Starting phenix.real_space_refine on Tue Jun 24 19:47:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q3k_18129/06_2025/8q3k_18129.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q3k_18129/06_2025/8q3k_18129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q3k_18129/06_2025/8q3k_18129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q3k_18129/06_2025/8q3k_18129.map" model { file = "/net/cci-nas-00/data/ceres_data/8q3k_18129/06_2025/8q3k_18129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q3k_18129/06_2025/8q3k_18129.cif" } resolution = 2.92 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= -0.001 sd= 1.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 Mg 1 5.21 5 S 172 5.16 5 C 18422 2.51 5 N 4975 2.21 5 O 5356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28932 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 11322 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1420, 11312 Classifications: {'peptide': 1420} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 64, 'TRANS': 1353} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 1420, 11312 Classifications: {'peptide': 1420} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 64, 'TRANS': 1353} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 11520 Chain: "B" Number of atoms: 8030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 8030 Classifications: {'peptide': 1020} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 44, 'TRANS': 975} Chain breaks: 10 Chain: "C" Number of atoms: 2910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2910 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 338} Chain: "D" Number of atoms: 2692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2692 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain: "E" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1657 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 192} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 863 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "I" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 816 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "J" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 635 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 74} 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: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "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 450 SG CYS A 59 107.816 98.761 42.488 1.00 86.41 S ATOM 471 SG CYS A 62 107.021 100.522 45.334 1.00 71.92 S ATOM 531 SG CYS A 69 105.716 97.274 45.051 1.00 83.49 S ATOM 775 SG CYS A 99 66.131 105.363 20.547 1.00118.51 S ATOM 797 SG CYS A 102 66.932 109.014 21.076 1.00134.38 S ATOM 1049 SG CYS A 134 63.296 107.900 20.505 1.00138.90 S ATOM 1074 SG CYS A 137 65.955 108.142 17.713 1.00146.89 S ATOM 18871 SG CYS B1180 96.584 111.901 46.458 1.00 69.85 S ATOM 18896 SG CYS B1183 94.249 109.844 44.214 1.00 75.61 S ATOM 19012 SG CYS B1198 97.672 110.530 43.165 1.00 75.44 S ATOM 19034 SG CYS B1201 95.261 113.410 43.086 1.00 87.59 S ATOM 27505 SG CYS I 4 37.849 51.884 23.230 1.00173.47 S ATOM 27525 SG CYS I 7 41.188 51.316 21.533 1.00178.88 S ATOM 27659 SG CYS I 24 40.029 54.848 22.764 1.00192.87 S ATOM 27671 SG CYS I 26 38.522 53.280 19.696 1.00192.54 S ATOM 28041 SG CYS I 73 41.829 24.796 67.709 1.00121.59 S ATOM 28062 SG CYS I 76 42.988 21.889 65.445 1.00132.46 S ATOM 28219 SG CYS I 96 44.923 25.332 65.739 1.00121.17 S ATOM 28236 SG CYS I 98 41.671 24.997 63.871 1.00113.90 S ATOM 28341 SG CYS J 7 107.789 44.797 91.326 1.00 68.06 S ATOM 28365 SG CYS J 10 107.668 45.778 95.201 1.00 82.43 S ATOM 28788 SG CYS J 65 104.960 44.579 93.889 1.00 63.37 S ATOM 28794 SG CYS J 66 107.933 42.068 94.022 1.00 65.98 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A 356 " occ=0.46 ... (18 atoms not shown) pdb=" NE2BHIS A 356 " occ=0.54 Time building chain proxies: 21.41, per 1000 atoms: 0.74 Number of scatterers: 28932 At special positions: 0 Unit cell: (147.384, 172.224, 138.276, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 172 16.00 Mg 1 11.99 O 5356 8.00 N 4975 7.00 C 18422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.32 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A 72 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 69 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 62 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 59 " pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 137 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 134 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 99 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1198 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1183 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1180 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1201 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 4 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 26 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 24 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 98 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 73 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 96 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 76 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 65 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 66 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " Number of angles added : 33 7188 Ramachandran restraints generated. 3594 Oldfield, 0 Emsley, 3594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6874 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 42 sheets defined 43.8% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.25 Creating SS restraints... Processing helix chain 'A' and resid 17 through 25 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 87 through 98 Processing helix chain 'A' and resid 108 through 114 removed outlier: 3.799A pdb=" N TYR A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N HIS A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 127 removed outlier: 4.361A pdb=" N LEU A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 removed outlier: 3.740A pdb=" N ARG A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 186 removed outlier: 3.545A pdb=" N VAL A 182 " --> pdb=" O THR A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 Proline residue: A 193 - end of helix Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 225 through 240 removed outlier: 3.948A pdb=" N VAL A 229 " --> pdb=" O ASP A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 272 Processing helix chain 'A' and resid 299 through 303 removed outlier: 3.563A pdb=" N ARG A 302 " --> pdb=" O ILE A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 342 through 348 Processing helix chain 'A' and resid 358 through 369 Proline residue: A 364 - end of helix Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'A' and resid 450 through 455 removed outlier: 4.051A pdb=" N TYR A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 482 through 488 removed outlier: 4.205A pdb=" N ILE A 488 " --> pdb=" O ASN A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 512 Processing helix chain 'A' and resid 524 through 531 removed outlier: 3.867A pdb=" N PHE A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 561 Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.568A pdb=" N MET A 582 " --> pdb=" O ALA A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 590 removed outlier: 4.383A pdb=" N SER A 590 " --> pdb=" O LYS A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 615 through 625 Processing helix chain 'A' and resid 625 through 647 removed outlier: 3.786A pdb=" N ASN A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 657 Processing helix chain 'A' and resid 659 through 687 Processing helix chain 'A' and resid 696 through 709 Processing helix chain 'A' and resid 715 through 723 removed outlier: 3.904A pdb=" N ILE A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 781 through 785 Processing helix chain 'A' and resid 797 through 834 removed outlier: 4.119A pdb=" N TYR A 824 " --> pdb=" O SER A 820 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA A 825 " --> pdb=" O SER A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 858 Processing helix chain 'A' and resid 876 through 885 Processing helix chain 'A' and resid 891 through 918 removed outlier: 3.898A pdb=" N GLU A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 945 Processing helix chain 'A' and resid 953 through 971 Processing helix chain 'A' and resid 972 through 976 Processing helix chain 'A' and resid 977 through 984 removed outlier: 3.732A pdb=" N GLU A 981 " --> pdb=" O ASN A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1006 removed outlier: 4.340A pdb=" N LEU A 997 " --> pdb=" O ARG A 993 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N MET A 998 " --> pdb=" O ALA A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1034 removed outlier: 3.552A pdb=" N LEU A1034 " --> pdb=" O TYR A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1064 Proline residue: A1052 - end of helix removed outlier: 4.207A pdb=" N GLN A1055 " --> pdb=" O GLU A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1082 Processing helix chain 'A' and resid 1085 through 1089 Processing helix chain 'A' and resid 1106 through 1118 removed outlier: 3.589A pdb=" N ALA A1110 " --> pdb=" O ASN A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 4.090A pdb=" N SER A1150 " --> pdb=" O ASP A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1162 removed outlier: 3.511A pdb=" N THR A1156 " --> pdb=" O VAL A1152 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP A1157 " --> pdb=" O GLU A1153 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU A1159 " --> pdb=" O MET A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1189 Processing helix chain 'A' and resid 1191 through 1203 Processing helix chain 'A' and resid 1229 through 1234 removed outlier: 3.571A pdb=" N ARG A1234 " --> pdb=" O SER A1230 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1237 No H-bonds generated for 'chain 'A' and resid 1235 through 1237' Processing helix chain 'A' and resid 1242 through 1257 Processing helix chain 'A' and resid 1299 through 1306 Processing helix chain 'A' and resid 1310 through 1314 removed outlier: 3.836A pdb=" N ILE A1314 " --> pdb=" O PRO A1311 " (cutoff:3.500A) Processing helix chain 'A' and resid 1318 through 1326 Processing helix chain 'A' and resid 1327 through 1344 removed outlier: 3.539A pdb=" N GLY A1344 " --> pdb=" O ARG A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1349 through 1361 removed outlier: 3.955A pdb=" N LEU A1353 " --> pdb=" O ASN A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1378 Processing helix chain 'A' and resid 1381 through 1389 Processing