Starting phenix.real_space_refine on Sun Aug 9 23:54:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e6z_27931/08_2026/8e6z_27931_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e6z_27931/08_2026/8e6z_27931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8e6z_27931/08_2026/8e6z_27931_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e6z_27931/08_2026/8e6z_27931_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e6z_27931/08_2026/8e6z_27931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e6z_27931/08_2026/8e6z_27931.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 97 5.49 5 Mg 1 5.21 5 S 113 5.16 5 C 17415 2.51 5 N 4980 2.21 5 O 5658 1.98 5 H 11239 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39505 Number of models: 1 Model: "" Number of chains: 10 Chain: "5" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 913 Classifications: {'DNA': 33} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 32} Chain breaks: 1 Chain: "6" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 1029 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "7" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 676 Classifications: {'RNA': 27} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 9, 'rna3p_pyr': 13} Link IDs: {'rna2p': 5, 'rna3p': 21} Chain: "A" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1280} Chain: "B" Number of atoms: 21000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 21000 Classifications: {'peptide': 1335} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 54, 'TRANS': 1277} Chain breaks: 2 Chain: "C" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1698 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1677 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 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: "E" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 550 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "F" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1392 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 164} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14070 SG CYS B 70 106.877 63.429 62.635 1.00 45.60 S ATOM 14329 SG CYS B 85 111.495 64.726 62.469 1.00 49.94 S ATOM 25911 SG CYS B 814 77.254 78.320 122.735 1.00 22.38 S ATOM 27048 SG CYS B 888 76.943 78.146 118.214 1.00 20.48 S ATOM 27139 SG CYS B 895 76.573 75.353 120.516 1.00 14.28 S ATOM 27176 SG CYS B 898 74.004 77.643 121.396 1.00 16.02 S Time building chain proxies: 6.86, per 1000 atoms: 0.17 Number of scatterers: 39505 At special positions: 0 Unit cell: (166.764, 162.488, 160.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 113 16.00 P 97 15.00 Mg 1 11.99 O 5658 8.00 N 4980 7.00 C 17415 6.00 H 11239 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 72 " - pdb=" SG CYS B 88 " distance=2.12 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 Atom "ATOM 311 O5' DA 5 100 .*. O " rejected from bonding due to valence issues. Atom "ATOM 311 O5' DA 5 100 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.62 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1502 " pdb="ZN ZN B1502 " - pdb=" SG CYS B 70 " pdb="ZN ZN B1502 " - pdb=" SG CYS B 85 " pdb=" ZN B1503 " pdb="ZN ZN B1503 " - pdb=" SG CYS B 888 " pdb="ZN ZN B1503 " - pdb=" SG CYS B 895 " pdb="ZN ZN B1503 " - pdb=" SG CYS B 814 " pdb="ZN ZN B1503 " - pdb=" SG CYS B 898 " Number of angles added : 6 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6194 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 48 sheets defined 35.6% alpha, 15.0% beta 28 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 5.83 Creating SS restraints... Processing helix chain 'A' and resid 4 through 8 Processing helix chain 'A' and resid 28 through 39 Processing helix chain 'A' and resid 48 through 56 removed outlier: 4.129A pdb=" N ALA A 52 " --> pdb=" O GLY A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 163 through 167 removed outlier: 3.840A pdb=" N SER A 166 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER A 167 " --> pdb=" O THR A 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 163 through 167' Processing helix chain 'A' and resid 206 through 213 removed outlier: 4.057A pdb=" N LEU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 225 Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.579A pdb=" N ARG A 247 " --> pdb=" O GLU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'A' and resid 318 through 327 removed outlier: 3.688A pdb=" N GLN A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 358 through 371 Processing helix chain 'A' and resid 377 through 389 removed outlier: 4.129A pdb=" N PHE A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 408 Processing helix chain 'A' and resid 421 through 438 removed outlier: 3.758A pdb=" N ILE A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 480 removed outlier: 4.512A pdb=" N SER A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 508 Processing helix chain 'A' and resid 519 through 527 Processing helix chain 'A' and resid 609 through 614 removed outlier: 4.046A pdb=" N ASN A 613 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 609 through 614' Processing helix chain 'A' and resid 670 through 674 Processing helix chain 'A' and resid 675 through 688 Processing helix chain 'A' and resid 704 through 711 Processing helix chain 'A' and resid 738 through 741 removed outlier: 3.792A pdb=" N MET A 741 " --> pdb=" O GLU A 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 738 through 741' Processing helix chain 'A' and resid 820 through 825 Processing helix chain 'A' and resid 858 through 863 Processing helix chain 'A' and resid 896 through 901 Processing helix chain 'A' and resid 902 through 907 removed outlier: 3.932A pdb=" N PHE A 906 " --> pdb=" O LEU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 981 removed outlier: 4.146A pdb=" N ALA A 981 " --> pdb=" O ALA A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 998 removed outlier: 3.589A pdb=" N LEU A 998 " --> pdb=" O ASP A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1038 removed outlier: 3.627A pdb=" N GLN A1038 " --> pdb=" O ARG A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1106 removed outlier: 4.548A pdb=" N SER A1105 " --> pdb=" O LEU A1101 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A1106 " --> pdb=" O GLY A1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1101 through 1106' Processing helix chain 'A' and resid 1109 through 1134 removed outlier: 3.695A pdb=" N LEU A1113 " --> pdb=" O ILE A1109 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A1134 " --> pdb=" O ALA A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1151 removed outlier: 3.879A pdb=" N LEU A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU A1151 " --> pdb=" O ARG A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1164 removed outlier: 4.191A pdb=" N THR A1163 " --> pdb=" O ASP A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1167 through 1177 Processing helix chain 'A' and resid 1191 through 1202 removed outlier: 3.552A pdb=" N GLY A1202 " --> pdb=" O LEU A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1281 removed outlier: 3.625A pdb=" N TYR A1281 " --> pdb=" O ALA A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1292 Processing helix chain 'A' and resid 1297 through 1310 Processing helix chain 'A' and resid 1320 through 1332 removed outlier: 3.651A pdb=" N ASN A1324 " --> pdb=" O PRO A1320 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 33 Processing helix chain 'B' and resid 131 through 140 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 180 through 191 removed outlier: 3.745A pdb=" N ALA B 184 " --> pdb=" O MET B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 207 Processing helix chain 'B' and resid 210 through 230 removed outlier: 3.777A pdb=" N ARG B 220 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU B 223 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 236 Processing