pdb=" O ASN H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.848A pdb=" N TYR H 94 " --> pdb=" O LYS H 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 90 through 94' Processing helix chain 'H' and resid 102 through 114 Processing helix chain 'H' and resid 117 through 128 Processing helix chain 'H' and resid 133 through 142 Processing helix chain 'H' and resid 230 through 254 Processing helix chain 'H' and resid 255 through 271 removed outlier: 3.905A pdb=" N LYS H 259 " --> pdb=" O ASN H 255 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA H 271 " --> pdb=" O HIS H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 287 Processing helix chain 'H' and resid 313 through 317 Processing helix chain 'H' and resid 338 through 365 removed outlier: 3.670A pdb=" N SER H 365 " --> pdb=" O THR H 361 " (cutoff:3.500A) Processing helix chain 'H' and resid 372 through 382 Processing helix chain 'I' and resid 20 through 24 Processing helix chain 'I' and resid 46 through 60 removed outlier: 3.518A pdb=" N GLN I 60 " --> pdb=" O ARG I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 79 Processing helix chain 'I' and resid 92 through 105 removed outlier: 3.629A pdb=" N TYR I 96 " --> pdb=" O ILE I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 118 Processing helix chain 'I' and resid 118 through 124 Processing helix chain 'I' and resid 130 through 143 Processing helix chain 'I' and resid 154 through 166 Processing helix chain 'I' and resid 176 through 178 No H-bonds generated for 'chain 'I' and resid 176 through 178' Processing helix chain 'I' and resid 179 through 201 Processing helix chain 'I' and resid 208 through 235 Processing helix chain 'I' and resid 249 through 256 Processing helix chain 'I' and resid 256 through 270 removed outlier: 3.811A pdb=" N THR I 270 " --> pdb=" O GLU I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 276 through 286 removed outlier: 3.848A pdb=" N TYR I 286 " --> pdb=" O THR I 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 23 Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 37 through 47 Processing helix chain 'O' and resid 2 through 8 removed outlier: 3.644A pdb=" N VAL O 6 " --> pdb=" O ALA O 3 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 25 Processing helix chain 'O' and resid 46 through 57 removed outlier: 3.876A pdb=" N LEU O 50 " --> pdb=" O PRO O 46 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR O 51 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 85 No H-bonds generated for 'chain 'O' and resid 83 through 85' Processing helix chain 'O' and resid 91 through 98 Processing helix chain 'O' and resid 133 through 140 removed outlier: 5.312A pdb=" N SER O 139 " --> pdb=" O LYS O 136 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 182 removed outlier: 3.624A pdb=" N HIS O 178 " --> pdb=" O SER O 174 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 221 Processing helix chain 'O' and resid 243 through 248 removed outlier: 3.910A pdb=" N VAL O 248 " --> pdb=" O GLN O 245 " (cutoff:3.500A) Processing helix chain 'O' and resid 326 through 338 Processing helix chain 'O' and resid 358 through 373 removed outlier: 3.656A pdb=" N VAL O 362 " --> pdb=" O THR O 358 " (cutoff:3.500A) Proline residue: O 371 - end of helix Processing helix chain 'O' and resid 384 through 387 Processing helix chain 'O' and resid 466 through 469 Processing helix chain 'O' and resid 493 through 503 Processing helix chain 'O' and resid 510 through 523 removed outlier: 3.922A pdb=" N SER O 522 " --> pdb=" O LEU O 518 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE O 523 " --> pdb=" O ARG O 519 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 51 Processing helix chain 'S' and resid 71 through 79 removed outlier: 4.489A pdb=" N GLY S 75 " --> pdb=" O LYS S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 85 removed outlier: 6.578A pdb=" N ARG S 83 " --> pdb=" O LYS S 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 109 Processing helix chain 'S' and resid 112 through 131 Processing helix chain 'S' and resid 144 through 148 Processing sheet with id=AA1, first strand: chain 'A' and resid 1229 through 1231 removed outlier: 6.003A pdb=" N ILE A 4 " --> pdb=" O GLU B1143 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N GLU B1143 " --> pdb=" O ILE A 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 67 Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 144 removed outlier: 4.077A pdb=" N PHE A 151 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 280 through 281 Processing sheet with id=AA6, first strand: chain 'B' and resid 1027 through 1029 removed outlier: 7.674A pdb=" N ILE A 402 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL A 289 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE A 404 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLY A 291 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 316 removed outlier: 6.911A pdb=" N TRP A 365 " --> pdb=" O TYR A 337 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR A 337 " --> pdb=" O TRP A 365 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLU A 367 " --> pdb=" O LYS A 335 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 518 through 519 Processing sheet with id=AA9, first strand: chain 'A' and resid 684 through 685 Processing sheet with id=AB1, first strand: chain 'A' and resid 767 through 768 removed outlier: 6.517A pdb=" N VAL A 774 " --> pdb=" O ILE A 781 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 796 through 799 Processing sheet with id=AB3, first strand: chain 'A' and resid 825 through 826 Processing sheet with id=AB4, first strand: chain 'A' and