helix chain 'A' and resid 1390 through 1402 Processing helix chain 'A' and resid 1410 through 1416 Processing helix chain 'A' and resid 1422 through 1426 Processing helix chain 'A' and resid 1432 through 1440 Processing helix chain 'B' and resid 22 through 38 removed outlier: 3.796A pdb=" N LEU B 27 " --> pdb=" O GLU B 23 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHE B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE B 30 " --> pdb=" O MET B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 53 Processing helix chain 'B' and resid 53 through 61 removed outlier: 3.540A pdb=" N GLN B 61 " --> pdb=" O GLN B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 175 through 183 Processing helix chain 'B' and resid 272 through 280 removed outlier: 3.523A pdb=" N PHE B 279 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 293 removed outlier: 3.691A pdb=" N VAL B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 314 removed outlier: 3.516A pdb=" N GLU B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 340 removed outlier: 3.730A pdb=" N LEU B 336 " --> pdb=" O ILE B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 372 removed outlier: 3.730A pdb=" N THR B 366 " --> pdb=" O GLU B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 377 Processing helix chain 'B' and resid 382 through 403 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 420 through 439 removed outlier: 3.746A pdb=" N ALA B 428 " --> pdb=" O SER B 424 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 431 " --> pdb=" O LYS B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 488 removed outlier: 4.228A pdb=" N ARG B 480 " --> pdb=" O SER B 476 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 522 Processing helix chain 'B' and resid 526 through 532 Processing helix chain 'B' and resid 538 through 543 Processing helix chain 'B' and resid 582 through 593 removed outlier: 3.556A pdb=" N LEU B 586 " --> pdb=" O GLU B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 611 removed outlier: 3.817A pdb=" N VAL B 608 " --> pdb=" O ASN B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 642 Processing helix chain 'B' and resid 679 through 696 Processing helix chain 'B' and resid 700 through 705 removed outlier: 4.023A pdb=" N HIS B 704 " --> pdb=" O ASP B 700 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 705 " --> pdb=" O TRP B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 700 through 705' Processing helix chain 'B' and resid 715 through 725 Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 754 through 761 Processing helix chain 'B' and resid 774 through 779 removed outlier: 3.504A pdb=" N ILE B 778 " --> pdb=" O PRO B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 785 Processing helix chain 'B' and resid 788 through 792 Processing helix chain 'B' and resid 836 through 841 Processing helix chain 'B' and resid 869 through 875 removed outlier: 3.627A pdb=" N GLY B 875 " --> pdb=" O PHE B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 1032 through 1037 removed outlier: 3.639A pdb=" N ARG B1036 " --> pdb=" O SER B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1038 through 1055 removed outlier: 3.636A pdb=" N MET B1042 " --> pdb=" O THR B1038 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA B1050 " --> pdb=" O THR B1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1079 Processing helix chain 'B' and resid 1114 through 1119 removed outlier: 3.873A pdb=" N ASP B1118 " --> pdb=" O PHE B1114 " (cutoff:3.500A) Processing helix chain 'B' and resid 1148 through 1159 Processing helix chain 'B' and resid 1160 through 1170 Processing helix chain 'B' and resid 1214 through 1226 Processing helix chain 'C' and resid 19 through 30 Processing helix chain 'C' and resid 51 through 64 Processing helix chain 'C' and resid 89 through 99 Processing helix chain 'C' and resid 128 through 130 No H-bonds generated for 'chain 'C' and resid 128 through 130' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 230 through 259 Processing helix chain 'C' and resid 287 through 302 Processing helix chain 'C' and resid 328 through 359 removed outlier: 3.721A pdb=" N ASP C 355 " --> pdb=" O GLU C 351 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA C 359 " --> pdb=" O ASP C 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 118 through 123 removed outlier: 3.682A pdb=" N ASN D 122 " --> pdb=" O GLU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 195 removed outlier: 3.932A pdb=" N ASN D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS D 180 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU D 181 " --> pdb=" O ASN D 177 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS D 194 " --> pdb=" O GLU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 208 removed outlier: 3.670A pdb=" N ILE D 200 " --> pdb=" O ASP D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 247 Processing helix chain 'D' and resid 288 through 314 Processing helix chain 'D' and resid 316 through 323 removed outlier: 3.555A pdb=" N ILE D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 334 removed outlier: 3.630A pdb=" N ARG D 333 " --> pdb=" O LEU D 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 17 removed outlier: 4.180A pdb=" N TYR E 11 " --> pdb=" O PHE E 7 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU E 12 " --> pdb=" O THR E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 39 Processing helix chain 'E' and resid 62 through 67 Processing helix chain 'E' and resid 67 through 81 removed outlier: 3.538A pdb=" N MET E 71 " --> pdb=" O HIS E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 99 removed outlier: 3.615A pdb=" N LEU E 97 " --> pdb=" O ASP E 93 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER E 98 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS E 99 " --> pdb=" O PRO E 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 93 through 99' Processing helix chain 'E' and resid 99 through 113 removed outlier: 3.724A pdb=" N LEU E 103 " --> pdb=" O LYS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 126 No H-bonds generated for 'chain 'E' and resid 124 through 126' Processing helix chain 'E' and resid 129 through 133 Processing helix chain 'E' and resid 143 through 155 Processing helix chain 'E' and resid 157 through 161 Processing helix chain 'E' and resid 168 through 175 Processing helix chain 'F' and resid 44 through 49 removed outlier: 3.689A pdb=" N GLY F 48 " --> pdb=" O SER F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 65 removed outlier: 3.544A pdb=" N ARG F 65 " --> pdb=" O ASP F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 90 Processing helix chain 'F' and resid 101 through 112 Processing helix chain 'I' and resid 33 through 38 removed outlier: 4.140A pdb=" N LEU I 38 " --> pdb=" O GLN I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 60 Processing helix chain 'I' and resid 61 through 63 No H-bonds generated for 'chain 'I' and resid 61 through 63' Processing helix chain 'J' and resid 13 through 16 Processing helix chain 'J' and resid 17 through 34 Processing helix chain 'J' and resid 42 through 47 Processing helix chain 'J' and resid 51 through 59 removed outlier: 3.529A pdb=" N LEU J 58 " --> pdb=" O LEU J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 73 removed outlier: 3.506A pdb=" N THR J 73 " --> pdb=" O HIS J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 80 removed outlier: 3.518A pdb=" N TYR J 79 " --> pdb=" O ASP J 75 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.245A pdb=" N GLY A 4 " --> pdb=" O MET B1209 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ASP B1211 " --> pdb=" O GLY A 4 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU B1185 " --> pdb=" O CYS B1180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1404 through 1406 removed outlier: 6.569A pdb=" N VAL B1233 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL A 11 " --> pdb=" O THR B1231 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR B1231 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE A 13 " --> pdb=" O ASN B1229 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASN B1229 " --> pdb=" O PHE A 13 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 27 through 28 removed outlier: 6.661A pdb=" N MET A 27 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLN A 77 " --> pdb=" O MET A 27 " (cutoff:3.500A) removed outlier: 10.612A pdb=" N ALA A 80 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA A 200 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 146 removed outlier: 4.719A pdb=" N PHE A 154 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 317 through 319 Processing sheet with id=AA6, first strand: chain 'B' and resid 1120 through 1121 removed outlier: 6.074A pdb=" N VAL A 338 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU A 436 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TYR A 340 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N PHE A 444 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR A 326 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N MET A 446 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N CYS A 328 " --> pdb=" O MET A 446 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 349 through 353 removed outlier: 4.061A pdb=" N ARG A 378 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASP A 408 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N CYS A 376 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 386 " --> pdb=" O LYS A 381 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 521 through 523 Processing sheet with id=AA9, first strand: chain 'A' and resid 567 through 569 removed outlier: 6.729A pdb=" N GLN A 592 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 753 through 754 Processing sheet with id=AB2, first strand: chain 'A' and resid 837 through 838 removed outlier: 6.482A pdb=" N VAL A 844 " --> pdb=" O VAL A 851 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 866 through 869 Processing sheet with id=AB4, first strand: chain 'A' and resid 1268 through 1278 removed outlier: 3.771A pdb=" N ILE A1290 " --> pdb=" O LEU A1273 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ARG A1275 " --> pdb=" O ASP A1288 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ASP A1288 " --> pdb=" O ARG A1275 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ARG A1277 " --> pdb=" O ARG A1286 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ARG A1286 " --> pdb=" O ARG A1277 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N MET A1094 " --> pdb=" O THR A1295 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A1315 " --> pdb=" O LEU A1095 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB6, first strand: chain 'A' and resid 1206 through 1209 removed outlier: 