helix chain 'B' and resid 246 through 250 Processing helix chain 'B' and resid 263 through 285 removed outlier: 3.808A pdb=" N ASP B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 308 removed outlier: 3.904A pdb=" N ASN B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 332 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 370 through 377 Processing helix chain 'B' and resid 377 through 389 removed outlier: 3.547A pdb=" N GLY B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 404 removed outlier: 3.689A pdb=" N ALA B 397 " --> pdb=" O THR B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 417 removed outlier: 3.566A pdb=" N ILE B 411 " --> pdb=" O VAL B 407 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG B 417 " --> pdb=" O ASP B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 432 No H-bonds generated for 'chain 'B' and resid 430 through 432' Processing helix chain 'B' and resid 450 through 458 removed outlier: 3.649A pdb=" N CYS B 454 " --> pdb=" O HIS B 450 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA B 455 " --> pdb=" O PRO B 451 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 483 Processing helix chain 'B' and resid 504 through 514 removed outlier: 3.521A pdb=" N LEU B 508 " --> pdb=" O GLN B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 539 Processing helix chain 'B' and resid 573 through 581 removed outlier: 3.610A pdb=" N ALA B 577 " --> pdb=" O THR B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 592 Processing helix chain 'B' and resid 598 through 613 Processing helix chain 'B' and resid 614 through 636 removed outlier: 3.645A pdb=" N GLY B 636 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 670 removed outlier: 3.533A pdb=" N SER B 670 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 703 Processing helix chain 'B' and resid 720 through 728 Processing helix chain 'B' and resid 733 through 742 removed outlier: 3.861A pdb=" N ILE B 737 " --> pdb=" O SER B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 805 removed outlier: 3.851A pdb=" N GLY B 782 " --> pdb=" O GLY B 778 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA B 791 " --> pdb=" O ALA B 787 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN B 792 " --> pdb=" O LEU B 788 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN B 805 " --> pdb=" O VAL B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 839 removed outlier: 3.642A pdb=" N ARG B 838 " --> pdb=" O PRO B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 876 removed outlier: 3.797A pdb=" N ASN B 875 " --> pdb=" O LEU B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 895 through 900 removed outlier: 3.522A pdb=" N TYR B 899 " --> pdb=" O CYS B 895 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY B 900 " --> pdb=" O ALA B 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 895 through 900' Processing helix chain 'B' and resid 914 through 925 removed outlier: 4.007A pdb=" N ILE B 918 " --> pdb=" O ALA B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 928 No H-bonds generated for 'chain 'B' and resid 926 through 928' Processing helix chain 'B' and resid 1137 through 1146 Processing helix chain 'B' and resid 1216 through 1224 Processing helix chain 'B' and resid 1225 through 1244 removed outlier: 4.195A pdb=" N VAL B1240 " --> pdb=" O GLU B1236 " (cutoff:3.500A) Processing helix chain 'B' and resid 1250 through 1261 Processing helix chain 'B' and resid 1282 through 1294 removed outlier: 3.542A pdb=" N ALA B1294 " --> pdb=" O ARG B1290 " (cutoff:3.500A) Processing helix chain 'B' and resid 1308 through 1315 Processing helix chain 'B' and resid 1327 through 1339 removed outlier: 3.828A pdb=" N VAL B1331 " --> pdb=" O GLU B1327 " (cutoff:3.500A) Processing helix chain 'B' and resid 1346 through 1353 removed outlier: 3.806A pdb=" N ASN B1350 " --> pdb=" O GLY B1346 " (cutoff:3.500A) Processing helix chain 'B' and resid 1361 through 1372 removed outlier: 4.419A pdb=" N TYR B1365 " --> pdb=" O THR B1361 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 50 removed outlier: 3.548A pdb=" N THR C 38 " --> pdb=" O GLY C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 87 Processing helix chain 'C' and resid 212 through 228 Processing helix chain 'C' and resid 229 through 232 removed outlier: 3.840A pdb=" N VAL C 232 " --> pdb=" O GLU C 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 229 through 232' Processing helix chain 'D' and resid 34 through 50 removed outlier: 4.040A pdb=" N THR D 38 " --> pdb=" O GLY D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 87 removed outlier: 3.560A pdb=" N GLY D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 115 No H-bonds generated for 'chain 'D' and resid 113 through 115' Processing helix chain 'D' and resid 212 through 227 Processing helix chain 'E' and resid 6 through 12 Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.527A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 60 through 71 Processing helix chain 'F' and resid 18 through 33 Processing helix chain 'F' and resid 35 through 39 removed outlier: 3.816A pdb=" N PHE F 39 " --> pdb=" O GLU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 86 Processing helix chain 'F' and resid 105 through 117 removed outlier: 3.647A pdb=" N ASP F 109 " --> pdb=" O ASP F 105 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU F 115 " --> pdb=" O ILE F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 178 No H-bonds generated for 'chain 'F' and resid 176 through 178' Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 6.570A pdb=" N LYS A 13 " --> pdb=" O ALA A1183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.927A pdb=" N LYS A 99 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR A 73 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ARG A 97 " --> pdb=" O TYR A 73 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU A 75 " --> pdb=" O PRO A 95 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ALA A 94 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLU A 126 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU A 96 " --> pdb=" O MET A 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA4, first strand: chain 'A' and resid 451 through 454 removed outlier: 6.321A pdb=" N SER A 147 " --> pdb=" O SER A 531 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 158 removed outlier: 3.580A pdb=" N LEU A 184 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 228 through 231 Processing sheet with id=AA7, first strand: chain 'A' and resid 239 through 240 Processing sheet with id=AA8, first strand: chain 'A' and resid 255 through 257 removed outlier: 6.576A pdb=" N ALA A 257 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N VAL A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 302 removed outlier: 7.193A pdb=" N TYR A 301 " --> pdb=" O ILE A 310 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 580 through 581 removed outlier: 3.687A pdb=" N GLU A 588 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A 593 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLU A 602 " --> pdb=" O LYS A 593 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 580 through 581 removed outlier: 3.687A pdb=" N GLU A 588 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 748 through 752 removed outlier: 6.632A pdb=" N ARG A 731 " --> pdb=" O VAL A 727 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL A 727 " --> pdb=" O ARG A 731 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL A 733 " --> pdb=" O GLN A 725 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 757 through 758 removed outlier: 3.995A pdb=" N THR A 757 " --> pdb=" O ILE A 765 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 768 through 769 Processing sheet with id=AB6, first strand: chain 'A' and resid 789 through 790 removed outlier: 3.590A pdb=" N ASP A 790 " --> pdb=" O GLU A 793 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1066 through 1067 