resid 1106 through 1111 Processing sheet with id=AB5, first strand: chain 'A' and resid 998 through 999 Processing sheet with id=AB6, first strand: chain 'A' and resid 1006 through 1012 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1015 through 1023 current: chain 'A' and resid 1065 through 1074 Processing sheet with id=AB7, first strand: chain 'A' and resid 1253 through 1256 removed outlier: 3.831A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 136 through 138 current: chain 'G' and resid 43 through 50 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 43 through 50 current: chain 'G' and resid 66 through 77 Processing sheet with id=AB8, first strand: chain 'B' and resid 54 through 59 removed outlier: 5.509A pdb=" N ILE B 68 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL B 73 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR B 97 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL B 75 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU B 95 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N PHE B 98 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLU B 121 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL B 100 " --> pdb=" O SER B 119 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER B 119 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE B 102 " --> pdb=" O ILE B 117 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 112 through 121 current: chain 'H' and resid 70 through 75 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 70 through 75 current: chain 'H' and resid 159 through 165 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 187 through 190 current: chain 'H' and resid 209 through 213 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 218 through 222 current: chain 'H' and resid 330 through 336 Processing sheet with id=AB9, first strand: chain 'B' and resid 157 through 158 Processing sheet with id=AC1, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.319A pdb=" N ASN B 169 " --> pdb=" O GLY B 445 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 179 through 184 removed outlier: 6.411A pdb=" N SER B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 418 through 419 Processing sheet with id=AC4, first strand: chain 'B' and resid 493 through 494 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 627 through 631 current: chain 'B' and resid 660 through 661 Processing sheet with id=AC5, first strand: chain 'B' and resid 535 through 540 removed outlier: 6.628A pdb=" N ILE B 530 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER B 539 " --> pdb=" O PHE B 528 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N PHE B 528 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ILE B 580 " --> pdb=" O PRO B 529 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR B 531 " --> pdb=" O ILE B 580 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.752A pdb=" N ILE B 772 " --> pdb=" O ARG B 875 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 870 " --> pdb=" O ARG B 856 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ARG B 856 " --> pdb=" O LEU B 870 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N MET B 872 " --> pdb=" O VAL B 854 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VAL B 854 " --> pdb=" O MET B 872 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N GLU B 874 " --> pdb=" O SER B 852 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N SER B 852 " --> pdb=" O GLU B 874 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 723 through 724 Processing sheet with id=AC8, first strand: chain 'B' and resid 992 through 993 removed outlier: 6.506A pdb=" N ILE B 758 " --> pdb=" O ALA B 894 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL B 896 " --> pdb=" O ILE B 758 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE B 760 " --> pdb=" O VAL B 896 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N VAL B 913 " --> pdb=" O HIS B 741 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR B 743 " --> pdb=" O VAL B 913 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ILE B 915 " --> pdb=" O THR B 743 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ALA B 745 " --> pdb=" O ILE B 915 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE B1009 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 823 through 827 Processing sheet with id=AD1, first strand: chain 'B' and resid 996 through 997 removed outlier: 3.615A pdb=" N LYS B1002 " --> pdb=" O ASP B 997 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1086 through 1087 Processing sheet with id=AD3, first strand: chain 'B' and resid 1095 through 1096 Processing sheet with id=AD4, first strand: chain 'C' and resid 4 through 12 Processing sheet with id=AD5, first strand: chain 'C' and resid 31 through 32 Processing sheet with id=AD6, first strand: chain 'C' and resid 36 through 42 removed outlier: 3.714A pdb=" N ILE C 36 " --> pdb=" O PHE C 143 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLU C 139 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASN C 42 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR C 137 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AD8, first strand: chain 'C' and resid 244 through 245 Processing sheet with id=AD9, first strand: chain 'E' and resid 35 through 38 Processing sheet with id=AE1, first strand: chain 'E' and resid 63 through 65 removed outlier: 6.356A pdb=" N ILE E 83 " --> pdb=" O PHE E 95 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 113 through 115 removed outlier: 6.228A pdb=" N MET E 142 " --> pdb=" O ILE E 181 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 84 through 91 removed