3.641A pdb=" N ARG A1224 " --> pdb=" O MET A1209 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE A1223 " --> pdb=" O ILE A1176 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE A1176 " --> pdb=" O ILE A1223 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE A1225 " --> pdb=" O TRP A1174 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TRP A1174 " --> pdb=" O ILE A1225 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU A1227 " --> pdb=" O ALA A1172 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N CYS A1175 " --> pdb=" O LEU A1131 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LEU A1131 " --> pdb=" O CYS A1175 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG A1177 " --> pdb=" O TRP A1129 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TRP A1129 " --> pdb=" O ARG A1177 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLU A1179 " --> pdb=" O LEU A1127 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1428 through 1431 removed outlier: 6.993A pdb=" N ILE F 132 " --> pdb=" O ILE F 123 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL F 125 " --> pdb=" O GLN F 130 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLN F 130 " --> pdb=" O VAL F 125 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR F 56 " --> pdb=" O LYS F 131 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL F 133 " --> pdb=" O THR F 56 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL F 58 " --> pdb=" O VAL F 133 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE F 135 " --> pdb=" O VAL F 58 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE B1239 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ILE F 59 " --> pdb=" O PHE B1239 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 193 through 195 removed outlier: 3.539A pdb=" N ALA B 195 " --> pdb=" O GLY B 198 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 416 through 419 removed outlier: 6.436A pdb=" N LEU B 204 " --> pdb=" O ASN B 525 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 214 through 216 removed outlier: 3.939A pdb=" N ILE B 228 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 257 " --> pdb=" O ARG B 249 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 576 through 577 removed outlier: 3.515A pdb=" N ARG B 671 " --> pdb=" O ILE B 741 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 710 through 712 removed outlier: 3.760A pdb=" N ASP B 677 " --> pdb=" O ASN B 711 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 596 through 598 removed outlier: 5.350A pdb=" N TRP B 621 " --> pdb=" O ILE B 617 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE B 617 " --> pdb=" O TRP B 621 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY B 623 " --> pdb=" O VAL B 615 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B 659 " --> pdb=" O ASP B 654 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 824 through 826 removed outlier: 6.143A pdb=" N ARG B 983 " --> pdb=" O ASP B 966 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 834 through 835 Processing sheet with id=AC7, first strand: chain 'B' and resid 1085 through 1086 removed outlier: 6.993A pdb=" N VAL B 865 " --> pdb=" O ALA B1007 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ALA B1009 " --> pdb=" O VAL B 865 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL B 867 " --> pdb=" O ALA B1009 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 866 " --> pdb=" O ILE B1027 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N PHE B1102 " --> pdb=" O TYR B 853 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1017 through 1018 Processing sheet with id=AC9, first strand: chain 'B' and resid 1188 through 1190 Processing sheet with id=AD1, first strand: chain 'C' and resid 5 through 12 removed outlier: 5.291A pdb=" N PHE C 5 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LYS C 48 " --> pdb=" O PHE C 5 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN C 7 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL C 39 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA C 225 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N CYS C 222 " --> pdb=" O LYS C 181 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LYS C 181 " --> pdb=" O CYS C 222 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 67 through 73 removed outlier: 4.856A pdb=" N ILE C 159 " --> pdb=" O LYS C 79 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 67 through 73 removed outlier: 4.237A pdb=" N ASP C 162 " --> pdb=" O PHE C 111 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE C 111 " --> pdb=" O ASP C 162 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL C 110 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 123 through 126 Processing sheet with id=AD5, first strand: chain 'C' and resid 267 through 272 Processing sheet with id=AD6, first strand: chain 'D' and resid 2 through 13 removed outlier: 6.368A pdb=" N SER D 75 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL D 51 " --> pdb=" O SER D 75 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N VAL D 77 " --> pdb=" O THR D 49 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N THR D 49 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N SER D 79 " --> pdb=" O ASN D 47 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N ASN D 47 " --> pdb=" O SER D 79 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 2 through 13 Processing sheet with id=AD8, first strand: chain 'D' and resid 86 through 87 removed outlier: 3.579A pdb=" N GLY D 152 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N VAL D 110 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE D 100 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU D 101 " --> pdb=" O ILE D 93 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 164 through 166 Processing sheet with id=AE1, first strand: chain 'D' and resid 237 through 238 Processing sheet with id=AE2, first strand: chain 'E' and resid 20 through 21 removed outlier: 6.627A pdb=" N ILE E 52 " --> pdb=" O GLU E 87 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ILE E 89 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N SER E 54 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE E 91 " --> pdb=" O SER E 54 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N PHE E 56 " --> pdb=" O ILE E 91 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLU E 86 " --> pdb=" O VAL E 117 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ASN E 119 " --> pdb=" O GLU E 86 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU E 88 " --> pdb=" O ASN E 119 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N TYR E 121 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU E 90 " --> pdb=" O TYR E 121 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 138 through 142 removed outlier: 3.885A pdb=" N LYS E 138 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N PHE E 181 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N MET E 162 " --> pdb=" O PHE E 199 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N THR E 201 " --> pdb=" O MET E 162 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE E 164 " --> pdb=" O THR E 201 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 12 through 15 removed outlier: 3.834A pdb=" N THR I 14 " --> pdb=" O ILE I 21 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE I 21 " --> pdb=" O THR I 14 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 68 through 69 Processing sheet with id=AE6, first strand: chain 'I' and resid 85 through 86 1265 hydrogen bonds defined for protein. 3495 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 17.09 Time building geometry restraints manager: 8.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7676 1.33 - 1.46: 6119 1.46 - 1.58: 15413 1.58 - 1.71: 0 1.71 - 1.83: 281 Bond restraints: 29489 Sorted by residual: bond pdb=" N ILE E 130 " pdb=" CA ILE E 130 " ideal model delta sigma weight residual 1.464 1.498 -0.034 1.23e-02 6.61e+03 7.78e+00 bond pdb=" C PRO E 131 " pdb=" O PRO E 131 " ideal model delta sigma weight residual 1.237 1.207 0.030 1.26e-02 6.30e+03 5.68e+00 bond pdb=" N LYS E 132 " pdb=" CA LYS E 132 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.40e-02 5.10e+03 5.55e+00 bond pdb=" N ARG B1224 " pdb=" CA ARG B1224 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.21e-02 6.83e+03 3.72e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.11e+00 ... (remaining 29484 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 39106 1.49 - 2.97: 618 2.97 - 4.46: 171 4.46 - 5.94: 12 5.94 - 7.43: 5 Bond angle restraints: 39912 Sorted by residual: angle pdb=" C ASN E 129 " pdb=" N ILE E 130 " pdb=" CA ILE E 130 " ideal model delta sigma weight residual 120.24 122.45 -2.21 6.30e-01 2.52e+00 1.23e+01 angle pdb=" CG LYS F 107 " pdb=" CD LYS F 107 " pdb=" CE LYS F 107 " ideal model delta sigma weight residual 111.30 118.73 -7.43 2.30e+00 1.89e-01 1.04e+01 angle pdb=" C ILE E 130 " pdb=" CA ILE E 130 " pdb=" CB ILE E 130 " ideal model delta sigma weight residual 114.35 111.50 2.85 1.06e+00 8.90e-01 7.24e+00 angle pdb=" N ARG B1224 " pdb=" CA ARG B1224 " pdb=" C ARG B1224 " ideal model delta sigma weight residual 111.28 108.37 2.91 1.09e+00 8.42e-01 7.13e+00 angle pdb=" N GLY A 71 " pdb=" CA GLY A 71 " pdb=" C GLY A 71 " ideal model delta sigma weight residual 113.18 107.51 5.67 2.37e+00 1.78e-01 5.72e+00 ... (remaining 39907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.16: 16081 18.16 - 36.31: 1529 36.31 - 54.47: 294 54.47 - 72.63: 70 72.63 - 90.78: 22 Dihedral angle restraints: 17996 sinusoidal: 7373 harmonic: 10623 Sorted by residual: dihedral pdb=" CA ALA B1123 " pdb=" C ALA B1123 " pdb=" N SER B1124 " pdb=" CA SER B1124 " ideal model delta harmonic sigma weight residual 180.00 157.70 22.30 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA LEU J 37 " pdb=" C LEU J 37 " pdb=" N PRO J 38 " pdb=" CA PRO J 38 " ideal model delta harmonic sigma weight residual 180.00 159.67 20.33 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA ASN A 358 " pdb=" C ASN A 358 " pdb=" N ILE A 359 " pdb=" CA ILE A 359 " ideal model delta harmonic sigma weight residual -180.00 -160.56 -19.44 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 17993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3116 0.034 - 0.068: 896 0.068 - 0.102: 298 0.102 - 0.136: 226 0.136 - 0.170: 10 Chirality restraints: 4546 Sorted by residual: chirality pdb=" CA HIS A 72 " pdb=" N HIS A 72 " pdb=" C HIS A 72 " pdb=" CB HIS A 72 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" CA ILE A1176 " pdb=" N ILE A1176 " pdb=" C ILE A1176 " pdb=" CB ILE A1176 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA ILE E 128 " pdb=" N ILE E 128 " pdb=" C ILE E 128 " pdb=" CB ILE E 128 