removed outlier: 4.452A pdb=" N THR A1226 " --> pdb=" O PHE A 804 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N ILE A1096 " --> pdb=" O ASN A 799 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ARG A 801 " --> pdb=" O ILE A1096 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU A1098 " --> pdb=" O ARG A 801 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA A 803 " --> pdb=" O LEU A1098 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 817 " --> pdb=" O VAL A1097 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE A 816 " --> pdb=" O SER A1077 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE A1079 " --> pdb=" O ILE A 816 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 818 " --> pdb=" O ILE A1079 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1066 through 1067 Processing sheet with id=AB9, first strand: chain 'A' and resid 846 through 847 removed outlier: 6.412A pdb=" N ASP A 842 " --> pdb=" O VAL A1046 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL A1046 " --> pdb=" O ASP A 842 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP A 930 " --> pdb=" O TYR A1053 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA A1055 " --> pdb=" O VAL A 928 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N VAL A 928 " --> pdb=" O ALA A1055 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 882 through 884 removed outlier: 3.626A pdb=" N VAL A 884 " --> pdb=" O LEU A 918 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 887 through 889 Processing sheet with id=AC3, first strand: chain 'A' and resid 1244 through 1246 Processing sheet with id=AC4, first strand: chain 'A' and resid 1269 through 1270 Processing sheet with id=AC5, first strand: chain 'A' and resid 1335 through 1337 Processing sheet with id=AC6, first strand: chain 'B' and resid 34 through 37 removed outlier: 4.452A pdb=" N SER B 34 " --> pdb=" O MET B 102 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N HIS B 104 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLY B 36 " --> pdb=" O HIS B 104 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N GLU B 106 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 107 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR B 240 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 10.938A pdb=" N SER B 109 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N ILE B 238 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AC8, first strand: chain 'B' and resid 253 through 254 removed outlier: 4.414A pdb=" N VAL B 253 " --> pdb=" O ALA B 261 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 526 through 527 Processing sheet with id=AD1, first strand: chain 'B' and resid 706 through 708 removed outlier: 3.685A pdb=" N GLU B 714 " --> pdb=" O ILE B 707 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 821 through 822 Processing sheet with id=AD3, first strand: chain 'B' and resid 849 through 850 removed outlier: 4.608A pdb=" N ASP B 855 " --> pdb=" O LYS B 850 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 957 through 961 removed outlier: 3.803A pdb=" N THR B 980 " --> pdb=" O VAL B 997 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 965 through 967 Processing sheet with id=AD6, first strand: chain 'B' and resid 1034 through 1038 removed outlier: 3.619A pdb=" N ARG B1036 " --> pdb=" O LYS B1079 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS B1079 " --> pdb=" O ARG B1036 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1046 through 1049 removed outlier: 4.089A pdb=" N GLN B1049 " --> pdb=" O SER B1058 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER B1058 " --> pdb=" O GLN B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1187 through 1190 Processing sheet with id=AD9, first strand: chain 'B' and resid 1279 through 1281 removed outlier: 7.344A pdb=" N THR B1301 " --> pdb=" O VAL B1267 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 12 through 13 removed outlier: 6.340A pdb=" N ASP C 199 " --> pdb=" O PRO C 30 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 202 " --> pdb=" O ASN C 186 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 52 through 53 removed outlier: 3.521A pdb=" N GLY C 53 " --> pdb=" O GLY C 149 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 115 through 116 removed outlier: 4.248A pdb=" N THR C 101 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N SER C 141 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ILE C 61 " --> pdb=" O SER C 141 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG C 143 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL C 59 " --> pdb=" O ARG C 143 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS C 145 " --> pdb=" O THR C 57 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 90 through 91 Processing sheet with id=AE5, first strand: chain 'C' and resid 108 through 111 removed outlier: 3.837A pdb=" N CYS C 131 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 23 through 31 removed outlier: 7.013A pdb=" N ASP D 199 " --> pdb=" O PRO D 30 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG D 182 " --> pdb=" O GLU D 206 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 53 through 61 removed outlier: 4.075A pdb=" N ALA D 55 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LYS D 145 " --> pdb=" O THR D 57 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL D 59 " --> pdb=" O ARG D 143 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ARG D 143 " --> pdb=" O VAL D 59 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 90 through 91 Processing sheet with id=AE9, first strand: chain 'D' and resid 108 through 111 removed outlier: 4.050A pdb=" N CYS D 131 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 152 through 153 removed outlier: 3.624A pdb=" N VAL D 153 " --> pdb=" O ALA D 175 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 68 through 73 removed outlier: 7.688A pdb=" N VAL F 11 " --> pdb=" O PHE F 92 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N PHE F 92 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLN F 13 " --> pdb=" O MET F 90 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 133 through 134 removed outlier: 3.685A pdb=" N GLU F 149 " --> pdb=" O LYS F 159 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LYS F 159 " --> pdb=" O GLU F 149 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL F 171 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL F 162 " --> pdb=" O THR F 169 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE F 164 " --> pdb=" O ARG F 167 " (cutoff:3.500A) 1009 hydrogen bonds defined for protein. 2835 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 73 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 9.97 Time building geometry restraints manager: 4.