outlier: 3.917A pdb=" N THR G 88 " --> pdb=" O GLN G 100 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N VAL G 97 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N VAL G 153 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ALA G 144 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU G 155 " --> pdb=" O MET G 142 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR G 138 " --> pdb=" O VAL G 159 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 114 through 116 Processing sheet with id=AE5, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AE6, first strand: chain 'O' and resid 34 through 42 removed outlier: 6.625A pdb=" N LEU O 121 " --> pdb=" O GLU O 112 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU O 112 " --> pdb=" O LEU O 121 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU O 123 " --> pdb=" O VAL O 110 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N VAL O 103 " --> pdb=" O LYS O 79 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LYS O 79 " --> pdb=" O VAL O 103 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LEU O 143 " --> pdb=" O LEU O 166 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LEU O 38 " --> pdb=" O PHE O 195 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 227 through 229 removed outlier: 4.242A pdb=" N TYR O 284 " --> pdb=" O PHE O 279 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE O 279 " --> pdb=" O TYR O 284 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL O 299 " --> pdb=" O LEU O 317 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU O 317 " --> pdb=" O VAL O 299 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE O 301 " --> pdb=" O ILE O 315 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL O 305 " --> pdb=" O THR O 311 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP O 310 " --> pdb=" O VAL O 346 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LYS O 348 " --> pdb=" O TRP O 310 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL O 312 " --> pdb=" O LYS O 348 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 238 through 241 removed outlier: 7.268A pdb=" N ILE O 389 " --> pdb=" O TYR O 381 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N TYR O 381 " --> pdb=" O ILE O 389 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 398 through 405 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 398 through 405 current: chain 'O' and resid 422 through 431 removed outlier: 7.035A pdb=" N ILE O 422 " --> pdb=" O VAL O 445 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL O 445 " --> pdb=" O ILE O 422 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL O 424 " --> pdb=" O LYS O 443 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LYS O 443 " --> pdb=" O VAL O 424 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TYR O 426 " --> pdb=" O SER O 441 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER O 441 " --> pdb=" O TYR O 426 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N LYS O 428 " --> pdb=" O TYR O 439 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 436 through 445 current: chain 'O' and resid 489 through 492 Processing sheet with id=AF1, first strand: chain 'O' and resid 458 through 465 removed outlier: 7.842A pdb=" N LYS O 471 " --> pdb=" O ASN O 463 " (cutoff:3.500A) 1622 hydrogen bonds defined for protein. 4467 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 34.81 Time building geometry restraints manager: 18.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 37839 1.03 - 1.22: 94 1.22 - 1.42: 16236 1.42 - 1.61: 22613 1.61 - 1.81: 262 Bond restraints: 77044 Sorted by residual: bond pdb=" C LEU B1158 " pdb=" N LYS B1159 " ideal model delta sigma weight residual 1.329 1.302 0.026 1.60e-02 3.91e+03 2.74e+00 bond pdb=" C ILE G 91 " pdb=" N GLU G 92 " ideal model delta sigma weight residual 1.331 1.309 0.023 1.40e-02 5.10e+03 2.67e+00 bond pdb=" N GLN C 1 " pdb=" CA GLN C 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.56e+00 bond pdb=" C THR B 279 " pdb=" N ASP B 280 " ideal model delta sigma weight residual 1.332 1.311 0.020 1.29e-02 6.01e+03 2.46e+00 bond pdb=" CA ASP C 90 " pdb=" CB ASP C 90 " ideal model delta sigma weight residual 1.528 1.487 0.041 2.61e-02 1.47e+03 2.46e+00 ... (remaining 77039 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 133734 1.21 - 2.41: 5475 2.41 - 3.62: 283 3.62 - 4.83: 62 4.83 - 6.04: 5 Bond angle restraints: 139559 Sorted by residual: angle pdb=" N ILE F 62 " pdb=" CA ILE F 62 " pdb=" C ILE F 62 " ideal model delta sigma weight residual 111.81 107.55 4.26 8.60e-01 1.35e+00 2.45e+01 angle pdb=" N HIS B 126 " pdb=" CA HIS B 126 " pdb=" C HIS B 126 " ideal model delta sigma weight residual 109.76 105.48 4.28 1.59e+00 3.96e-01 7.24e+00 angle pdb=" C3' DT T 54 " pdb=" C2' DT T 54 " pdb=" C1' DT T 54 " ideal model delta sigma weight residual 101.60 105.61 -4.01 1.50e+00 4.44e-01 7.15e+00 angle pdb=" N ASN A 410 " pdb=" CA ASN A 410 " pdb=" CB ASN A 410 " ideal model delta sigma weight residual 110.12 114.02 -3.90 1.47e+00 4.63e-01 7.04e+00 angle pdb=" C GLU B 781 " pdb=" N ILE B 782 " pdb=" CA ILE B 782 " ideal model delta sigma weight residual 123.33 121.11 2.22 8.70e-01 1.32e+00 6.52e+00 ... (remaining 139554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.23: 35051 34.23 - 68.45: 759 68.45 - 102.68: 12 102.68 - 136.90: 2 136.90 - 171.13: 1 Dihedral angle restraints: 35825 sinusoidal: 20094 harmonic: 15731 Sorted by residual: dihedral pdb=" C4' DA N 38 " pdb=" C3' DA N 38 " pdb=" O3' DA N 38 " pdb=" P DA N 39 " ideal model delta sinusoidal sigma weight residual 220.00 48.87 171.13 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA GLU O 319 " pdb=" C GLU O 319 " pdb=" N PRO O 320 " pdb=" CA PRO O 320 " ideal model delta harmonic sigma weight residual 180.00 161.10 18.90 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ASP B 573 " pdb=" C ASP B 573 " pdb=" N HIS B 574 " pdb=" CA HIS B 574 " ideal model delta harmonic sigma weight residual 180.00 161.32 18.68 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 35822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 4137 0.036 - 0.073: 1297 0.073 - 0.109: 503 0.109 - 0.146: 116 0.146 - 0.182: 6 Chirality restraints: 6059 Sorted by residual: chirality pdb=" CB THR J 9 " pdb=" CA THR J 9 " pdb=" OG1 THR J 9 " pdb=" CG2 THR J 9 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.30e-01 chirality pdb=" CA ILE C 103 " pdb=" N ILE C 103 " pdb=" C ILE C 103 " pdb=" CB ILE C 103 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA ILE G 91 " pdb=" N ILE G 91 " pdb=" C ILE G 91 " pdb=" CB ILE G 91 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.75e-01 ... (remaining 6056 not shown) Planarity restraints: 10893 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 410 " -0.005 2.00e-02 2.50e+03 2.78e-02 1.16e+01 pdb=" CG ASN A 410 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN A 410 " -0.033 2.00e-02 2.50e+03 pdb=" ND2 ASN A 410 " 0.016 2.00e-02 2.50e+03 pdb="HD21 ASN A 410 " 0.005 2.00e-02 2.50e+03 pdb="HD22 ASN A 410 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER I 180 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.85e+00 pdb=" C SER I 180 " 0.042 2.00e-02 2.50e+03 pdb=" O SER I 180 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR I 181 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 41 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.70e+00 pdb=" C PHE B 41 " -0.041 2.00e-02 2.50e+03 pdb=" O PHE B 41 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE B 42 " 0.014 2.00e-02 2.50e+03 ... (remaining 10890 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 1588 2.08 - 2.71: 134422 2.71 - 3.34: 228518 3.34 - 3.97: 299139 3.97 - 4.60: 472968 Nonbonded interactions: 1136635 Sorted by model distance: nonbonded pdb=" OE1 GLU O 225 " pdb=" H GLU O 225 " model vdw 1.454 2.450 nonbonded pdb=" OE1 GLU E 18 " pdb=" HH TYR E 35 " model vdw 1.482 2.450 nonbonded pdb=" OE2 GLU B 533 " pdb=" H ILE B 582 " model vdw 1.488 2.450 nonbonded pdb=" H LEU G 89 " pdb=" O SER G 135 " model vdw 1.514 2.450 nonbonded pdb=" H LYS O 91 " pdb=" OE1 GLN O 94 " model vdw 1.527 2.450 ... (remaining 1136630 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.26 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: 3.170 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: 0.990 Extract box with map and model: 2.170 Check model and map are aligned: 0.440 Set scattering table: 0.540 Process input model: 187.080 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.270 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:11.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 206.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 : 0.006 0.047 39152 Z= 0.368 Angle : 0.572 6.035 53219 Z= 0.338 Chirality : 0.042 0.182 6059 Planarity : 0.003 0.038 6473 Dihedral : 11.638 171.126 14976 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.77 % Allowed : 3.21 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.13), residues: 4512 helix: 2.04 (0.13), residues: 1692 sheet: 0.21 (0.20), residues: 730 loop : -0.14 (0.14), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 310 HIS 0.007 0.001 HIS A 62 PHE 0.026 0.001 PHE A 938 TYR 0.014 0.001 TYR B 377 ARG 0.005 0.001 ARG A1029 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 229 time to evaluate : 4.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 683 TYR cc_start: 0.9304 (OUTLIER) cc_final: 0.9094 (t80) REVERT: A 695 THR cc_start: 0.8947 (p) cc_final: 0.8669 (t) REVERT: A 741 GLN cc_start: 0.8843 (mt0) cc_final: 0.8537 (mm110) REVERT: A 959 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9212 (mm) REVERT: O 1 MET cc_start: 0.5107 (mtt) cc_final: 0.4645 (mpp) REVERT: S 49 SER cc_start: 0.8782 (t) cc_final: 0.8036 (p) REVERT: S 134 TYR cc_start: 0.8119 (p90) cc_final: 0.7872 (p90) REVERT: S 141 ASP cc_start: 0.7260 (t0) cc_final: 0.6855 (p0) outliers start: 32 outliers final: 12 residues processed: 261 average time/residue: 3.1463 time to fit residues: 983.6744 Evaluate side-chains 178 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 164 time to evaluate : 4.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 296 LYS Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 281 HIS Chi-restraints excluded: chain O residue 333 TYR Chi-restraints excluded: chain O residue 362 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 455 random chunks: chunk 384 optimal weight: 4.9990 chunk 344 optimal weight: 40.0000 chunk 191 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 232 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 356 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 chunk 216 optimal weight: 6.9990 chunk 265 optimal weight: 10.0000 chunk 413 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 GLN A 962 ASN G 127 ASN I 123 ASN ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 229 GLN I 257 ASN O 21 ASN O 52 ASN O 254 ASN S 97 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 39152 Z= 0.409 Angle : 0.579 6.997 53219 Z= 0.327 Chirality : 0.043 0.182 6059 Planarity : 0.004 0.048 6473 Dihedral : 13.680 172.104 5834 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.79 % Allowed : 5.76 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.13), residues: 4512 helix: 1.68 (0.13), residues: 1725 sheet: -0.18 (0.19), residues: 762 loop : -0.36 (0.14), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 310 HIS 0.011 0.001 HIS B1064 PHE 0.024 0.002 PHE A 938 TYR 0.014 0.001 TYR C 169 ARG 0.008 0.001 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 167 time to evaluate : 4.