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.34e-01 ... (remaining 4543 not shown) Planarity restraints: 5132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B1224 " -0.454 9.50e-02 1.11e+02 2.04e-01 2.55e+01 pdb=" NE ARG B1224 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B1224 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG B1224 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B1224 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU J 37 " -0.080 5.00e-02 4.00e+02 1.22e-01 2.36e+01 pdb=" N PRO J 38 " 0.210 5.00e-02 4.00e+02 pdb=" CA PRO J 38 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO J 38 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 42 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C TYR B 42 " -0.041 2.00e-02 2.50e+03 pdb=" O TYR B 42 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN B 43 " 0.014 2.00e-02 2.50e+03 ... (remaining 5129 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 134 2.44 - 3.05: 20221 3.05 - 3.67: 43037 3.67 - 4.28: 67648 4.28 - 4.90: 112211 Nonbonded interactions: 243251 Sorted by model distance: nonbonded pdb=" OD2 ASP A 457 " pdb=" OD2 ASP A 459 " model vdw 1.824 3.040 nonbonded pdb=" OD1 ASP A 457 " pdb="MG MG A1503 " model vdw 2.017 2.170 nonbonded pdb=" OD1 ASP A 459 " pdb="MG MG A1503 " model vdw 2.020 2.170 nonbonded pdb=" O ALA B 431 " pdb=" OG1 THR B 435 " model vdw 2.022 3.040 nonbonded pdb=" OD1 ASP A 108 " pdb=" NZ LYS A 110 " model vdw 2.034 3.120 ... (remaining 243246 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=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.210 Check model and map are aligned: 0.240 Set scattering table: 0.260 Process input model: 84.760 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.240 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: 0.030 Load rotamer database and sin/cos tables:16.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.366 29513 Z= 0.167 Angle : 0.541 20.999 39945 Z= 0.267 Chirality : 0.043 0.170 4546 Planarity : 0.005 0.204 5132 Dihedral : 14.832 90.782 11122 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.15 % Allowed : 14.24 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.61 (0.14), residues: 3594 helix: 1.59 (0.14), residues: 1348 sheet: -0.84 (0.23), residues: 495 loop : -0.06 (0.15), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 223 HIS 0.006 0.001 HIS A 526 PHE 0.021 0.001 PHE D 278 TYR 0.013 0.001 TYR E 123 ARG 0.008 0.000 ARG B 796 Details of bonding type rmsd hydrogen bonds : bond 0.19740 ( 1247) hydrogen bonds : angle 7.13313 ( 3495) metal coordination : bond 0.11812 ( 24) metal coordination : angle 5.97115 ( 33) covalent geometry : bond 0.00266 (29489) covalent geometry : angle 0.51332 (39912) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7188 Ramachandran restraints generated. 3594 Oldfield, 0 Emsley, 3594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7188 Ramachandran restraints generated. 3594 Oldfield, 0 Emsley, 3594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 459 time to evaluate : 3.513 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: A 963 MET cc_start: 0.9097 (mtt) cc_final: 0.8881 (mtm) REVERT: A 1055 GLN cc_start: 0.8416 (tt0) cc_final: 0.7889 (pt0) REVERT: B 163 MET cc_start: 0.7850 (ttm) cc_final: 0.7622 (ttm) REVERT: B 281 MET cc_start: 0.8019 (tpt) cc_final: 0.7739 (tpt) REVERT: B 659 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7207 (mm-30) REVERT: C 257 TYR cc_start: 0.8319 (m-80) cc_final: 0.7980 (m-80) REVERT: D 103 GLU cc_start: 0.8220 (pt0) cc_final: 0.7723 (pp20) REVERT: E 80 ASN cc_start: 0.9090 (m-40) cc_final: 0.8584 (m110) REVERT: F 100 SER cc_start: 0.8372 (p) cc_final: 0.7925 (t) REVERT: I 11 MET cc_start: 0.8366 (mmm) cc_final: 0.8143 (mmm) REVERT: I 42 LYS cc_start: 0.8879 (tptm) cc_final: 0.8634 (tptp) REVERT: I 52 LYS cc_start: 0.9037 (tttm) cc_final: 0.8773 (tttm) REVERT: I 86 ILE cc_start: 0.8999 (mm) cc_final: 0.8759 (pt) REVERT: I 91 ILE cc_start: 0.8591 (mm) cc_final: 0.8035 (mm) outliers start: 5 outliers final: 2 residues processed: 464 average time/residue: 1.3187 time to fit residues: 724.0689 Evaluate side-chains 410 residues out of total 3230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 408 time to evaluate : 3.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1205 ASN Chi-restraints excluded: chain I residue 16 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 304 optimal weight: 30.0000 chunk 273 optimal weight: 2.9990 chunk 151 optimal weight: 50.0000 chunk 93 optimal weight: 0.0370 chunk 184 optimal weight: 4.9990 chunk 146 optimal weight: 30.0000 chunk 282 optimal weight: 0.0670 chunk 109 optimal weight: 10.0000 chunk 172 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 327 optimal weight: 4.9990 overall best weight: 2.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 681 ASN A 742 ASN A 744 ASN A 765 GLN A 914 ASN A1090 GLN A1111 GLN A1115 ASN ** A1210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN B 245 GLN B 375 HIS ** B1162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN E 37 ASN E 109 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.124668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.076537 restraints weight = 75034.939| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.37 r_work: 0.2650 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29513 Z= 0.186 Angle : 0.635 20.906 39945 Z= 0.321 Chirality : 0.046 0.207 4546 Planarity : 0.004 0.090 5132 Dihedral : 4.496 78.316 3944 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.86 % Allowed : 16.13 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 (0.14), residues: 3594 helix: 1.64 (0.14), residues: 1373 sheet: -0.73 (0.23), residues: 488 loop : 0.03 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1129 HIS 0.006 0.001 HIS A 56 PHE 0.025 0.002 PHE A 918 TYR 0.021 0.001 TYR A1145 ARG 0.008 0.001 ARG D 322 Details of bonding type rmsd hydrogen bonds : bond 0.05282 ( 1247) hydrogen bonds : angle 5.42594 ( 3495) metal coordination : bond 0.01358 ( 24) metal coordination : angle 5.99466 ( 33) covalent geometry : bond 0.00429 (29489) covalent geometry : angle 0.61163 (39912) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7188 Ramachandran restraints generated. 3594 Oldfield, 0 Emsley, 3594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7188 Ramachandran restraints generated. 3594 Oldfield, 0 Emsley, 3594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 472 time to evaluate : 4.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 678 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8535 (mm-30) REVERT: A 760 GLN cc_start: 0.8218 (tp40) cc_final: 0.7963 (tp40) REVERT: A 781 GLU cc_start: 0.8191 (pt0) cc_final: 0.7909 (pm20) REVERT: A 963 MET cc_start: 0.9099 (mtt) cc_final: 0.8891 (mtm) REVERT: A 1055 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7731 (pt0) REVERT: A 1129 TRP cc_start: 0.8644 (p-90) cc_final: 0.8350 (p-90) REVERT: A 1145 TYR cc_start: 0.9088 (t80) cc_final: 0.8868 (t80) REVERT: A 1209 MET cc_start: 0.8614 (mtp) cc_final: 0.7911 (mmm) REVERT: A 1370 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8726 (mt-10) REVERT: A 1371 LYS cc_start: 0.8632 (tppt) cc_final: 0.8326 (tptm) REVERT: A 1393 GLN cc_start: 0.8305 (mp10) cc_final: 0.8090 (mp10) REVERT: B 192 TYR cc_start: 0.7584 (p90) cc_final: 0.7187 (p90) REVERT: B 206 GLU cc_start: 0.7960 (pm20) cc_final: 0.7512 (pm20) REVERT: B 281 MET cc_start: 0.8056 (tpt) cc_final: 0.7598 (tpt) REVERT: B 523 THR cc_start: 0.8108 (m) cc_final: 0.7886 (m) REVERT: B 557 GLN cc_start: 0.7188 (tp40) cc_final: 0.6939 (tm130) REVERT: B 659 GLU cc_start: 0.7370 (mm-30) cc_final: 0.6934 (mm-30) REVERT: B 665 ASP cc_start: 0.8239 (t0) cc_final: 0.8039 (t0) REVERT: B 718 MET cc_start: 0.8787 (mtm) cc_final: 0.8528 (mtm) REVERT: B 982 MET cc_start: 0.6771 (tpp) cc_final: 0.6514 (tpp) REVERT: B 1129 ASP cc_start: 0.8739 (t0) cc_final: 0.8431 (t0) REVERT: D 103 GLU cc_start: 0.8100 (pt0) cc_final: 0.7510 (pp20) REVERT: D 187 MET cc_start: 0.8948 (mmm) cc_final: 0.8597 (mpp) REVERT: D 217 ILE cc_start: 0.4972 (OUTLIER) cc_final: 0.4215 (pp) REVERT: D 218 LEU cc_start: 0.8561 (tt) cc_final: 0.8358 (tt) REVERT: D 327 TRP cc_start: 0.8783 (m100) cc_final: 0.8475 (m100) REVERT: F 100 SER cc_start: 0.8605 (p) cc_final: 0.8156 (t) REVERT: I 11 MET cc_start: 0.8308 (mmm) cc_final: 0.7201 (mmm) REVERT: I 22 PHE cc_start: 0.8062 (m-80) cc_final: 0.7565 (m-80) REVERT: I 58 LYS cc_start: 0.9066 (tmmt) cc_final: 0.8853 (tppp) REVERT: I 63 ASP cc_start: 0.8720 (t0) cc_final: 0.8497 (t0) outliers start: 60 outliers final: 18 residues processed: 505 average time/residue: 1.3205 time to fit residues: 795.1040 Evaluate side-chains 443 residues out of total 3230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 421 time to evaluate : 3.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 789 CYS Chi-restraints excluded: chain A residue 1055 GLN Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1370 GLU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 325 HIS Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain J residue 46 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 52 optimal weight: 0.9990 chunk 277 optimal weight: 7.9990 chunk 356 optimal weight: 8.9990 chunk 273 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 245 optimal weight: 1.9990 chunk 228 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 336 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN A 814 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN B 704 HIS ** B1162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN E 37 ASN I 68 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.124914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.077048 restraints weight = 62219.715| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 2.99 r_work: 0.2681 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29513 Z= 0.176 Angle : 0.612 20.344 39945 Z= 0.306 Chirality : 0.045 0.185 4546 Planarity : 0.004 0.073 5132 Dihedral : 4.519 78.080 3942 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.38 % Allowed : 17.06 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 (0.14), residues: 3594 helix: 1.59 (0.14), residues: 1371 sheet: -0.69 (0.22), residues: 504 loop : -0.02 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1154 HIS 0.007 0.001 HIS B 375 PHE 0.024 0.002 PHE A 918 TYR 0.018 0.001 TYR B 273 ARG 0.010 0.000 ARG D 322 Details of bonding type rmsd hydrogen bonds : bond 0.04667 ( 1247) hydrogen bonds : angle 5.14257 ( 3495) metal coordination : bond 0.00828 ( 24) metal coordination : angle 5.89706 ( 33) covalent geometry : bond 0.00411 (29489) covalent geometry : angle 0.58793 (39912) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7188 Ramachandran restraints generated. 