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11195 1.03 - 1.23: 464 1.23 - 1.42: 11396 1.42 - 1.62: 16870 1.62 - 1.82: 203 Bond restraints: 40128 Sorted by residual: bond pdb=" C PHE A 828 " pdb=" N THR A 829 " ideal model delta sigma weight residual 1.331 1.535 -0.205 1.43e-02 4.89e+03 2.05e+02 bond pdb=" C PRO F 102 " pdb=" N ILE F 103 " ideal model delta sigma weight residual 1.332 1.522 -0.190 1.36e-02 5.41e+03 1.95e+02 bond pdb=" CA THR B 93 " pdb=" C THR B 93 " ideal model delta sigma weight residual 1.523 1.687 -0.164 1.34e-02 5.57e+03 1.50e+02 bond pdb=" N3 U 7 17 " pdb=" H3 U 7 17 " ideal model delta sigma weight residual 0.860 1.041 -0.181 2.00e-02 2.50e+03 8.17e+01 bond pdb=" N3 DT 6 24 " pdb=" H3 DT 6 24 " ideal model delta sigma weight residual 0.860 1.041 -0.181 2.00e-02 2.50e+03 8.15e+01 ... (remaining 40123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.68: 65040 9.68 - 19.35: 30 19.35 - 29.03: 1 29.03 - 38.70: 1 38.70 - 48.38: 2 Bond angle restraints: 65074 Sorted by residual: angle pdb=" O3' DG 6 27 " pdb=" P DA 6 28 " pdb=" O5' DA 6 28 " ideal model delta sigma weight residual 104.00 147.99 -43.99 1.90e+00 2.77e-01 5.36e+02 angle pdb=" H2' DA 5 110 " pdb=" C2' DA 5 110 " pdb="H2'' DA 5 110 " ideal model delta sigma weight residual 109.00 75.98 33.02 1.50e+00 4.44e-01 4.85e+02 angle pdb=" O3' DG 6 27 " pdb=" P DA 6 28 " pdb=" OP1 DA 6 28 " ideal model delta sigma weight residual 108.00 59.62 48.38 3.00e+00 1.11e-01 2.60e+02 angle pdb=" C3' DA 6 28 " pdb=" O3' DA 6 28 " pdb=" P DT 6 29 " ideal model delta sigma weight residual 119.70 136.30 -16.60 1.20e+00 6.94e-01 1.91e+02 angle pdb=" CA PRO F 102 " pdb=" C PRO F 102 " pdb=" N ILE F 103 " ideal model delta sigma weight residual 115.12 131.74 -16.62 1.25e+00 6.40e-01 1.77e+02 ... (remaining 65069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 20084 35.99 - 71.98: 876 71.98 - 107.97: 28 107.97 - 143.96: 2 143.96 - 179.95: 9 Dihedral angle restraints: 20999 sinusoidal: 10953 harmonic: 10046 Sorted by residual: dihedral pdb=" CA VAL C 192 " pdb=" C VAL C 192 " pdb=" N GLU C 193 " pdb=" CA GLU C 193 " ideal model delta harmonic sigma weight residual -180.00 -126.65 -53.35 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" O4' U 7 16 " pdb=" C1' U 7 16 " pdb=" N1 U 7 16 " pdb=" C2 U 7 16 " ideal model delta sinusoidal sigma weight residual 200.00 43.62 156.38 1 1.50e+01 4.44e-03 8.18e+01 dihedral pdb=" CA GLN B1326 " pdb=" C GLN B1326 " pdb=" N GLU B1327 " pdb=" CA GLU B1327 " ideal model delta harmonic sigma weight residual -180.00 -138.06 -41.94 0 5.00e+00 4.00e-02 7.03e+01 ... (remaining 20996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 4118 0.113 - 0.227: 369 0.227 - 0.340: 19 0.340 - 0.454: 4 0.454 - 0.567: 2 Chirality restraints: 4512 Sorted by residual: chirality pdb=" C3' U 7 17 " pdb=" C4' U 7 17 " pdb=" O3' U 7 17 " pdb=" C2' U 7 17 " both_signs ideal model delta sigma weight residual False -2.74 -2.18 -0.57 2.00e-01 2.50e+01 8.04e+00 chirality pdb=" CB ILE A1079 " pdb=" CA ILE A1079 " pdb=" CG1 ILE A1079 " pdb=" CG2 ILE A1079 " both_signs ideal model delta sigma weight residual False 2.64 2.10 0.54 2.00e-01 2.50e+01 7.28e+00 chirality pdb=" CA TYR B 46 " pdb=" N TYR B 46 " pdb=" C TYR B 46 " pdb=" CB TYR B 46 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.85e+00 ... (remaining 4509 not shown) Planarity restraints: 6142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 232 " 0.211 2.00e-02 2.50e+03 2.51e-01 9.44e+02 pdb=" CG ASN B 232 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN B 232 " -0.203 2.00e-02 2.50e+03 pdb=" ND2 ASN B 232 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN B 232 " 0.385 2.00e-02 2.50e+03 pdb="HD22 ASN B 232 " -0.379 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 285 " -0.032 2.00e-02 2.50e+03 6.04e-02 3.64e+01 pdb=" N ALA B 286 " 0.104 2.00e-02 2.50e+03 pdb=" CA ALA B 286 " -0.027 2.00e-02 2.50e+03 pdb=" H ALA B 286 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 41 " 0.028 2.00e-02 2.50e+03 6.00e-02 3.59e+01 pdb=" C GLU F 41 " -0.103 2.00e-02 2.50e+03 pdb=" O GLU F 41 " 0.043 2.00e-02 2.50e+03 pdb=" N VAL F 42 " 0.032 2.00e-02 2.50e+03 ... (remaining 6139 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.75: 97 1.75 - 2.46: 15019 2.46 - 3.18: 81511 3.18 - 3.89: 122426 3.89 - 4.60: 189298 Nonbonded interactions: 408351 Sorted by model distance: nonbonded pdb=" C5' DA 5 100 " pdb=" OG SER F 16 " model vdw 1.038 3.100 nonbonded pdb=" O PRO A 847 " pdb=" CB PRO A 889 " model vdw 1.117 3.100 nonbonded pdb=" O5' DA 5 100 " pdb=" CB SER F 16 " model vdw 1.140 3.100 nonbonded pdb=" C4' DA 5 100 " pdb=" OG SER F 16 " model vdw 1.219 3.100 nonbonded pdb=" H42 DC 6 18 " pdb=" H1 G 7 32 " model vdw 1.266 2.100 ... (remaining 408346 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 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 7 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 158 or resid 169 through 232)) selection = (chain 'D' and (resid 7 through 190 or (resid 191 through 192 and (name N or nam \ e CA or name C or name O or name CB )) or resid 193 or (resid 194 and (name N or \ name CA or name C or name O or name CB )) or resid 195 through 232)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.320 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 47.920 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5796 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 : 0.011 0.498 28896 Z= 0.556 Angle : 1.217 48.381 39438 Z= 0.730 Chirality : 0.067 0.567 4512 Planarity : 0.008 0.081 4824 Dihedral : 16.108 163.715 11425 Min Nonbonded Distance : 1.038 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.78 % Favored : 90.59 % Rotamer: Outliers : 4.31 % Allowed : 4.69 % Favored : 91.00 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.71 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.36 (0.11), residues: 3338 helix: -2.92 (0.11), residues: 1101 sheet: -2.25 (0.24), residues: 409 loop : -3.11 (0.12), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 8 TYR 0.038 0.003 TYR A1229 PHE 0.035 0.003 PHE B 620 TRP 0.043 0.004 TRP A 183 HIS 0.018 0.002 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.01006 / 0.54 (28889) covalent geometry : angle 1.19595 / 0.73 (39430) SS BOND : bond 0.09312 / 4.66 ( 1) SS BOND : angle 5.97336 / 10.28 ( 2) hydrogen bonds : bond 0.17855 / 19.30 ( 1079) hydrogen bonds : angle 7.45990 / 9.90 ( 2981) metal coordination : bond 0.27728 / 17.26 ( 6) metal coordination : angle 18.03350 / 34.65 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 542 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.6710 (mt) cc_final: 0.6148 (mt) REVERT: A 469 VAL cc_start: 0.7968 (m) cc_final: 0.6852 (t) REVERT: A 516 ASP cc_start: 0.7051 (p0) cc_final: 0.6712 (p0) REVERT: A 681 MET cc_start: 0.6853 (mtp) cc_final: 0.6222 (mtm) REVERT: A 1308 ILE cc_start: 0.7312 (mm) cc_final: 0.6914 (mm) REVERT: B 70 CYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7332 (t) REVERT: B 119 SER cc_start: 0.6413 (OUTLIER) cc_final: 0.5927 (p) REVERT: B 363 LEU cc_start: 0.7461 (pp) cc_final: 0.6997 (pp) REVERT: F 44 VAL cc_start: 0.7149 (OUTLIER) cc_final: 0.6817 (t) REVERT: F 123 ARG cc_start: -0.0724 (OUTLIER) cc_final: -0.1179 (mtt180) outliers start: 123 outliers final: 28 residues processed: 643 average time/residue: 0.3245 time to fit residues: 316.4265 Evaluate side-chains 322 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 290 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.0670 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 3.9990 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN A 86 GLN A 150 HIS A 314 ASN A 330 HIS ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 604 HIS A 618 GLN A 686 GLN A 688 GLN A 761 GLN ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1268 GLN B 294 ASN B 606 ASN ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 HIS D 117 HIS D 227 GLN E 29 GLN F 33 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.074930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.055265 restraints weight = 357287.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.057154 restraints weight = 185724.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.058378 restraints weight = 119837.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.059193 restraints weight = 89350.