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 683 TYR cc_start: 0.9209 (OUTLIER) cc_final: 0.8918 (t80) REVERT: A 695 THR cc_start: 0.8996 (p) cc_final: 0.8729 (t) REVERT: H 46 MET cc_start: 0.7884 (tpp) cc_final: 0.6966 (tpp) REVERT: O 1 MET cc_start: 0.5142 (mtt) cc_final: 0.4635 (mpp) REVERT: S 46 GLU cc_start: 0.9256 (tm-30) cc_final: 0.9000 (tm-30) REVERT: S 49 SER cc_start: 0.8701 (t) cc_final: 0.8168 (p) REVERT: S 141 ASP cc_start: 0.7499 (t0) cc_final: 0.7047 (p0) outliers start: 33 outliers final: 14 residues processed: 195 average time/residue: 3.2183 time to fit residues: 752.3273 Evaluate side-chains 174 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 159 time to evaluate : 4.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 356 MET Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain O residue 281 HIS Chi-restraints excluded: chain O residue 333 TYR Chi-restraints excluded: chain O residue 362 VAL Chi-restraints excluded: chain S residue 134 TYR Chi-restraints excluded: chain S residue 136 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 455 random chunks: chunk 229 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 343 optimal weight: 8.9990 chunk 281 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 413 optimal weight: 20.0000 chunk 447 optimal weight: 20.0000 chunk 368 optimal weight: 3.9990 chunk 410 optimal weight: 9.9990 chunk 141 optimal weight: 2.9990 chunk 332 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 139 GLN I 178 GLN I 229 GLN I 257 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 39152 Z= 0.212 Angle : 0.508 10.640 53219 Z= 0.283 Chirality : 0.042 0.167 6059 Planarity : 0.004 0.065 6473 Dihedral : 13.646 172.469 5822 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.75 % Favored : 96.23 % Rotamer: Outliers : 0.55 % Allowed : 6.45 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.13), residues: 4512 helix: 1.83 (0.13), residues: 1721 sheet: -0.24 (0.19), residues: 725 loop : -0.43 (0.14), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1148 HIS 0.009 0.001 HIS B1064 PHE 0.024 0.001 PHE A 938 TYR 0.069 0.001 TYR S 134 ARG 0.005 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 166 time to evaluate : 4.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7203 (tpp) cc_final: 0.7000 (tpp) REVERT: A 536 MET cc_start: 0.8785 (mmt) cc_final: 0.8561 (mmm) REVERT: A 683 TYR cc_start: 0.9158 (OUTLIER) cc_final: 0.8901 (t80) REVERT: A 695 THR cc_start: 0.9060 (p) cc_final: 0.8420 (t) REVERT: H 46 MET cc_start: 0.7922 (tpp) cc_final: 0.7098 (tpp) REVERT: O 1 MET cc_start: 0.5148 (mtt) cc_final: 0.4655 (mpp) REVERT: S 43 TRP cc_start: 0.7699 (t60) cc_final: 0.6747 (t60) REVERT: S 49 SER cc_start: 0.8679 (t) cc_final: 0.8147 (p) REVERT: S 64 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7942 (mt-10) REVERT: S 141 ASP cc_start: 0.7459 (t0) cc_final: 0.7011 (p0) outliers start: 23 outliers final: 12 residues processed: 182 average time/residue: 3.2860 time to fit residues: 719.0744 Evaluate side-chains 169 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 156 time to evaluate : 4.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain I residue 81 LYS Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain O residue 281 HIS Chi-restraints excluded: chain O residue 333 TYR Chi-restraints excluded: chain O residue 362 VAL Chi-restraints excluded: chain S residue 134 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 455 random chunks: chunk 408 optimal weight: 0.9980 chunk 311 optimal weight: 20.0000 chunk 214 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 197 optimal weight: 9.9990 chunk 277 optimal weight: 0.0170 chunk 415 optimal weight: 9.9990 chunk 439 optimal weight: 8.9990 chunk 217 optimal weight: 8.9990 chunk 393 optimal weight: 5.9990 chunk 118 optimal weight: 0.1980 overall best weight: 2.4422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 822 GLN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 139 GLN ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 229 GLN I 257 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39152 Z= 0.215 Angle : 0.503 8.521 53219 Z= 0.277 Chirality : 0.041 0.165 6059 Planarity : 0.003 0.062 6473 Dihedral : 13.622 172.336 5818 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.28 % Favored : 95.70 % Rotamer: Outliers : 0.46 % Allowed : 6.93 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.13), residues: 4512 helix: 1.91 (0.13), residues: 1721 sheet: -0.33 (0.19), residues: 733 loop : -0.46 (0.14), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 205 HIS 0.005 0.001 HIS A 62 PHE 0.024 0.001 PHE A 938 TYR 0.029 0.001 TYR S 134 ARG 0.008 0.000 ARG B1047 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 163 time to evaluate : 4.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 536 MET cc_start: 0.8791 (mmt) cc_final: 0.8552 (mmm) REVERT: A 683 TYR cc_start: 0.9183 (OUTLIER) cc_final: 0.8873 (t80) REVERT: B 755 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8346 (tp30) REVERT: H 46 MET cc_start: 0.7987 (tpp) cc_final: 0.7279 (tpp) REVERT: O 1 MET cc_start: 0.5011 (mtt) cc_final: 0.4551 (mpp) REVERT: S 43 TRP cc_start: 0.7762 (t60) cc_final: 0.6842 (t60) REVERT: S 49 SER cc_start: 0.8648 (t) cc_final: 0.8098 (p) REVERT: S 141 ASP cc_start: 0.7536 (t0) cc_final: 0.7077 (p0) outliers start: 19 outliers final: 12 residues processed: 179 average time/residue: 3.1853 time to fit residues: 686.6053 Evaluate side-chains 170 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 157 time to evaluate : 4.