3594 Oldfield, 0 Emsley, 3594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7188 Ramachandran restraints generated. 3594 Oldfield, 0 Emsley, 3594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 448 time to evaluate : 3.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ARG cc_start: 0.8876 (mmm-85) cc_final: 0.8595 (mtp85) REVERT: A 760 GLN cc_start: 0.8256 (tp40) cc_final: 0.7910 (tp40) REVERT: A 781 GLU cc_start: 0.8145 (pt0) cc_final: 0.7931 (pm20) REVERT: A 963 MET cc_start: 0.9057 (mtt) cc_final: 0.8842 (mtm) REVERT: A 1055 GLN cc_start: 0.8367 (tt0) cc_final: 0.7801 (pt0) REVERT: A 1129 TRP cc_start: 0.8605 (p-90) cc_final: 0.8281 (p-90) REVERT: A 1144 MET cc_start: 0.7594 (ptp) cc_final: 0.7162 (ptt) REVERT: A 1145 TYR cc_start: 0.8974 (t80) cc_final: 0.8751 (t80) REVERT: A 1185 MET cc_start: 0.8854 (mtp) cc_final: 0.8653 (mtm) REVERT: A 1222 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8442 (mp) REVERT: A 1240 MET cc_start: 0.8215 (ppp) cc_final: 0.7958 (tpt) REVERT: A 1370 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8707 (mt-10) REVERT: A 1371 LYS cc_start: 0.8609 (tppt) cc_final: 0.8325 (tptm) REVERT: A 1393 GLN cc_start: 0.8289 (mp10) cc_final: 0.8062 (mp10) REVERT: B 192 TYR cc_start: 0.7980 (p90) cc_final: 0.7215 (p90) REVERT: B 206 GLU cc_start: 0.7980 (pm20) cc_final: 0.7586 (pm20) REVERT: B 251 MET cc_start: 0.7693 (mmm) cc_final: 0.7447 (mmm) REVERT: B 281 MET cc_start: 0.8072 (tpt) cc_final: 0.7670 (tpt) REVERT: B 567 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.6800 (mmm) REVERT: B 659 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6932 (mm-30) REVERT: B 982 MET cc_start: 0.6878 (tpp) cc_final: 0.6661 (tpp) REVERT: B 1129 ASP cc_start: 0.8777 (t0) cc_final: 0.8434 (t0) REVERT: C 2 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7844 (pm20) REVERT: C 88 MET cc_start: 0.9397 (mmp) cc_final: 0.9094 (mmp) REVERT: D 187 MET cc_start: 0.8980 (mmm) cc_final: 0.8578 (mpp) REVERT: D 210 TYR cc_start: 0.8857 (m-10) cc_final: 0.8650 (m-10) REVERT: D 217 ILE cc_start: 0.5151 (OUTLIER) cc_final: 0.4542 (pp) REVERT: D 327 TRP cc_start: 0.8775 (m100) cc_final: 0.8520 (m100) REVERT: F 100 SER cc_start: 0.8662 (p) cc_final: 0.8240 (t) REVERT: I 2 LYS cc_start: 0.7515 (mttp) cc_final: 0.7018 (mtmt) REVERT: I 58 LYS cc_start: 0.9069 (tmmt) cc_final: 0.8824 (tppp) REVERT: I 63 ASP cc_start: 0.8725 (t0) cc_final: 0.8433 (t0) REVERT: I 68 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7804 (mt0) outliers start: 77 outliers final: 25 residues processed: 486 average time/residue: 1.3682 time to fit residues: 788.3301 Evaluate side-chains 455 residues out of total 3230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 424 time to evaluate : 3.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 789 CYS Chi-restraints excluded: chain A residue 1155 MET Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1222 ILE Chi-restraints excluded: chain A residue 1370 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 325 HIS Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 68 GLN Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 46 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 203 optimal weight: 1.9990 chunk 174 optimal weight: 8.9990 chunk 154 optimal weight: 20.0000 chunk 195 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 242 optimal weight: 10.0000 chunk 198 optimal weight: 0.9980 chunk 256 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1162 HIS ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN ** B1162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 GLN E 37 ASN E 109 GLN I 36 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.124732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.076756 restraints weight = 75466.427| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.24 r_work: 0.2650 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 29513 Z= 0.204 Angle : 0.617 21.219 39945 Z= 0.306 Chirality : 0.046 0.180 4546 Planarity : 0.004 0.059 5132 Dihedral : 4.537 77.644 3942 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.57 % Allowed : 17.28 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.66 (0.14), residues: 3594 helix: 1.57 (0.14), residues: 1369 sheet: -0.67 (0.22), residues: 494 loop : -0.05 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 200 HIS 0.009 0.001 HIS B 216 PHE 0.025 0.002 PHE A 918 TYR 0.015 0.001 TYR E 123 ARG 0.013 0.001 ARG D 322 Details of bonding type rmsd hydrogen bonds : bond 0.04491 ( 1247) hydrogen bonds : angle 5.05540 ( 3495) metal coordination : bond 0.00832 ( 24) metal coordination : angle 6.19704 ( 33) covalent geometry : bond 0.00480 (29489) covalent geometry : angle 0.59129 (39912) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7188 Ramachandran restraints generated. 3594 Oldfield, 0 Emsley, 3594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7188 Ramachandran restraints generated. 3594 Oldfield, 0 Emsley, 3594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 439 time to evaluate : 4.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ARG cc_start: 0.8863 (mmm-85) cc_final: 0.8616 (mtp85) REVERT: A 756 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8083 (pp20) REVERT: A 760 GLN cc_start: 0.8288 (tp40) cc_final: 0.7896 (tp40) REVERT: A 963 MET cc_start: 0.9064 (mtt) cc_final: 0.8845 (mtm) REVERT: A 1055 GLN cc_start: 0.8306 (tt0) cc_final: 0.7785 (pt0) REVERT: A 1129 TRP cc_start: 0.8672 (p-90) cc_final: 0.8338 (p-90) REVERT: A 1144 MET cc_start: 0.7595 (ptp) cc_final: 0.7164 (ptt) REVERT: A 1145 TYR cc_start: 0.9022 (t80) cc_final: 0.8746 (t80) REVERT: A 1209 MET cc_start: 0.8610 (mtp) cc_final: 0.7964 (mmm) REVERT: A 1370 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8700 (mt-10) REVERT: A 1371 LYS cc_start: 0.8596 (tppt) cc_final: 0.8290 (tptm) REVERT: A 1393 GLN cc_start: 0.8273 (mp10) cc_final: 0.8022 (mp10) REVERT: B 192 TYR cc_start: 0.8115 (p90) cc_final: 0.6950 (p90) REVERT: B 193 PHE cc_start: 0.8587 (m-80) cc_final: 0.8205 (m-80) REVERT: B 206 GLU cc_start: 0.7998 (pm20) cc_final: 0.7638 (pm20) REVERT: B 281 MET cc_start: 0.8104 (tpt) cc_final: 0.7785 (tpt) REVERT: B 410 ARG cc_start: 0.8539 (mtm-85) cc_final: 0.8246 (tpp-160) REVERT: B 523 THR cc_start: 0.7991 (m) cc_final: 0.7753 (m) REVERT: B 567 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6837 (mmm) REVERT: B 597 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7628 (mt0) REVERT: B 659 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6936 (mm-30) REVERT: B 982 MET cc_start: 0.6994 (tpp) cc_final: 0.6722 (tpp) REVERT: B 1129 ASP cc_start: 0.8809 (t0) cc_final: 0.8457 (t0) REVERT: C 2 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7861 (pm20) REVERT: C 88 MET cc_start: 0.9427 (mmp) cc_final: 0.9074 (mmp) REVERT: C 210 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8099 (mmm) REVERT: D 187 MET cc_start: 0.9032 (mmm) cc_final: 0.8617 (mpp) REVERT: D 210 TYR cc_start: 0.8912 (m-10) cc_final: 0.8703 (m-10) REVERT: D 217 ILE cc_start: 0.5347 (OUTLIER) cc_final: 0.4815 (pp) REVERT: D 244 TYR cc_start: 0.9179 (OUTLIER) cc_final: 0.8852 (t80) REVERT: F 100 SER cc_start: 0.8768 (p) cc_final: 0.8340 (t) REVERT: I 58 LYS cc_start: 0.9101 (tmmt) cc_final: 0.8828 (tppp) REVERT: I 63 ASP cc_start: 0.8779 (t0) cc_final: 0.8475 (t0) REVERT: I 79 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.7692 (t0) outliers start: 83 outliers final: 33 residues processed: 482 average time/residue: 1.4090 time to fit residues: 811.2413 Evaluate side-chains 451 residues out of total 3230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 409 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 789 CYS Chi-restraints excluded: chain A residue 1061 HIS Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1155 MET Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1370 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 325 HIS Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 597 GLN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 46 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 208 optimal weight: 3.9990 chunk 355 optimal weight: 1.9990 chunk 340 optimal weight: 2.9990 chunk 331 optimal weight: 1.9990 chunk 306 optimal weight: 30.0000 chunk 343 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 296 optimal weight: 4.9990 chunk 325 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 326 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 497 ASN A1162 HIS ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN ** B1162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN E 109 GLN I 36 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.125447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.077494 restraints weight = 69035.675| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.16 r_work: 0.2685 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29513 Z= 0.142 Angle : 0.598 19.192 39945 Z= 0.294 Chirality : 0.044 0.185 4546 Planarity : 0.004 0.057 5132 Dihedral : 4.440 77.781 3942 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.72 % Allowed : 17.68 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 (0.14), residues: 3594 helix: 1.64 (0.14), residues: 1372 sheet: -0.64 (0.23), residues: 486 loop : -0.00 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 200 HIS 0.007 0.001 HIS B 375 PHE 0.025 0.001 PHE A 918 TYR 0.013 0.001 TYR B 192 ARG 0.012 0.000 ARG D 322 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 1247) hydrogen bonds : angle 4.89561 ( 3495) metal coordination : bond 0.00691 ( 24) metal coordination : angle 5.50694 ( 33) covalent geometry : bond 0.00329 (29489) covalent geometry : angle 0.57693 (39912) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7188 Ramachandran restraints generated. 3594 Oldfield, 0 Emsley, 3594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7188 Ramachandran restraints generated. 3594 Oldfield, 0 Emsley, 3594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 462 time to evaluate : 3.