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.059626 restraints weight = 73459.751| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.161 28896 Z= 0.163 Angle : 0.683 9.046 39438 Z= 0.370 Chirality : 0.045 0.243 4512 Planarity : 0.006 0.094 4824 Dihedral : 17.234 168.007 4859 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 22.79 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.92 % Favored : 92.81 % Rotamer: Outliers : 0.11 % Allowed : 2.63 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 1.43 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.13), residues: 3338 helix: -0.86 (0.14), residues: 1118 sheet: -2.09 (0.24), residues: 416 loop : -2.75 (0.13), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1033 TYR 0.029 0.001 TYR F 68 PHE 0.034 0.002 PHE F 64 TRP 0.009 0.001 TRP F 9 HIS 0.007 0.001 HIS B 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (28889) covalent geometry : angle 0.68091 / 0.37 (39430) SS BOND : bond 0.01143 / 0.57 ( 1) SS BOND : angle 4.13646 / 7.92 ( 2) hydrogen bonds : bond 0.05060 / 5.44 ( 1079) hydrogen bonds : angle 5.51057 / 7.10 ( 2981) metal coordination : bond 0.00836 / 0.60 ( 6) metal coordination : angle 3.90728 / 6.96 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 344 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.7702 (ttp) cc_final: 0.7396 (ttp) REVERT: A 315 MET cc_start: 0.8507 (ttm) cc_final: 0.8071 (tpp) REVERT: A 420 LEU cc_start: 0.8020 (mt) cc_final: 0.7816 (mt) REVERT: A 459 MET cc_start: 0.8287 (mmp) cc_final: 0.8006 (mmp) REVERT: A 573 ASN cc_start: 0.8980 (m110) cc_final: 0.8736 (m110) REVERT: A 1329 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8423 (mt-10) REVERT: B 42 GLU cc_start: 0.8683 (mp0) cc_final: 0.8432 (mp0) REVERT: B 49 PHE cc_start: 0.7933 (m-10) cc_final: 0.7606 (m-80) REVERT: B 147 ILE cc_start: 0.7952 (pt) cc_final: 0.7322 (tp) REVERT: B 169 LEU cc_start: 0.9378 (tt) cc_final: 0.9128 (mt) REVERT: B 330 MET cc_start: 0.9188 (mmm) cc_final: 0.8787 (tpt) REVERT: B 363 LEU cc_start: 0.8862 (pp) cc_final: 0.8609 (pp) REVERT: B 381 ILE cc_start: 0.9534 (mt) cc_final: 0.9302 (mt) REVERT: B 437 PHE cc_start: 0.9218 (m-80) cc_final: 0.9002 (m-80) REVERT: B 499 ILE cc_start: 0.9377 (tp) cc_final: 0.9125 (tp) REVERT: B 513 MET cc_start: 0.9424 (ttp) cc_final: 0.9187 (ttp) REVERT: B 698 MET cc_start: 0.9658 (tpp) cc_final: 0.9429 (tpp) REVERT: B 765 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8737 (mp0) REVERT: B 1223 LEU cc_start: 0.8146 (mt) cc_final: 0.7805 (mt) REVERT: B 1260 MET cc_start: 0.8067 (mtp) cc_final: 0.7845 (mtp) REVERT: C 82 LEU cc_start: 0.9582 (mt) cc_final: 0.9370 (mt) REVERT: C 177 TYR cc_start: 0.7142 (m-80) cc_final: 0.6722 (m-80) REVERT: D 144 ILE cc_start: 0.9515 (tt) cc_final: 0.9289 (tt) REVERT: E 7 GLN cc_start: 0.7209 (tp40) cc_final: 0.6737 (tt0) REVERT: E 17 PHE cc_start: 0.8743 (m-10) cc_final: 0.8498 (m-80) REVERT: E 19 LEU cc_start: 0.9348 (pp) cc_final: 0.8930 (mp) REVERT: E 66 VAL cc_start: 0.9184 (t) cc_final: 0.8914 (t) REVERT: F 28 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8552 (mm-30) REVERT: F 175 PHE cc_start: 0.4216 (m-80) cc_final: 0.3471 (m-10) outliers start: 3 outliers final: 1 residues processed: 347 average time/residue: 0.2890 time to fit residues: 160.6365 Evaluate side-chains 269 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 268 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 114 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 chunk 236 optimal weight: 8.9990 chunk 64 optimal weight: 0.2980 chunk 338 optimal weight: 10.0000 chunk 295 optimal weight: 5.9990 chunk 245 optimal weight: 6.9990 chunk 247 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 36 optimal weight: 0.2980 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN A 618 GLN A 628 HIS ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 ASN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 GLN ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 ASN ** B 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1279 GLN C 227 GLN ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.067737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.048352 restraints weight = 376641.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.049976 restraints weight = 197886.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.051051 restraints weight = 130661.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.051746 restraints weight = 99051.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.052084 restraints weight = 82864.374| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 28896 Z= 0.284 Angle : 0.782 17.492 39438 Z= 0.409 Chirality : 0.044 0.195 4512 Planarity : 0.006 0.082 4824 Dihedral : 17.041 171.518 4859 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 30.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.61 % Favored : 92.24 % Rotamer: Outliers : 0.11 % Allowed : 2.14 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 1.43 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.14), residues: 3338 helix: 0.06 (0.15), residues: 1119 sheet: -1.94 (0.24), residues: 447 loop : -2.43 (0.13), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B1222 TYR 0.026 0.002 TYR F 68 PHE 0.025 0.002 PHE F 65 TRP 0.019 0.001 TRP F 9 HIS 0.015 0.002 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.28 (28889) covalent geometry : angle 0.78101 / 0.41 (39430) SS BOND : bond 0.01690 / 0.84 ( 1) SS BOND : angle 1.41163 / 2.71 ( 2) hydrogen bonds : bond 0.04882 / 5.44 ( 1079) hydrogen bonds : angle 5.22228 / 6.77 ( 2981) metal coordination : bond 0.00798 / 0.70 ( 6) metal coordination : angle 3.74415 / 7.48 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 278 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ASP cc_start: 0.8811 (t0) cc_final: 0.8610 (t70) REVERT: A 239 MET cc_start: 0.7725 (ttp) cc_final: 0.7272 (ttp) REVERT: A 515 MET cc_start: 0.8791 (ttp) cc_final: 0.8333 (ttp) REVERT: A 1243 MET cc_start: 0.9051 (tmm) cc_final: 0.8829 (tmm) REVERT: A 1325 VAL cc_start: 0.9793 (t) cc_final: 0.9553 (t) REVERT: A 1329 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8486 (mt-10) REVERT: B 42 GLU cc_start: 0.8851 (mp0) cc_final: 0.8622 (mp0) REVERT: B 49 PHE cc_start: 0.7769 (m-80) cc_final: 0.7553 (m-80) REVERT: B 96 LYS cc_start: 0.8995 (ptpt) cc_final: 0.8715 (pptt) REVERT: B 147 ILE cc_start: 0.8365 (pt) cc_final: 0.8037 (tp) REVERT: B 330 MET cc_start: 0.9481 (mmm) cc_final: 0.8921 (mmm) REVERT: B 466 MET cc_start: 0.8983 (mtp) cc_final: 0.8352 (mtp) REVERT: B 497 GLU cc_start: 0.8918 (mp0) cc_final: 0.8566 (mp0) REVERT: B 499 ILE cc_start: 0.9459 (tp) cc_final: 0.9218 (tp) REVERT: B 625 MET cc_start: 0.9280 (ttt) cc_final: 0.9024 (tmm) REVERT: B 913 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8227 (mp0) REVERT: B 1151 LYS cc_start: 0.9406 (mtpp) cc_final: 0.8946 (mmmt) REVERT: C 82 LEU cc_start: 0.9577 (mt) cc_final: 0.9323 (mt) REVERT: C 177 TYR cc_start: 0.7562 (m-80) cc_final: 0.7031 (m-80) REVERT: C 199 ASP cc_start: 0.7765 (m-30) cc_final: 0.7473 (m-30) REVERT: C 205 MET cc_start: 0.8781 (pmm) cc_final: 0.8577 (pmm) REVERT: D 25 LYS cc_start: 0.8984 (tmtt) cc_final: 0.8759 (tmmt) REVERT: D 144 ILE cc_start: 0.9605 (tt) cc_final: 0.9264 (tt) REVERT: E 7 GLN cc_start: 0.7380 (tp40) cc_final: 0.6857 (tt0) REVERT: E 68 GLU cc_start: 0.8390 (tp30) cc_final: 0.8159 (tp30) REVERT: F 35 MET cc_start: 0.8165 (mmp) cc_final: 0.7743 (mmm) REVERT: F 175 PHE cc_start: 0.5223 (m-80) cc_final: 0.4378 (m-80) outliers start: 3 outliers final: 3 residues processed: 281 average time/residue: 0.2899 time to fit residues: 129.2204 Evaluate side-chains 233 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 230 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 54 optimal weight: 0.6980 chunk 283 optimal weight: 0.8980 chunk 282 optimal weight: 2.9990 chunk 171 optimal weight: 7.9990 chunk 335 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 246 optimal weight: 10.0000 chunk 258 optimal weight: 10.0000 chunk 6 optimal weight: 40.0000 chunk 17 optimal weight: 5.9990 chunk 21 optimal weight: 0.0870 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 HIS A 686 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN ** B 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1218 HIS ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.068189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.048984 restraints weight = 363775.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.050638 restraints weight = 191246.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.051728 restraints weight = 125433.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.052427 restraints weight = 94674.