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain H residue 218 MET Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain O residue 281 HIS Chi-restraints excluded: chain O residue 333 TYR Chi-restraints excluded: chain O residue 362 VAL Chi-restraints excluded: chain S residue 134 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 455 random chunks: chunk 366 optimal weight: 20.0000 chunk 249 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 327 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 chunk 375 optimal weight: 50.0000 chunk 304 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 224 optimal weight: 0.3980 chunk 394 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN B 314 ASN C 136 GLN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39152 Z= 0.219 Angle : 0.501 8.509 53219 Z= 0.275 Chirality : 0.041 0.158 6059 Planarity : 0.003 0.062 6473 Dihedral : 13.611 172.281 5817 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.24 % Favored : 95.74 % Rotamer: Outliers : 0.46 % Allowed : 7.27 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.13), residues: 4512 helix: 1.90 (0.13), residues: 1730 sheet: -0.32 (0.19), residues: 742 loop : -0.48 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1148 HIS 0.007 0.001 HIS H 310 PHE 0.024 0.001 PHE A 938 TYR 0.024 0.001 TYR S 134 ARG 0.008 0.000 ARG B1047 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 160 time to evaluate : 4.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 536 MET cc_start: 0.8810 (mmt) cc_final: 0.8571 (mmm) REVERT: A 683 TYR cc_start: 0.9206 (OUTLIER) cc_final: 0.8918 (t80) REVERT: B 755 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8317 (tp30) REVERT: C 112 MET cc_start: 0.7980 (ttm) cc_final: 0.7653 (ttm) REVERT: H 1 MET cc_start: 0.5959 (ttt) cc_final: 0.5422 (ptt) REVERT: H 46 MET cc_start: 0.7874 (tpp) cc_final: 0.7267 (tpp) REVERT: O 1 MET cc_start: 0.4982 (mtt) cc_final: 0.4556 (mpp) REVERT: S 49 SER cc_start: 0.8658 (t) cc_final: 0.8133 (p) REVERT: S 141 ASP cc_start: 0.7556 (t0) cc_final: 0.7119 (p0) outliers start: 19 outliers final: 12 residues processed: 175 average time/residue: 3.1001 time to fit residues: 658.2708 Evaluate side-chains 170 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 157 time to evaluate : 4.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain H residue 218 MET Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain O residue 281 HIS Chi-restraints excluded: chain O residue 333 TYR Chi-restraints excluded: chain O residue 362 VAL Chi-restraints excluded: chain S residue 134 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 455 random chunks: chunk 147 optimal weight: 7.9990 chunk 396 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 258 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 440 optimal weight: 20.0000 chunk 365 optimal weight: 9.9990 chunk 203 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 231 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 641 ASN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 39152 Z= 0.293 Angle : 0.518 8.251 53219 Z= 0.286 Chirality : 0.041 0.160 6059 Planarity : 0.003 0.057 6473 Dihedral : 13.631 172.341 5817 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.57 % Favored : 95.41 % Rotamer: Outliers : 0.50 % Allowed : 7.39 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.13), residues: 4512 helix: 1.83 (0.13), residues: 1736 sheet: -0.35 (0.19), residues: 742 loop : -0.54 (0.14), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 365 HIS 0.007 0.001 HIS H 310 PHE 0.024 0.001 PHE A 938 TYR 0.019 0.001 TYR S 134 ARG 0.010 0.000 ARG B1047 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 158 time to evaluate : 4.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 536 MET cc_start: 0.8870 (mmt) cc_final: 0.8629 (mmm) REVERT: A 683 TYR cc_start: 0.9210 (OUTLIER) cc_final: 0.8939 (t80) REVERT: B 256 MET cc_start: 0.8755 (mmt) cc_final: 0.8388 (mmt) REVERT: B 755 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8357 (tp30) REVERT: C 112 MET cc_start: 0.7993 (ttm) cc_final: 0.7676 (ttm) REVERT: H 1 MET cc_start: 0.6145 (ttt) cc_final: 0.5643 (ptt) REVERT: H 46 MET cc_start: 0.7870 (tpp) cc_final: 0.7303 (tpp) REVERT: O 1 MET cc_start: 0.4990 (mtt) cc_final: 0.4577 (mpp) REVERT: S 49 SER cc_start: 0.8694 (t) cc_final: 0.8170 (p) REVERT: S 141 ASP cc_start: 0.7404 (t0) cc_final: 0.6983 (p0) outliers start: 21 outliers final: 16 residues processed: 174 average time/residue: 3.0522 time to fit residues: 643.0508 Evaluate side-chains 173 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 156 time to evaluate : 4.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain H residue 218 MET Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 356 MET Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain O residue 281 HIS Chi-restraints excluded: chain O residue 333 TYR Chi-restraints excluded: chain O residue 362 VAL Chi-restraints excluded: chain S residue 102 THR Chi-restraints excluded: chain S residue 134 TYR Chi-restraints excluded: chain S residue 136 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 455 random chunks: chunk 424 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 250 optimal weight: 1.9990 chunk 321 optimal weight: 20.0000 chunk 249 optimal weight: 0.9990 chunk 370 optimal weight: 30.0000 chunk 245 optimal weight: 2.9990 chunk 438 optimal weight: 5.9990 chunk 274 optimal weight: 6.9990 chunk 267 optimal weight: 5.9990 chunk 202 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 39152 Z= 0.205 Angle : 0.496 8.094 53219 Z= 0.273 Chirality : 0.041 0.159 6059 Planarity : 0.003 0.059 6473 Dihedral : 13.616 172.661 5817 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.17 % Favored : 95.81 % Rotamer: Outliers : 0.55 % Allowed : 7.63 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.13), residues: 4512 helix: 1.92 (0.13), residues: 1739 sheet: -0.37 (0.19), residues: 743 loop : -0.50 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1148 HIS 0.011 0.001 HIS H 310 PHE 0.023 0.001 PHE A 938 TYR 0.012 0.001 TYR C 169 ARG 0.009 0.000 ARG B1047 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 160 time to evaluate : 4.