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ARG cc_start: 0.8859 (mmm-85) cc_final: 0.8579 (mtp85) REVERT: A 455 ASN cc_start: 0.9274 (t0) cc_final: 0.8843 (t0) REVERT: A 695 LEU cc_start: 0.8731 (mt) cc_final: 0.8510 (pt) REVERT: A 756 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8060 (pp20) REVERT: A 760 GLN cc_start: 0.8299 (tp40) cc_final: 0.7904 (tp40) REVERT: A 963 MET cc_start: 0.9066 (mtt) cc_final: 0.8851 (mtm) REVERT: A 1055 GLN cc_start: 0.8292 (tt0) cc_final: 0.7791 (pt0) REVERT: A 1129 TRP cc_start: 0.8650 (p-90) cc_final: 0.8321 (p-90) REVERT: A 1144 MET cc_start: 0.7598 (ptp) cc_final: 0.7141 (ptt) REVERT: A 1145 TYR cc_start: 0.9028 (t80) cc_final: 0.8771 (t80) REVERT: A 1209 MET cc_start: 0.8568 (mtp) cc_final: 0.7880 (mmm) REVERT: A 1228 ARG cc_start: 0.8477 (mtp-110) cc_final: 0.8200 (mtp-110) REVERT: A 1240 MET cc_start: 0.8320 (ppp) cc_final: 0.8011 (tpt) REVERT: A 1370 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8685 (mt-10) REVERT: A 1371 LYS cc_start: 0.8523 (tppt) cc_final: 0.8235 (tptm) REVERT: A 1393 GLN cc_start: 0.8270 (mp10) cc_final: 0.8021 (mp10) REVERT: B 206 GLU cc_start: 0.8000 (pm20) cc_final: 0.7624 (pm20) REVERT: B 278 MET cc_start: 0.9081 (mtp) cc_final: 0.8820 (mtt) REVERT: B 281 MET cc_start: 0.8060 (tpt) cc_final: 0.7746 (tpt) REVERT: B 410 ARG cc_start: 0.8479 (mtm-85) cc_final: 0.8182 (tpp-160) REVERT: B 523 THR cc_start: 0.7987 (m) cc_final: 0.7748 (m) REVERT: B 567 MET cc_start: 0.7193 (OUTLIER) cc_final: 0.6914 (mmm) REVERT: B 596 ILE cc_start: 0.8656 (mp) cc_final: 0.8245 (tp) REVERT: B 659 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6915 (mm-30) REVERT: B 744 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7952 (pm20) REVERT: B 982 MET cc_start: 0.7008 (tpp) cc_final: 0.6716 (tpp) REVERT: B 1129 ASP cc_start: 0.8793 (t0) cc_final: 0.8456 (t0) REVERT: C 2 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7853 (pm20) REVERT: C 88 MET cc_start: 0.9421 (mmp) cc_final: 0.9053 (mmp) REVERT: D 87 ILE cc_start: 0.8998 (mm) cc_final: 0.8773 (mp) REVERT: D 187 MET cc_start: 0.9071 (mmm) cc_final: 0.8716 (mpp) REVERT: D 217 ILE cc_start: 0.5523 (OUTLIER) cc_final: 0.5056 (pp) REVERT: D 244 TYR cc_start: 0.9173 (OUTLIER) cc_final: 0.8873 (t80) REVERT: D 327 TRP cc_start: 0.8831 (m100) cc_final: 0.8459 (m100) REVERT: F 100 SER cc_start: 0.8746 (p) cc_final: 0.8332 (t) REVERT: I 2 LYS cc_start: 0.7478 (mttp) cc_final: 0.7172 (mttp) REVERT: I 28 GLU cc_start: 0.7120 (tm-30) cc_final: 0.6860 (tm-30) REVERT: I 37 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7774 (mm) REVERT: I 63 ASP cc_start: 0.8769 (t0) cc_final: 0.8446 (t0) REVERT: J 52 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8354 (tttp) outliers start: 88 outliers final: 36 residues processed: 501 average time/residue: 1.2717 time to fit residues: 758.7666 Evaluate side-chains 482 residues out of total 3230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 437 time to evaluate : 3.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 789 CYS Chi-restraints excluded: chain A residue 1061 HIS Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain A residue 1155 MET Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1370 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 325 HIS Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 822 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 52 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 353 optimal weight: 1.9990 chunk 180 optimal weight: 40.0000 chunk 174 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 183 optimal weight: 0.0040 chunk 214 optimal weight: 20.0000 chunk 275 optimal weight: 0.8980 chunk 344 optimal weight: 20.0000 chunk 341 optimal weight: 1.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 760 GLN A1078 GLN A1162 HIS ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 HIS B 245 GLN ** B1162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN E 109 GLN F 86 GLN I 36 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.126217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.078409 restraints weight = 67162.888| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.12 r_work: 0.2713 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29513 Z= 0.129 Angle : 0.591 17.950 39945 Z= 0.291 Chirality : 0.044 0.188 4546 Planarity : 0.004 0.062 5132 Dihedral : 4.376 77.639 3942 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.51 % Allowed : 18.48 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.80 (0.14), residues: 3594 helix: 1.69 (0.14), residues: 1372 sheet: -0.56 (0.22), residues: 510 loop : 0.02 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 200 HIS 0.007 0.001 HIS B 375 PHE 0.024 0.001 PHE A 918 TYR 0.019 0.001 TYR B 192 ARG 0.015 0.000 ARG D 322 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 1247) hydrogen bonds : angle 4.82398 ( 3495) metal coordination : bond 0.00656 ( 24) metal coordination : angle 5.26018 ( 33) covalent geometry : bond 0.00297 (29489) covalent geometry : angle 0.57144 (39912) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7188 Ramachandran restraints generated. 3594 Oldfield, 0 Emsley, 3594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7188 Ramachandran restraints generated. 3594 Oldfield, 0 Emsley, 3594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 463 time to evaluate : 3.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8898 (tt0) cc_final: 0.8629 (tm-30) REVERT: A 111 ARG cc_start: 0.8811 (mmm-85) cc_final: 0.8540 (mtp85) REVERT: A 153 THR cc_start: 0.8752 (m) cc_final: 0.8423 (p) REVERT: A 455 ASN cc_start: 0.9237 (t0) cc_final: 0.8839 (t0) REVERT: A 810 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7488 (m-80) REVERT: A 963 MET cc_start: 0.9054 (mtt) cc_final: 0.8828 (mtm) REVERT: A 1055 GLN cc_start: 0.8252 (tt0) cc_final: 0.7825 (pt0) REVERT: A 1129 TRP cc_start: 0.8642 (p-90) cc_final: 0.8292 (p-90) REVERT: A 1144 MET cc_start: 0.7553 (ptp) cc_final: 0.7117 (ptt) REVERT: A 1145 TYR cc_start: 0.9007 (t80) cc_final: 0.8737 (t80) REVERT: A 1209 MET cc_start: 0.8536 (mtp) cc_final: 0.7866 (mmm) REVERT: A 1370 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8674 (mt-10) REVERT: A 1371 LYS cc_start: 0.8469 (tppt) cc_final: 0.8264 (tptm) REVERT: A 1393 GLN cc_start: 0.8256 (mp10) cc_final: 0.7989 (mp10) REVERT: B 192 TYR cc_start: 0.7932 (p90) cc_final: 0.7135 (p90) REVERT: B 206 GLU cc_start: 0.7992 (pm20) cc_final: 0.7627 (pm20) REVERT: B 264 LYS cc_start: 0.7538 (mmmm) cc_final: 0.7228 (mptt) REVERT: B 281 MET cc_start: 0.8026 (tpt) cc_final: 0.7688 (tpt) REVERT: B 389 PHE cc_start: 0.8049 (t80) cc_final: 0.7787 (t80) REVERT: B 410 ARG cc_start: 0.8529 (mtm-85) cc_final: 0.8249 (tpp-160) REVERT: B 523 THR cc_start: 0.8028 (m) cc_final: 0.7782 (m) REVERT: B 567 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6935 (mmm) REVERT: B 597 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7622 (mt0) REVERT: B 659 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6924 (mm-30) REVERT: B 744 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7914 (pm20) REVERT: B 821 MET cc_start: 0.4869 (OUTLIER) cc_final: 0.4632 (mmm) REVERT: B 982 MET cc_start: 0.7040 (tpp) cc_final: 0.6764 (tpp) REVERT: B 1129 ASP cc_start: 0.8779 (t0) cc_final: 0.8445 (t0) REVERT: C 2 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7820 (pm20) REVERT: C 88 MET cc_start: 0.9406 (mmp) cc_final: 0.9034 (mmp) REVERT: D 85 ASP cc_start: 0.8998 (m-30) cc_final: 0.8667 (m-30) REVERT: D 87 ILE cc_start: 0.9012 (mm) cc_final: 0.8792 (mp) REVERT: D 187 MET cc_start: 0.9072 (mmm) cc_final: 0.8731 (mpp) REVERT: D 217 ILE cc_start: 0.5472 (OUTLIER) cc_final: 0.4997 (pp) REVERT: D 327 TRP cc_start: 0.8883 (m100) cc_final: 0.8510 (m100) REVERT: F 100 SER cc_start: 0.8731 (p) cc_final: 0.8342 (t) REVERT: I 14 THR cc_start: 0.7708 (OUTLIER) cc_final: 0.7314 (p) REVERT: I 28 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6904 (tm-30) REVERT: I 44 TYR cc_start: 0.8248 (m-80) cc_final: 0.7691 (m-80) REVERT: I 63 ASP cc_start: 0.8764 (t0) cc_final: 0.8458 (t0) REVERT: I 71 LYS cc_start: 0.8351 (mttt) cc_final: 0.8091 (mtpm) REVERT: J 52 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8322 (tttp) outliers start: 81 outliers final: 38 residues processed: 504 average time/residue: 1.2736 time to fit residues: 768.3903 Evaluate side-chains 499 residues out of total 3230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 451 time to evaluate : 3.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 1061 HIS Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1252 ASP Chi-restraints excluded: chain A residue 1258 THR Chi-restraints excluded: chain A residue 1370 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 325 HIS Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 597 GLN Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 821 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 52 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 59 optimal weight: 6.9990 chunk 308 optimal weight: 8.9990 chunk 179 optimal weight: 8.9990 chunk 176 optimal weight: 30.0000 chunk 332 optimal weight: 0.0770 chunk 45 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 304 optimal weight: 20.0000 chunk 219 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 191 optimal weight: 0.9980 overall best weight: 2.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1162 HIS A1197 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN E 109 GLN F 86 GLN I 36 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.124863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.076484 restraints weight = 73044.166| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.24 r_work: 0.2665 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 29513 Z= 0.194 Angle : 0.632 20.492 39945 Z= 0.310 Chirality : 0.046 0.200 4546 Planarity : 0.004 0.064 5132 Dihedral : 4.443 76.947 3942 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.54 % Allowed : 19.20 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.72 (0.14), residues: 3594 helix: 1.63 (0.14), residues: 1378 sheet: -0.51 (0.23), residues: 488 loop : -0.07 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 701 HIS 0.005 0.001 HIS C 315 PHE 0.024 0.002 PHE A 952 TYR 0.015 0.001 TYR B 273 ARG 0.015 0.001 ARG D 322 Details of bonding type rmsd hydrogen bonds : bond 0.04182 ( 1247) hydrogen bonds : angle 4.88777 ( 3495) metal coordination : bond 0.00750 ( 24) metal coordination : angle 5.54160 ( 33) covalent geometry : bond 0.00458 (29489) covalent geometry : angle 0.61171 (39912) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7188 Ramachandran restraints generated. 3594 Oldfield, 0 Emsley, 3594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7188 Ramachandran restraints generated. 3594 Oldfield, 0 Emsley, 3594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 453 time to evaluate : 3.