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.052848 restraints weight = 79082.191| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28896 Z= 0.132 Angle : 0.565 14.460 39438 Z= 0.302 Chirality : 0.041 0.216 4512 Planarity : 0.005 0.092 4824 Dihedral : 16.966 171.284 4859 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 26.53 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.17 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.71 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.14), residues: 3338 helix: 0.63 (0.16), residues: 1115 sheet: -1.77 (0.24), residues: 439 loop : -2.20 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 123 TYR 0.022 0.001 TYR F 68 PHE 0.037 0.001 PHE F 65 TRP 0.012 0.001 TRP F 9 HIS 0.009 0.001 HIS F 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (28889) covalent geometry : angle 0.56110 / 0.30 (39430) SS BOND : bond 0.00161 / 0.08 ( 1) SS BOND : angle 6.07235 / 10.48 ( 2) hydrogen bonds : bond 0.03965 / 4.37 ( 1079) hydrogen bonds : angle 4.79963 / 6.21 ( 2981) metal coordination : bond 0.00509 / 0.42 ( 6) metal coordination : angle 4.49284 / 7.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.8987 (ttt) cc_final: 0.8750 (ttt) REVERT: A 370 MET cc_start: 0.8998 (mmp) cc_final: 0.8720 (mmm) REVERT: A 515 MET cc_start: 0.8787 (ttp) cc_final: 0.7294 (ttp) REVERT: A 800 MET cc_start: 0.8105 (mpp) cc_final: 0.7905 (mpp) REVERT: A 1119 MET cc_start: 0.9216 (tpp) cc_final: 0.8831 (tpp) REVERT: A 1315 MET cc_start: 0.8352 (ppp) cc_final: 0.7945 (ppp) REVERT: A 1325 VAL cc_start: 0.9794 (t) cc_final: 0.9593 (t) REVERT: A 1329 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8712 (mt-10) REVERT: B 42 GLU cc_start: 0.8799 (mp0) cc_final: 0.8572 (mp0) REVERT: B 49 PHE cc_start: 0.7819 (m-80) cc_final: 0.7563 (m-80) REVERT: B 96 LYS cc_start: 0.8973 (ptpt) cc_final: 0.8672 (pptt) REVERT: B 499 ILE cc_start: 0.9483 (tp) cc_final: 0.9224 (tp) REVERT: B 513 MET cc_start: 0.9410 (ttp) cc_final: 0.9169 (ttp) REVERT: B 899 TYR cc_start: 0.8987 (t80) cc_final: 0.7741 (t80) REVERT: C 177 TYR cc_start: 0.7558 (m-80) cc_final: 0.7007 (m-80) REVERT: C 199 ASP cc_start: 0.7946 (m-30) cc_final: 0.7621 (m-30) REVERT: D 144 ILE cc_start: 0.9557 (tt) cc_final: 0.9268 (tt) REVERT: E 7 GLN cc_start: 0.7343 (tp40) cc_final: 0.6836 (tt0) REVERT: E 49 ILE cc_start: 0.9420 (pt) cc_final: 0.9190 (pt) REVERT: E 70 GLN cc_start: 0.8409 (tm-30) cc_final: 0.8101 (pp30) REVERT: F 28 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8647 (mm-30) REVERT: F 35 MET cc_start: 0.8049 (mmp) cc_final: 0.7578 (mmm) REVERT: F 59 LYS cc_start: 0.8949 (pttt) cc_final: 0.8719 (pttm) REVERT: F 73 MET cc_start: 0.8346 (tmm) cc_final: 0.7588 (ppp) REVERT: F 175 PHE cc_start: 0.5122 (m-80) cc_final: 0.4299 (m-80) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.2956 time to fit residues: 125.1661 Evaluate side-chains 217 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 286 optimal weight: 0.9980 chunk 256 optimal weight: 7.9990 chunk 269 optimal weight: 3.9990 chunk 307 optimal weight: 9.9990 chunk 35 optimal weight: 0.0270 chunk 12 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 180 optimal weight: 0.5980 chunk 191 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN A 686 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN B 545 HIS ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 921 GLN ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.067541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.048164 restraints weight = 368918.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.049811 restraints weight = 191709.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.050877 restraints weight = 125626.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.051570 restraints weight = 95330.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.051892 restraints weight = 80010.728| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 28896 Z= 0.128 Angle : 0.520 12.390 39438 Z= 0.281 Chirality : 0.040 0.153 4512 Planarity : 0.004 0.090 4824 Dihedral : 16.813 171.369 4859 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 28.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.04 % Favored : 92.81 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 1.43 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.14), residues: 3338 helix: 0.95 (0.16), residues: 1120 sheet: -1.59 (0.25), residues: 432 loop : -2.04 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 114 TYR 0.018 0.001 TYR F 68 PHE 0.031 0.001 PHE F 65 TRP 0.009 0.001 TRP F 9 HIS 0.005 0.001 HIS B 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (28889) covalent geometry : angle 0.51844 / 0.28 (39430) SS BOND : bond 0.00667 / 0.33 ( 1) SS BOND : angle 3.14414 / 5.81 ( 2) hydrogen bonds : bond 0.03692 / 4.07 ( 1079) hydrogen bonds : angle 4.63418 / 6.02 ( 2981) metal coordination : bond 0.00611 / 0.73 ( 6) metal coordination : angle 2.56274 / 4.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8750 (m-80) cc_final: 0.8280 (m-10) REVERT: A 239 MET cc_start: 0.7827 (ttp) cc_final: 0.7262 (ttp) REVERT: A 370 MET cc_start: 0.8969 (mmp) cc_final: 0.8683 (mmm) REVERT: A 400 VAL cc_start: 0.8529 (t) cc_final: 0.8305 (p) REVERT: A 429 MET cc_start: 0.9339 (mtm) cc_final: 0.9111 (mtm) REVERT: A 515 MET cc_start: 0.7915 (ttp) cc_final: 0.7546 (ttp) REVERT: A 1007 LYS cc_start: 0.8554 (mttt) cc_final: 0.8331 (ttpp) REVERT: A 1119 MET cc_start: 0.9214 (tpp) cc_final: 0.8762 (tpp) REVERT: A 1243 MET cc_start: 0.9161 (tmm) cc_final: 0.8873 (tmm) REVERT: A 1315 MET cc_start: 0.8360 (ppp) cc_final: 0.7927 (ppp) REVERT: A 1329 GLU cc_start: 0.9261 (mt-10) cc_final: 0.8741 (mt-10) REVERT: B 42 GLU cc_start: 0.8812 (mp0) cc_final: 0.8584 (mp0) REVERT: B 96 LYS cc_start: 0.9040 (ptpt) cc_final: 0.8739 (pptt) REVERT: B 147 ILE cc_start: 0.7771 (tp) cc_final: 0.7363 (tt) REVERT: B 499 ILE cc_start: 0.9506 (tp) cc_final: 0.9259 (tp) REVERT: B 513 MET cc_start: 0.9390 (ttp) cc_final: 0.9181 (ttp) REVERT: B 525 MET cc_start: 0.8557 (mmp) cc_final: 0.8224 (mmm) REVERT: B 822 MET cc_start: 0.7637 (tpp) cc_final: 0.7436 (tpp) REVERT: C 96 ASP cc_start: 0.7689 (m-30) cc_final: 0.7160 (p0) REVERT: C 177 TYR cc_start: 0.7560 (m-80) cc_final: 0.6997 (m-80) REVERT: C 199 ASP cc_start: 0.7833 (m-30) cc_final: 0.7560 (m-30) REVERT: D 144 ILE cc_start: 0.9577 (tt) cc_final: 0.9290 (tt) REVERT: E 5 THR cc_start: 0.8230 (m) cc_final: 0.7860 (m) REVERT: E 7 GLN cc_start: 0.7397 (tp40) cc_final: 0.7176 (tt0) REVERT: E 8 ASP cc_start: 0.9060 (m-30) cc_final: 0.8841 (p0) REVERT: E 53 GLU cc_start: 0.8879 (mp0) cc_final: 0.8668 (mp0) REVERT: F 28 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8674 (mm-30) REVERT: F 35 MET cc_start: 0.8100 (mmp) cc_final: 0.7636 (mmm) REVERT: F 175 PHE cc_start: 0.5270 (m-80) cc_final: 0.4632 (m-80) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.2934 time to fit residues: 117.3809 Evaluate side-chains 220 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 215 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 125 optimal weight: 0.9980 chunk 287 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 318 optimal weight: 20.0000 chunk 272 optimal weight: 6.9990 chunk 188 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 GLN ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 688 GLN ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.063657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.044647 restraints weight = 382487.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.046111 restraints weight = 197127.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.047113 restraints weight = 129271.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.047740 restraints weight = 98507.