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7457 (tpp) cc_final: 0.7139 (tpp) REVERT: A 536 MET cc_start: 0.8832 (mmt) cc_final: 0.8595 (mmm) REVERT: A 683 TYR cc_start: 0.9181 (OUTLIER) cc_final: 0.8930 (t80) REVERT: A 959 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9342 (mm) REVERT: B 256 MET cc_start: 0.8746 (mmt) cc_final: 0.8367 (mmt) REVERT: B 755 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8335 (tp30) REVERT: B 819 MET cc_start: 0.9233 (mtm) cc_final: 0.8923 (mtm) REVERT: C 112 MET cc_start: 0.7996 (ttm) cc_final: 0.7677 (ttm) REVERT: H 1 MET cc_start: 0.6049 (ttt) cc_final: 0.5548 (ptt) REVERT: H 46 MET cc_start: 0.7868 (tpp) cc_final: 0.7369 (tpp) REVERT: S 49 SER cc_start: 0.8644 (t) cc_final: 0.8245 (p) REVERT: S 141 ASP cc_start: 0.7483 (t0) cc_final: 0.7034 (p0) outliers start: 23 outliers final: 15 residues processed: 177 average time/residue: 3.0037 time to fit residues: 645.7543 Evaluate side-chains 175 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 158 time to evaluate : 4.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain H residue 218 MET Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 356 MET Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain O residue 281 HIS Chi-restraints excluded: chain O residue 333 TYR Chi-restraints excluded: chain O residue 362 VAL Chi-restraints excluded: chain S residue 102 THR Chi-restraints excluded: chain S residue 134 TYR Chi-restraints excluded: chain S residue 136 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 455 random chunks: chunk 271 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 278 optimal weight: 7.9990 chunk 298 optimal weight: 4.9990 chunk 216 optimal weight: 0.5980 chunk 40 optimal weight: 8.9990 chunk 344 optimal weight: 50.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 39152 Z= 0.318 Angle : 0.529 10.568 53219 Z= 0.291 Chirality : 0.041 0.160 6059 Planarity : 0.003 0.063 6473 Dihedral : 13.645 172.822 5817 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.68 % Favored : 95.30 % Rotamer: Outliers : 0.55 % Allowed : 7.87 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.13), residues: 4512 helix: 1.82 (0.13), residues: 1739 sheet: -0.37 (0.19), residues: 744 loop : -0.57 (0.14), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 43 HIS 0.009 0.001 HIS H 310 PHE 0.024 0.001 PHE A 938 TYR 0.016 0.001 TYR O 409 ARG 0.009 0.000 ARG B1047 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 156 time to evaluate : 4.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7462 (tpp) cc_final: 0.7154 (tpp) REVERT: A 536 MET cc_start: 0.8892 (mmt) cc_final: 0.8658 (mmm) REVERT: A 683 TYR cc_start: 0.9198 (OUTLIER) cc_final: 0.8966 (t80) REVERT: A 959 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9349 (mm) REVERT: B 256 MET cc_start: 0.8770 (mmt) cc_final: 0.8410 (mmt) REVERT: B 755 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8355 (tp30) REVERT: C 112 MET cc_start: 0.8022 (ttm) cc_final: 0.7698 (ttm) REVERT: H 1 MET cc_start: 0.6188 (ttt) cc_final: 0.5797 (ptt) REVERT: H 46 MET cc_start: 0.7883 (tpp) cc_final: 0.7390 (tpp) REVERT: O 1 MET cc_start: 0.5048 (mtt) cc_final: 0.4642 (mpp) REVERT: S 49 SER cc_start: 0.8764 (t) cc_final: 0.8270 (p) REVERT: S 141 ASP cc_start: 0.7442 (t0) cc_final: 0.7007 (p0) outliers start: 23 outliers final: 18 residues processed: 173 average time/residue: 3.0686 time to fit residues: 649.6980 Evaluate side-chains 174 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 154 time to evaluate : 4.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain B residue 649 MET Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 356 MET Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain O residue 281 HIS Chi-restraints excluded: chain O residue 333 TYR Chi-restraints excluded: chain O residue 362 VAL Chi-restraints excluded: chain S residue 102 THR Chi-restraints excluded: chain S residue 134 TYR Chi-restraints excluded: chain S residue 136 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 455 random chunks: chunk 398 optimal weight: 6.9990 chunk 420 optimal weight: 9.9990 chunk 383 optimal weight: 5.9990 chunk 408 optimal weight: 0.7980 chunk 245 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 320 optimal weight: 20.0000 chunk 125 optimal weight: 0.9990 chunk 369 optimal weight: 20.0000 chunk 386 optimal weight: 10.0000 chunk 407 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 39152 Z= 0.219 Angle : 0.509 11.295 53219 Z= 0.278 Chirality : 0.041 0.159 6059 Planarity : 0.003 0.064 6473 Dihedral : 13.644 173.262 5817 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.28 % Favored : 95.70 % Rotamer: Outliers : 0.58 % Allowed : 7.72 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.13), residues: 4512 helix: 1.88 (0.13), residues: 1740 sheet: -0.45 (0.19), residues: 756 loop : -0.54 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 43 HIS 0.011 0.001 HIS A 62 PHE 0.023 0.001 PHE A 938 TYR 0.022 0.001 TYR O 409 ARG 0.011 0.000 ARG B1047 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 160 time to evaluate : 4.