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8934 (tt0) cc_final: 0.8646 (tm-30) REVERT: A 111 ARG cc_start: 0.8852 (mmm-85) cc_final: 0.8588 (mtp85) REVERT: A 153 THR cc_start: 0.8771 (m) cc_final: 0.8438 (p) REVERT: A 756 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8110 (pp20) REVERT: A 963 MET cc_start: 0.9067 (mtt) cc_final: 0.8849 (mtm) REVERT: A 1055 GLN cc_start: 0.8386 (tt0) cc_final: 0.7828 (pt0) REVERT: A 1129 TRP cc_start: 0.8575 (p-90) cc_final: 0.8290 (p-90) REVERT: A 1144 MET cc_start: 0.7586 (ptp) cc_final: 0.7134 (ptt) REVERT: A 1145 TYR cc_start: 0.9037 (t80) cc_final: 0.8775 (t80) REVERT: A 1209 MET cc_start: 0.8592 (mtp) cc_final: 0.7855 (mmm) REVERT: A 1370 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8707 (mt-10) REVERT: A 1371 LYS cc_start: 0.8588 (tppt) cc_final: 0.8329 (tptm) REVERT: A 1393 GLN cc_start: 0.8258 (mp10) cc_final: 0.8003 (mp10) REVERT: B 192 TYR cc_start: 0.8098 (p90) cc_final: 0.7813 (p90) REVERT: B 206 GLU cc_start: 0.8013 (pm20) cc_final: 0.7627 (pm20) REVERT: B 264 LYS cc_start: 0.7633 (mmmm) cc_final: 0.7323 (mptt) REVERT: B 281 MET cc_start: 0.8075 (tpt) cc_final: 0.7712 (tpt) REVERT: B 295 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8426 (mm) REVERT: B 389 PHE cc_start: 0.8225 (t80) cc_final: 0.8007 (t80) REVERT: B 410 ARG cc_start: 0.8502 (mtm-85) cc_final: 0.8207 (tpp-160) REVERT: B 544 ARG cc_start: 0.7594 (ptp90) cc_final: 0.7317 (ptp90) REVERT: B 567 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6914 (mmm) REVERT: B 584 LEU cc_start: 0.9125 (mp) cc_final: 0.8836 (tm) REVERT: B 597 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7592 (mt0) REVERT: B 659 GLU cc_start: 0.7346 (mm-30) cc_final: 0.6907 (mm-30) REVERT: B 744 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8006 (pm20) REVERT: B 982 MET cc_start: 0.7087 (tpp) cc_final: 0.6865 (tpp) REVERT: B 1129 ASP cc_start: 0.8810 (t0) cc_final: 0.8520 (t0) REVERT: C 2 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7835 (pm20) REVERT: C 88 MET cc_start: 0.9420 (mmp) cc_final: 0.9024 (mmp) REVERT: C 257 TYR cc_start: 0.8328 (m-80) cc_final: 0.7788 (t80) REVERT: C 343 ILE cc_start: 0.9365 (OUTLIER) cc_final: 0.8990 (mt) REVERT: D 85 ASP cc_start: 0.9000 (m-30) cc_final: 0.8639 (m-30) REVERT: D 187 MET cc_start: 0.9098 (mmm) cc_final: 0.8781 (mpp) REVERT: D 217 ILE cc_start: 0.5505 (OUTLIER) cc_final: 0.5045 (pp) REVERT: D 292 MET cc_start: 0.9131 (tmm) cc_final: 0.8778 (tmm) REVERT: D 327 TRP cc_start: 0.8940 (m100) cc_final: 0.8644 (m100) REVERT: F 100 SER cc_start: 0.8774 (p) cc_final: 0.8355 (t) REVERT: I 14 THR cc_start: 0.7633 (OUTLIER) cc_final: 0.7258 (p) REVERT: I 28 GLU cc_start: 0.7327 (tm-30) cc_final: 0.6963 (tm-30) REVERT: I 63 ASP cc_start: 0.8813 (t0) cc_final: 0.8494 (t0) REVERT: I 71 LYS cc_start: 0.8347 (mttt) cc_final: 0.8103 (mtpm) REVERT: J 52 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8356 (tttp) outliers start: 82 outliers final: 41 residues processed: 494 average time/residue: 1.2920 time to fit residues: 765.3423 Evaluate side-chains 494 residues out of total 3230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 443 time to evaluate : 3.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 1061 HIS Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1252 ASP Chi-restraints excluded: chain A residue 1258 THR Chi-restraints excluded: chain A residue 1370 GLU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 325 HIS Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 597 GLN Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 52 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 69 optimal weight: 0.8980 chunk 249 optimal weight: 4.9990 chunk 273 optimal weight: 3.9990 chunk 235 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 176 optimal weight: 40.0000 chunk 128 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1162 HIS ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 HIS B 245 GLN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN E 109 GLN I 36 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.126232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.078931 restraints weight = 64375.919| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.02 r_work: 0.2684 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 29513 Z= 0.172 Angle : 0.635 20.002 39945 Z= 0.312 Chirality : 0.045 0.253 4546 Planarity : 0.004 0.068 5132 Dihedral : 4.433 76.306 3942 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.54 % Allowed : 19.85 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.70 (0.14), residues: 3594 helix: 1.58 (0.14), residues: 1382 sheet: -0.52 (0.23), residues: 492 loop : -0.07 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 701 HIS 0.006 0.001 HIS B 375 PHE 0.025 0.001 PHE A 918 TYR 0.017 0.001 TYR B 273 ARG 0.017 0.001 ARG D 322 Details of bonding type rmsd hydrogen bonds : bond 0.04105 ( 1247) hydrogen bonds : angle 4.85729 ( 3495) metal coordination : bond 0.00727 ( 24) metal coordination : angle 5.52003 ( 33) covalent geometry : bond 0.00404 (29489) covalent geometry : angle 0.61525 (39912) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7188 Ramachandran restraints generated. 3594 Oldfield, 0 Emsley, 3594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7188 Ramachandran restraints generated. 3594 Oldfield, 0 Emsley, 3594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 444 time to evaluate : 3.733 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: A 28 GLU cc_start: 0.8912 (tt0) cc_final: 0.8636 (tm-30) REVERT: A 111 ARG cc_start: 0.8827 (mmm-85) cc_final: 0.8567 (mtp85) REVERT: A 153 THR cc_start: 0.8769 (m) cc_final: 0.8437 (p) REVERT: A 397 PHE cc_start: 0.8029 (t80) cc_final: 0.7656 (t80) REVERT: A 455 ASN cc_start: 0.9246 (t0) cc_final: 0.8878 (t0) REVERT: A 963 MET cc_start: 0.9062 (mtt) cc_final: 0.8843 (mtm) REVERT: A 1051 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8578 (tt0) REVERT: A 1055 GLN cc_start: 0.8353 (tt0) cc_final: 0.7817 (pt0) REVERT: A 1129 TRP cc_start: 0.8608 (p-90) cc_final: 0.8354 (p-90) REVERT: A 1144 MET cc_start: 0.7671 (ptp) cc_final: 0.7257 (ptt) REVERT: A 1145 TYR cc_start: 0.9022 (t80) cc_final: 0.8795 (t80) REVERT: A 1209 MET cc_start: 0.8628 (mtp) cc_final: 0.7987 (mmm) REVERT: A 1228 ARG cc_start: 0.8573 (mtp-110) cc_final: 0.8340 (mtm180) REVERT: A 1370 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8697 (mt-10) REVERT: A 1371 LYS cc_start: 0.8580 (tppt) cc_final: 0.8318 (tptm) REVERT: A 1393 GLN cc_start: 0.8239 (mp10) cc_final: 0.7989 (mp10) REVERT: B 163 MET cc_start: 0.7845 (ttm) cc_final: 0.7516 (mmm) REVERT: B 192 TYR cc_start: 0.8147 (p90) cc_final: 0.7735 (p90) REVERT: B 206 GLU cc_start: 0.8031 (pm20) cc_final: 0.7676 (pm20) REVERT: B 229 ARG cc_start: 0.6900 (OUTLIER) cc_final: 0.6521 (ptm160) REVERT: B 264 LYS cc_start: 0.7683 (mmmm) cc_final: 0.7387 (mptt) REVERT: B 281 MET cc_start: 0.8084 (tpt) cc_final: 0.7712 (tpt) REVERT: B 295 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8575 (mm) REVERT: B 410 ARG cc_start: 0.8513 (mtm-85) cc_final: 0.8210 (tpp-160) REVERT: B 523 THR cc_start: 0.7907 (m) cc_final: 0.7695 (m) REVERT: B 567 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6870 (mmm) REVERT: B 597 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7603 (mt0) REVERT: B 659 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6882 (mm-30) REVERT: B 744 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8002 (pm20) REVERT: B 821 MET cc_start: 0.4609 (OUTLIER) cc_final: 0.4103 (mmm) REVERT: B 982 MET cc_start: 0.7073 (tpp) cc_final: 0.6792 (tpp) REVERT: B 1129 ASP cc_start: 0.8794 (t0) cc_final: 0.8502 (t0) REVERT: C 88 MET cc_start: 0.9422 (mmp) cc_final: 0.9013 (mmp) REVERT: C 343 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.9005 (mt) REVERT: D 85 ASP cc_start: 0.8979 (m-30) cc_final: 0.8592 (m-30) REVERT: D 217 ILE cc_start: 0.5567 (OUTLIER) cc_final: 0.5211 (pp) REVERT: D 224 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7743 (mmtm) REVERT: F 100 SER cc_start: 0.8744 (p) cc_final: 0.8330 (t) REVERT: I 14 THR cc_start: 0.7585 (OUTLIER) cc_final: 0.7229 (p) REVERT: I 28 GLU cc_start: 0.7441 (tm-30) cc_final: 0.6938 (tm-30) REVERT: I 63 ASP cc_start: 0.8815 (t0) cc_final: 0.8505 (t0) REVERT: I 71 LYS cc_start: 0.8354 (mttt) cc_final: 0.8115 (mtpm) REVERT: J 52 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8307 (tttp) outliers start: 82 outliers final: 40 residues processed: 483 average time/residue: 1.3990 time to fit residues: 807.5846 Evaluate side-chains 486 residues out of total 3230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 434 time to evaluate : 3.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 1061 HIS Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1252 ASP Chi-restraints excluded: chain A residue 1370 GLU Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 325 HIS Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 597 GLN Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 821 MET Chi-restraints excluded: chain B residue 822 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 52 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 228 optimal weight: 3.9990 chunk 342 optimal weight: 0.9980 chunk 153 optimal weight: 20.0000 chunk 229 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 154 optimal weight: 9.9990 chunk 298 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 358 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1162 HIS ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN E 109 GLN I 36 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.125542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.077464 restraints weight = 62171.703| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.96 r_work: 0.2706 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 29513 Z= 0.183 Angle : 0.657 22.004 39945 Z= 0.319 Chirality : 0.046 0.278 4546 Planarity : 0.004 0.068 5132 Dihedral : 4.473 75.778 3942 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.23 % Allowed : 20.40 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 (0.14), residues: 3594 helix: 1.58 (0.14), residues: 1381 sheet: -0.48 (0.23), residues: 490 loop : -0.11 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 701 HIS 0.006 0.001 HIS B 375 PHE 0.031 0.002 PHE B 389 TYR 0.017 0.001 TYR B 273 ARG 0.017 0.001 ARG D 322 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 1247) hydrogen bonds : angle 4.88291 ( 3495) metal coordination : bond 0.00745 ( 24) metal coordination : angle 5.66464 ( 33) covalent geometry : bond 0.00432 (29489) covalent geometry : angle 0.63645 (39912) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7188 Ramachandran restraints generated. 3594 Oldfield, 0 Emsley, 3594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7188 Ramachandran restraints generated. 