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.048149 restraints weight = 83336.127| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 28896 Z= 0.221 Angle : 0.650 15.909 39438 Z= 0.341 Chirality : 0.042 0.339 4512 Planarity : 0.005 0.086 4824 Dihedral : 16.867 171.388 4859 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 34.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.79 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 1.43 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.14), residues: 3338 helix: 0.72 (0.15), residues: 1121 sheet: -1.60 (0.24), residues: 450 loop : -1.98 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 62 TYR 0.023 0.002 TYR F 68 PHE 0.052 0.002 PHE F 65 TRP 0.010 0.001 TRP B 686 HIS 0.009 0.002 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.22 (28889) covalent geometry : angle 0.64847 / 0.34 (39430) SS BOND : bond 0.01642 / 0.82 ( 1) SS BOND : angle 3.64301 / 6.08 ( 2) hydrogen bonds : bond 0.04075 / 4.50 ( 1079) hydrogen bonds : angle 4.78486 / 6.18 ( 2981) metal coordination : bond 0.00987 / 0.97 ( 6) metal coordination : angle 2.51239 / 4.82 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8807 (m-80) cc_final: 0.8175 (m-10) REVERT: A 369 MET cc_start: 0.9095 (ttt) cc_final: 0.8826 (ttt) REVERT: A 370 MET cc_start: 0.9025 (mmp) cc_final: 0.8777 (mmm) REVERT: A 425 ILE cc_start: 0.9339 (mp) cc_final: 0.9083 (mp) REVERT: A 429 MET cc_start: 0.9451 (mtm) cc_final: 0.8763 (mtm) REVERT: A 459 MET cc_start: 0.9001 (mmp) cc_final: 0.8656 (mmp) REVERT: A 768 MET cc_start: 0.8549 (tmm) cc_final: 0.8297 (tmm) REVERT: A 1274 GLU cc_start: 0.9344 (mp0) cc_final: 0.9014 (mp0) REVERT: A 1315 MET cc_start: 0.8401 (ppp) cc_final: 0.7964 (ppp) REVERT: A 1329 GLU cc_start: 0.9307 (mt-10) cc_final: 0.8785 (mt-10) REVERT: B 42 GLU cc_start: 0.8921 (mp0) cc_final: 0.8689 (mp0) REVERT: B 49 PHE cc_start: 0.7830 (m-80) cc_final: 0.7529 (m-80) REVERT: B 147 ILE cc_start: 0.8157 (tp) cc_final: 0.7843 (tt) REVERT: B 525 MET cc_start: 0.8497 (mmp) cc_final: 0.8217 (mmm) REVERT: B 822 MET cc_start: 0.7768 (tpp) cc_final: 0.7554 (tpp) REVERT: C 177 TYR cc_start: 0.7702 (m-80) cc_final: 0.7104 (m-80) REVERT: C 199 ASP cc_start: 0.8022 (m-30) cc_final: 0.7735 (m-30) REVERT: D 25 LYS cc_start: 0.9036 (tmtt) cc_final: 0.8808 (tmmt) REVERT: D 144 ILE cc_start: 0.9617 (tt) cc_final: 0.9301 (tt) REVERT: E 5 THR cc_start: 0.8395 (m) cc_final: 0.8042 (m) REVERT: E 7 GLN cc_start: 0.7553 (tp40) cc_final: 0.7258 (tt0) REVERT: E 8 ASP cc_start: 0.9116 (m-30) cc_final: 0.8815 (p0) REVERT: F 35 MET cc_start: 0.8030 (mmp) cc_final: 0.7656 (mmm) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2850 time to fit residues: 111.8294 Evaluate side-chains 206 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 143 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 252 optimal weight: 4.9990 chunk 221 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 165 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 GLN ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1256 GLN B 294 ASN ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.064375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.045128 restraints weight = 376456.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.046724 restraints weight = 191596.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.047756 restraints weight = 124596.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.048427 restraints weight = 94770.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.048728 restraints weight = 79830.650| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.5907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 28896 Z= 0.113 Angle : 0.521 17.594 39438 Z= 0.277 Chirality : 0.040 0.188 4512 Planarity : 0.004 0.097 4824 Dihedral : 16.776 171.577 4859 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 31.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.71 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.15), residues: 3338 helix: 1.14 (0.16), residues: 1120 sheet: -1.45 (0.24), residues: 448 loop : -1.78 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 52 TYR 0.039 0.001 TYR B 631 PHE 0.027 0.001 PHE F 65 TRP 0.012 0.001 TRP F 9 HIS 0.005 0.001 HIS B 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (28889) covalent geometry : angle 0.51658 / 0.28 (39430) SS BOND : bond 0.00809 / 0.40 ( 1) SS BOND : angle 3.45959 / 5.77 ( 2) hydrogen bonds : bond 0.03556 / 3.94 ( 1079) hydrogen bonds : angle 4.46841 / 5.79 ( 2981) metal coordination : bond 0.01591 / 2.01 ( 6) metal coordination : angle 5.09065 / 10.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8784 (m-80) cc_final: 0.8151 (m-10) REVERT: A 369 MET cc_start: 0.9156 (ttt) cc_final: 0.8907 (ttt) REVERT: A 370 MET cc_start: 0.9043 (mmp) cc_final: 0.8768 (mmm) REVERT: A 425 ILE cc_start: 0.9345 (mp) cc_final: 0.9024 (mp) REVERT: A 429 MET cc_start: 0.9457 (mtm) cc_final: 0.8754 (mtm) REVERT: A 459 MET cc_start: 0.8986 (mmp) cc_final: 0.8599 (mmp) REVERT: A 515 MET cc_start: 0.7419 (ttp) cc_final: 0.6320 (ttp) REVERT: A 745 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7832 (pt0) REVERT: A 1274 GLU cc_start: 0.9335 (mp0) cc_final: 0.9045 (mp0) REVERT: A 1315 MET cc_start: 0.8447 (ppp) cc_final: 0.8134 (ppp) REVERT: A 1329 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8678 (mt-10) REVERT: B 42 GLU cc_start: 0.8900 (mp0) cc_final: 0.8682 (mp0) REVERT: B 49 PHE cc_start: 0.7814 (m-80) cc_final: 0.7518 (m-80) REVERT: B 330 MET cc_start: 0.9223 (mmm) cc_final: 0.9019 (tpp) REVERT: B 525 MET cc_start: 0.8544 (mmp) cc_final: 0.8219 (mmm) REVERT: B 822 MET cc_start: 0.7900 (tpp) cc_final: 0.7656 (tpp) REVERT: B 837 ASP cc_start: 0.9011 (m-30) cc_final: 0.8761 (m-30) REVERT: C 177 TYR cc_start: 0.7533 (m-80) cc_final: 0.6867 (m-80) REVERT: C 199 ASP cc_start: 0.8023 (m-30) cc_final: 0.7746 (m-30) REVERT: D 144 ILE cc_start: 0.9604 (tt) cc_final: 0.9304 (tt) REVERT: E 5 THR cc_start: 0.8416 (m) cc_final: 0.8065 (m) REVERT: E 7 GLN cc_start: 0.7502 (tp40) cc_final: 0.7236 (tt0) REVERT: E 8 ASP cc_start: 0.9149 (m-30) cc_final: 0.8803 (p0) REVERT: F 28 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8835 (mm-30) REVERT: F 35 MET cc_start: 0.8166 (mmp) cc_final: 0.7865 (mmm) REVERT: F 73 MET cc_start: 0.8352 (ppp) cc_final: 0.8130 (ppp) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.2932 time to fit residues: 111.2853 Evaluate side-chains 213 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 332 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 249 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 258 optimal weight: 7.9990 chunk 162 optimal weight: 3.9990 chunk 214 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 336 optimal weight: 20.0000 chunk 217 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN B 545 HIS ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.061830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.042963 restraints weight = 381236.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.044417 restraints weight = 196351.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.045363 restraints weight = 129619.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.045971 restraints weight = 99789.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.046268 restraints weight = 84591.992| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.6487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 28896 Z= 0.221 Angle : 0.641 18.243 39438 Z= 0.332 Chirality : 0.041 0.194 4512 Planarity : 0.005 0.090 4824 Dihedral : 16.762 171.772 4859 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 37.21 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.36 % Favored : 91.46 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.71 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.15), residues: 3338 helix: 0.88 (0.16), residues: 1125 sheet: -1.44 (0.25), residues: 442 loop : -1.78 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1258 TYR 0.022 0.002 TYR B 269 PHE 0.025 0.002 PHE F 65 TRP 0.011 0.001 TRP F 9 HIS 0.007 0.002 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.22 (28889) covalent geometry : angle 0.63820 / 0.33 (39430) SS BOND : bond 0.01060 / 0.53 ( 1) SS BOND : angle 2.74399 / 4.57 ( 2) hydrogen bonds : bond 0.03894 / 4.32 ( 1079) hydrogen bonds : angle 4.69366 / 6.01 ( 2981) metal coordination : bond 0.01403 / 1.49 ( 6) metal coordination : angle 5.00178 / 9.