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7488 (tpp) cc_final: 0.7188 (tpp) REVERT: A 536 MET cc_start: 0.8864 (mmt) cc_final: 0.8583 (mmm) REVERT: A 683 TYR cc_start: 0.9195 (OUTLIER) cc_final: 0.8980 (t80) REVERT: A 959 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9342 (mm) REVERT: B 256 MET cc_start: 0.8787 (mmt) cc_final: 0.8441 (mmt) REVERT: B 650 MET cc_start: 0.7950 (ptp) cc_final: 0.7521 (ptp) REVERT: B 755 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8338 (tp30) REVERT: B 819 MET cc_start: 0.9260 (mtm) cc_final: 0.8995 (mtm) REVERT: C 112 MET cc_start: 0.8007 (ttm) cc_final: 0.7696 (ttm) REVERT: H 1 MET cc_start: 0.6213 (ttt) cc_final: 0.5803 (ptt) REVERT: H 46 MET cc_start: 0.7954 (tpp) cc_final: 0.7473 (tpp) REVERT: S 49 SER cc_start: 0.8700 (t) cc_final: 0.8280 (p) REVERT: S 141 ASP cc_start: 0.7436 (t0) cc_final: 0.6998 (p0) outliers start: 24 outliers final: 17 residues processed: 178 average time/residue: 3.0605 time to fit residues: 661.2164 Evaluate side-chains 175 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 156 time to evaluate : 4.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain B residue 649 MET Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 356 MET Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain O residue 281 HIS Chi-restraints excluded: chain O residue 333 TYR Chi-restraints excluded: chain O residue 362 VAL Chi-restraints excluded: chain S residue 134 TYR Chi-restraints excluded: chain S residue 136 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 455 random chunks: chunk 268 optimal weight: 1.9990 chunk 432 optimal weight: 0.8980 chunk 263 optimal weight: 6.9990 chunk 205 optimal weight: 0.9980 chunk 300 optimal weight: 10.0000 chunk 453 optimal weight: 10.0000 chunk 417 optimal weight: 10.0000 chunk 360 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 278 optimal weight: 6.9990 chunk 221 optimal weight: 5.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 39152 Z= 0.262 Angle : 0.525 11.747 53219 Z= 0.286 Chirality : 0.041 0.161 6059 Planarity : 0.003 0.058 6473 Dihedral : 13.645 172.772 5817 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.55 % Favored : 95.43 % Rotamer: Outliers : 0.46 % Allowed : 7.91 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.13), residues: 4512 helix: 1.83 (0.13), residues: 1741 sheet: -0.47 (0.19), residues: 756 loop : -0.57 (0.14), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP S 43 HIS 0.011 0.001 HIS A 62 PHE 0.024 0.001 PHE A 938 TYR 0.022 0.001 TYR O 409 ARG 0.011 0.000 ARG B1047 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 155 time to evaluate : 4.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7538 (tpp) cc_final: 0.7224 (tpp) REVERT: A 536 MET cc_start: 0.8874 (mmt) cc_final: 0.8596 (mmm) REVERT: A 959 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9343 (mm) REVERT: B 256 MET cc_start: 0.8759 (mmt) cc_final: 0.8400 (mmt) REVERT: B 650 MET cc_start: 0.7977 (ptp) cc_final: 0.7544 (ptp) REVERT: B 755 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8371 (tp30) REVERT: B 819 MET cc_start: 0.9275 (mtm) cc_final: 0.9022 (mtm) REVERT: C 112 MET cc_start: 0.7996 (ttm) cc_final: 0.7687 (ttm) REVERT: H 1 MET cc_start: 0.6242 (ttt) cc_final: 0.5842 (ptt) REVERT: H 46 MET cc_start: 0.7963 (tpp) cc_final: 0.7481 (tpp) REVERT: S 49 SER cc_start: 0.8698 (t) cc_final: 0.8413 (p) REVERT: S 141 ASP cc_start: 0.7450 (t0) cc_final: 0.7009 (p0) outliers start: 19 outliers final: 16 residues processed: 169 average time/residue: 2.9921 time to fit residues: 615.4117 Evaluate side-chains 171 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 154 time to evaluate : 4.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain B residue 649 MET Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 356 MET Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain O residue 281 HIS Chi-restraints excluded: chain O residue 333 TYR Chi-restraints excluded: chain O residue 362 VAL Chi-restraints excluded: chain S residue 134 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 455 random chunks: chunk 286 optimal weight: 0.2980 chunk 384 optimal weight: 0.1980 chunk 110 optimal weight: 0.7980 chunk 332 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 361 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 371 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 260 ASN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.058459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.045795 restraints weight = 966947.974| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 4.96 r_work: 0.3197 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 39152 Z= 0.153 Angle : 0.500 11.786 53219 Z= 0.270 Chirality : 0.042 0.160 6059 Planarity : 0.003 0.055 6473 Dihedral : 13.580 172.052 5815 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.88 % Favored : 96.10 % Rotamer: Outliers : 0.36 % Allowed : 7.96 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.13), residues: 4512 helix: 2.05 (0.13), residues: 1729 sheet: -0.45 (0.19), residues: 758 loop : -0.47 (0.14), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP S 43 HIS 0.009 0.001 HIS A 62 PHE 0.023 0.001 PHE A 938 TYR 0.018 0.001 TYR O 409 ARG 0.011 0.000 ARG B1047 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16189.27 seconds wall clock time: 278 minutes 46.62 seconds (16726.62 seconds total)