3594 Oldfield, 0 Emsley, 3594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 435 time to evaluate : 3.414 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: A 28 GLU cc_start: 0.8906 (tt0) cc_final: 0.8623 (tm-30) REVERT: A 111 ARG cc_start: 0.8816 (mmm-85) cc_final: 0.8561 (mtp85) REVERT: A 153 THR cc_start: 0.8794 (m) cc_final: 0.8474 (p) REVERT: A 455 ASN cc_start: 0.9207 (t0) cc_final: 0.8825 (t0) REVERT: A 963 MET cc_start: 0.9081 (mtt) cc_final: 0.8868 (mtm) REVERT: A 1055 GLN cc_start: 0.8367 (tt0) cc_final: 0.7848 (pt0) REVERT: A 1129 TRP cc_start: 0.8632 (p-90) cc_final: 0.8327 (p-90) REVERT: A 1144 MET cc_start: 0.7689 (ptp) cc_final: 0.7304 (ptt) REVERT: A 1145 TYR cc_start: 0.9021 (t80) cc_final: 0.8787 (t80) REVERT: A 1209 MET cc_start: 0.8659 (mtp) cc_final: 0.8048 (mmm) REVERT: A 1227 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8845 (mm) REVERT: A 1228 ARG cc_start: 0.8532 (mtp-110) cc_final: 0.8296 (mtm180) REVERT: A 1240 MET cc_start: 0.8254 (ppp) cc_final: 0.7896 (pmm) REVERT: A 1370 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8692 (mt-10) REVERT: A 1371 LYS cc_start: 0.8622 (tppt) cc_final: 0.8380 (tptm) REVERT: A 1393 GLN cc_start: 0.8302 (mp10) cc_final: 0.8074 (mp10) REVERT: B 163 MET cc_start: 0.7780 (ttm) cc_final: 0.7449 (mmm) REVERT: B 192 TYR cc_start: 0.8180 (p90) cc_final: 0.7748 (p90) REVERT: B 206 GLU cc_start: 0.8075 (pm20) cc_final: 0.7702 (pm20) REVERT: B 229 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.6650 (ptm160) REVERT: B 264 LYS cc_start: 0.7703 (mmmm) cc_final: 0.7426 (mptt) REVERT: B 281 MET cc_start: 0.8045 (tpt) cc_final: 0.7692 (tpt) REVERT: B 376 MET cc_start: 0.8062 (tpp) cc_final: 0.7779 (mmt) REVERT: B 410 ARG cc_start: 0.8508 (mtm-85) cc_final: 0.8246 (tpp-160) REVERT: B 523 THR cc_start: 0.7944 (m) cc_final: 0.7707 (m) REVERT: B 567 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6902 (mmm) REVERT: B 597 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7632 (mt0) REVERT: B 659 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6886 (mm-30) REVERT: B 744 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8011 (pm20) REVERT: B 821 MET cc_start: 0.4614 (OUTLIER) cc_final: 0.3951 (mmm) REVERT: B 982 MET cc_start: 0.7076 (tpp) cc_final: 0.6789 (tpp) REVERT: B 1129 ASP cc_start: 0.8827 (t0) cc_final: 0.8541 (t0) REVERT: C 88 MET cc_start: 0.9394 (mmp) cc_final: 0.8983 (mmp) REVERT: C 343 ILE cc_start: 0.9407 (OUTLIER) cc_final: 0.9061 (mt) REVERT: D 85 ASP cc_start: 0.8911 (m-30) cc_final: 0.8515 (m-30) REVERT: D 187 MET cc_start: 0.9051 (mmt) cc_final: 0.8731 (mpp) REVERT: D 217 ILE cc_start: 0.5573 (OUTLIER) cc_final: 0.5246 (pp) REVERT: D 224 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7699 (mmtm) REVERT: D 327 TRP cc_start: 0.8921 (m100) cc_final: 0.8570 (m100) REVERT: F 100 SER cc_start: 0.8763 (p) cc_final: 0.8361 (t) REVERT: I 14 THR cc_start: 0.7560 (OUTLIER) cc_final: 0.7203 (p) REVERT: I 63 ASP cc_start: 0.8818 (t0) cc_final: 0.8529 (t0) REVERT: I 71 LYS cc_start: 0.8394 (mttt) cc_final: 0.8159 (mtpm) REVERT: J 52 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8388 (tttp) outliers start: 72 outliers final: 46 residues processed: 475 average time/residue: 1.3629 time to fit residues: 773.9965 Evaluate side-chains 487 residues out of total 3230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 429 time to evaluate : 3.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 1061 HIS Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1252 ASP Chi-restraints excluded: chain A residue 1258 THR Chi-restraints excluded: chain A residue 1370 GLU Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 325 HIS Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 597 GLN Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 821 MET Chi-restraints excluded: chain B residue 822 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 52 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 91 optimal weight: 1.9990 chunk 142 optimal weight: 20.0000 chunk 170 optimal weight: 0.0980 chunk 13 optimal weight: 0.4980 chunk 182 optimal weight: 0.0470 chunk 167 optimal weight: 5.9990 chunk 208 optimal weight: 0.8980 chunk 234 optimal weight: 5.9990 chunk 237 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1162 HIS ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 HIS B 245 GLN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN I 36 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.127832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.080189 restraints weight = 63434.900| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 3.00 r_work: 0.2755 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 29513 Z= 0.120 Angle : 0.646 21.393 39945 Z= 0.314 Chirality : 0.045 0.254 4546 Planarity : 0.004 0.070 5132 Dihedral : 4.382 76.072 3942 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.67 % Allowed : 20.96 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.77 (0.14), residues: 3594 helix: 1.65 (0.14), residues: 1377 sheet: -0.45 (0.23), residues: 491 loop : -0.05 (0.15), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 701 HIS 0.006 0.001 HIS B 375 PHE 0.029 0.001 PHE B 389 TYR 0.023 0.001 TYR E 123 ARG 0.015 0.001 ARG D 322 Details of bonding type rmsd hydrogen bonds : bond 0.03735 ( 1247) hydrogen bonds : angle 4.79254 ( 3495) metal coordination : bond 0.00649 ( 24) metal coordination : angle 5.12027 ( 33) covalent geometry : bond 0.00275 (29489) covalent geometry : angle 0.62893 (39912) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7188 Ramachandran restraints generated. 3594 Oldfield, 0 Emsley, 3594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7188 Ramachandran restraints generated. 3594 Oldfield, 0 Emsley, 3594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 471 time to evaluate : 3.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8810 (tt0) cc_final: 0.8590 (tm-30) REVERT: A 111 ARG cc_start: 0.8798 (mmm-85) cc_final: 0.8557 (mtp85) REVERT: A 153 THR cc_start: 0.8760 (m) cc_final: 0.8453 (p) REVERT: A 455 ASN cc_start: 0.9180 (t0) cc_final: 0.8810 (t0) REVERT: A 963 MET cc_start: 0.9089 (mtt) cc_final: 0.8873 (mtm) REVERT: A 1055 GLN cc_start: 0.8327 (tt0) cc_final: 0.7803 (pt0) REVERT: A 1129 TRP cc_start: 0.8623 (p-90) cc_final: 0.8372 (p-90) REVERT: A 1144 MET cc_start: 0.7670 (ptp) cc_final: 0.7280 (ptt) REVERT: A 1145 TYR cc_start: 0.8968 (t80) cc_final: 0.8757 (t80) REVERT: A 1209 MET cc_start: 0.8631 (mtp) cc_final: 0.8052 (mmm) REVERT: A 1228 ARG cc_start: 0.8545 (mtp-110) cc_final: 0.8150 (mtp-110) REVERT: A 1240 MET cc_start: 0.8173 (ppp) cc_final: 0.7855 (pmm) REVERT: A 1393 GLN cc_start: 0.8275 (mp10) cc_final: 0.8060 (mp10) REVERT: B 163 MET cc_start: 0.7737 (ttm) cc_final: 0.7408 (mmm) REVERT: B 192 TYR cc_start: 0.8123 (p90) cc_final: 0.7742 (p90) REVERT: B 206 GLU cc_start: 0.8056 (pm20) cc_final: 0.7686 (pm20) REVERT: B 264 LYS cc_start: 0.7671 (mmmm) cc_final: 0.7403 (mptt) REVERT: B 281 MET cc_start: 0.8028 (tpt) cc_final: 0.7652 (tpt) REVERT: B 289 GLU cc_start: 0.8864 (tt0) cc_final: 0.8595 (tp30) REVERT: B 293 PHE cc_start: 0.8856 (m-80) cc_final: 0.8311 (m-80) REVERT: B 376 MET cc_start: 0.7993 (tpp) cc_final: 0.7663 (mmt) REVERT: B 410 ARG cc_start: 0.8461 (mtm-85) cc_final: 0.8180 (tpp-160) REVERT: B 525 ASN cc_start: 0.8162 (m110) cc_final: 0.7570 (m110) REVERT: B 567 MET cc_start: 0.7157 (OUTLIER) cc_final: 0.6893 (mmm) REVERT: B 597 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7630 (mt0) REVERT: B 659 GLU cc_start: 0.7356 (mm-30) cc_final: 0.6933 (mm-30) REVERT: B 744 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7968 (pm20) REVERT: B 821 MET cc_start: 0.4522 (OUTLIER) cc_final: 0.3837 (mmm) REVERT: B 982 MET cc_start: 0.7020 (tpp) cc_final: 0.6713 (tpp) REVERT: B 1129 ASP cc_start: 0.8800 (t0) cc_final: 0.8515 (t0) REVERT: C 88 MET cc_start: 0.9380 (mmp) cc_final: 0.8999 (mmp) REVERT: C 273 ASP cc_start: 0.8060 (t0) cc_final: 0.7726 (t0) REVERT: C 343 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.9053 (mt) REVERT: D 85 ASP cc_start: 0.8907 (m-30) cc_final: 0.8513 (m-30) REVERT: D 187 MET cc_start: 0.9036 (mmt) cc_final: 0.8698 (mpp) REVERT: D 217 ILE cc_start: 0.5785 (OUTLIER) cc_final: 0.5370 (pp) REVERT: D 224 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7657 (mmtm) REVERT: D 292 MET cc_start: 0.9109 (tmm) cc_final: 0.8431 (tmm) REVERT: D 296 LEU cc_start: 0.9524 (mt) cc_final: 0.9281 (mt) REVERT: D 327 TRP cc_start: 0.8894 (m100) cc_final: 0.8528 (m100) REVERT: F 100 SER cc_start: 0.8728 (p) cc_final: 0.8347 (t) REVERT: I 14 THR cc_start: 0.7481 (OUTLIER) cc_final: 0.7137 (p) REVERT: I 48 GLU cc_start: 0.7046 (tp30) cc_final: 0.6748 (tm-30) REVERT: I 63 ASP cc_start: 0.8735 (t0) cc_final: 0.8461 (t0) REVERT: I 71 LYS cc_start: 0.8360 (mttt) cc_final: 0.8121 (mtpm) outliers start: 54 outliers final: 30 residues processed: 496 average time/residue: 1.2594 time to fit residues: 747.2420 Evaluate side-chains 476 residues out of total 3230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 438 time to evaluate : 3.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 1061 HIS Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1252 ASP Chi-restraints excluded: chain A residue 1258 THR Chi-restraints excluded: chain B residue 325 HIS Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 597 GLN Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 821 MET Chi-restraints excluded: chain B residue 822 ASN Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1088 MET Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 181 optimal weight: 6.9990 chunk 321 optimal weight: 10.0000 chunk 255 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 214 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 267 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1162 HIS ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 HIS B1162 GLN B1227 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 GLN E 37 ASN I 36 ASN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.123941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.076233 restraints weight = 55036.004| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.78 r_work: 0.2686 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.119 29513 Z= 0.284 Angle : 0.709 22.993 39945 Z= 0.348 Chirality : 0.049 0.338 4546 Planarity : 0.004 0.066 5132 Dihedral : 4.546 75.470 3941 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.64 % Allowed : 21.70 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.61 (0.14), residues: 3594 helix: 1.53 (0.14), residues: 1377 sheet: -0.46 (0.23), residues: 470 loop : -0.18 (0.15), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 701 HIS 0.006 0.001 HIS B 375 PHE 0.025 0.002 PHE A 952 TYR 0.017 0.002 TYR B 273 ARG 0.017 0.001 ARG D 322 Details of bonding type rmsd hydrogen bonds : bond 0.04519 ( 1247) hydrogen bonds : angle 4.97837 ( 3495) metal coordination : bond 0.00942 ( 24) metal coordination : angle 5.99298 ( 33) covalent geometry : bond 0.00679 (29489) covalent geometry : angle 0.68843 (39912) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25753.57 seconds wall clock time: 441 minutes 32.60 seconds (26492.60 seconds total)