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8782 (m-80) cc_final: 0.8103 (m-10) REVERT: A 370 MET cc_start: 0.9039 (mmp) cc_final: 0.8722 (mmm) REVERT: A 429 MET cc_start: 0.9539 (mtm) cc_final: 0.9266 (mtm) REVERT: A 459 MET cc_start: 0.8983 (mmp) cc_final: 0.8612 (mmp) REVERT: A 1274 GLU cc_start: 0.9335 (mp0) cc_final: 0.9055 (mp0) REVERT: A 1315 MET cc_start: 0.8513 (ppp) cc_final: 0.8086 (tmm) REVERT: A 1329 GLU cc_start: 0.9312 (mt-10) cc_final: 0.8763 (mt-10) REVERT: B 49 PHE cc_start: 0.7809 (m-80) cc_final: 0.7495 (m-80) REVERT: B 525 MET cc_start: 0.8581 (mmp) cc_final: 0.8212 (mmm) REVERT: B 822 MET cc_start: 0.8071 (tpp) cc_final: 0.7827 (tpp) REVERT: C 177 TYR cc_start: 0.7739 (m-80) cc_final: 0.7118 (m-80) REVERT: D 25 LYS cc_start: 0.9111 (tmtt) cc_final: 0.8850 (tmmt) REVERT: D 144 ILE cc_start: 0.9595 (tt) cc_final: 0.9293 (tt) REVERT: E 5 THR cc_start: 0.8535 (m) cc_final: 0.8185 (m) REVERT: E 7 GLN cc_start: 0.7588 (tp40) cc_final: 0.7331 (tt0) REVERT: E 8 ASP cc_start: 0.9178 (m-30) cc_final: 0.8815 (p0) REVERT: F 35 MET cc_start: 0.8228 (mmp) cc_final: 0.7958 (mmm) REVERT: F 73 MET cc_start: 0.8263 (ppp) cc_final: 0.7750 (ppp) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.2904 time to fit residues: 105.4545 Evaluate side-chains 195 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 176 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 180 optimal weight: 0.7980 chunk 339 optimal weight: 6.9990 chunk 271 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 254 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.061870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.042824 restraints weight = 384762.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.044326 restraints weight = 195138.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.045289 restraints weight = 128062.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.045893 restraints weight = 98216.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.046183 restraints weight = 83304.562| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.6672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28896 Z= 0.153 Angle : 0.537 16.411 39438 Z= 0.286 Chirality : 0.040 0.172 4512 Planarity : 0.004 0.089 4824 Dihedral : 16.727 172.016 4859 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 34.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.25 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.71 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.15), residues: 3338 helix: 1.09 (0.16), residues: 1127 sheet: -1.43 (0.25), residues: 438 loop : -1.68 (0.15), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 26 TYR 0.015 0.001 TYR B 631 PHE 0.017 0.001 PHE F 65 TRP 0.012 0.001 TRP F 9 HIS 0.005 0.001 HIS B 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (28889) covalent geometry : angle 0.53349 / 0.29 (39430) SS BOND : bond 0.00837 / 0.42 ( 1) SS BOND : angle 2.71697 / 4.55 ( 2) hydrogen bonds : bond 0.03589 / 3.97 ( 1079) hydrogen bonds : angle 4.49628 / 5.76 ( 2981) metal coordination : bond 0.00817 / 0.86 ( 6) metal coordination : angle 4.43396 / 8.73 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8740 (m-80) cc_final: 0.8100 (m-10) REVERT: A 370 MET cc_start: 0.9040 (mmp) cc_final: 0.8747 (mmm) REVERT: A 459 MET cc_start: 0.8969 (mmp) cc_final: 0.8622 (mmp) REVERT: A 768 MET cc_start: 0.8423 (tmm) cc_final: 0.8004 (tmm) REVERT: A 1243 MET cc_start: 0.9255 (tmm) cc_final: 0.9012 (tmm) REVERT: A 1274 GLU cc_start: 0.9318 (mp0) cc_final: 0.9060 (mp0) REVERT: A 1315 MET cc_start: 0.8595 (ppp) cc_final: 0.8108 (tmm) REVERT: A 1329 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8719 (mt-10) REVERT: B 330 MET cc_start: 0.9197 (mmm) cc_final: 0.8996 (tpp) REVERT: B 525 MET cc_start: 0.8571 (mmp) cc_final: 0.8206 (mmm) REVERT: B 822 MET cc_start: 0.8107 (tpp) cc_final: 0.7891 (tpp) REVERT: B 1260 MET cc_start: 0.9372 (ttp) cc_final: 0.8486 (tpp) REVERT: C 177 TYR cc_start: 0.7578 (m-80) cc_final: 0.6938 (m-80) REVERT: D 25 LYS cc_start: 0.9086 (tmtt) cc_final: 0.8864 (tmmt) REVERT: D 144 ILE cc_start: 0.9575 (tt) cc_final: 0.9272 (tt) REVERT: E 5 THR cc_start: 0.8583 (m) cc_final: 0.8234 (m) REVERT: E 7 GLN cc_start: 0.7608 (tp40) cc_final: 0.7379 (tt0) REVERT: E 8 ASP cc_start: 0.9160 (m-30) cc_final: 0.8791 (p0) REVERT: E 67 ARG cc_start: 0.8333 (tmt-80) cc_final: 0.8086 (tmt170) REVERT: F 35 MET cc_start: 0.8265 (mmp) cc_final: 0.7979 (mmm) REVERT: F 73 MET cc_start: 0.8283 (ppp) cc_final: 0.7736 (ppp) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.2854 time to fit residues: 100.8362 Evaluate side-chains 191 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 95 optimal weight: 3.9990 chunk 336 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 49 optimal weight: 0.0270 chunk 148 optimal weight: 0.9980 chunk 193 optimal weight: 0.9980 chunk 300 optimal weight: 0.6980 chunk 326 optimal weight: 2.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.062312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.043516 restraints weight = 370775.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.045004 restraints weight = 189380.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.045976 restraints weight = 124062.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.046592 restraints weight = 94797.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.046905 restraints weight = 80181.546| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.6736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 28896 Z= 0.100 Angle : 0.503 14.049 39438 Z= 0.269 Chirality : 0.040 0.356 4512 Planarity : 0.004 0.088 4824 Dihedral : 16.616 172.048 4859 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 32.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.80 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.71 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.15), residues: 3338 helix: 1.46 (0.16), residues: 1125 sheet: -1.28 (0.25), residues: 432 loop : -1.53 (0.15), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 62 TYR 0.014 0.001 TYR B 631 PHE 0.024 0.001 PHE F 65 TRP 0.010 0.001 TRP F 9 HIS 0.005 0.001 HIS F 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (28889) covalent geometry : angle 0.50061 / 0.27 (39430) SS BOND : bond 0.00682 / 0.34 ( 1) SS BOND : angle 2.57154 / 4.34 ( 2) hydrogen bonds : bond 0.03385 / 3.75 ( 1079) hydrogen bonds : angle 4.29340 / 5.50 ( 2981) metal coordination : bond 0.00452 / 0.48 ( 6) metal coordination : angle 4.04569 / 8.01 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8740 (m-80) cc_final: 0.8077 (m-10) REVERT: A 369 MET cc_start: 0.9135 (ttt) cc_final: 0.8750 (tmm) REVERT: A 370 MET cc_start: 0.9060 (mmp) cc_final: 0.8676 (mmm) REVERT: A 429 MET cc_start: 0.9459 (mtm) cc_final: 0.9143 (mtp) REVERT: A 459 MET cc_start: 0.8950 (mmp) cc_final: 0.8555 (mmp) REVERT: A 768 MET cc_start: 0.8456 (tmm) cc_final: 0.8026 (tmm) REVERT: A 1230 MET cc_start: 0.8381 (tpp) cc_final: 0.7938 (tpp) REVERT: A 1243 MET cc_start: 0.9232 (tmm) cc_final: 0.8963 (tmm) REVERT: A 1274 GLU cc_start: 0.9359 (mp0) cc_final: 0.9073 (mp0) REVERT: A 1315 MET cc_start: 0.8619 (ppp) cc_final: 0.8079 (tmm) REVERT: A 1329 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8683 (mt-10) REVERT: B 525 MET cc_start: 0.8537 (mmp) cc_final: 0.8170 (mmm) REVERT: B 822 MET cc_start: 0.8075 (tpp) cc_final: 0.7852 (tpp) REVERT: B 1260 MET cc_start: 0.9356 (ttp) cc_final: 0.8452 (tpp) REVERT: B 1370 MET cc_start: 0.9407 (tmm) cc_final: 0.9175 (tmm) REVERT: C 177 TYR cc_start: 0.7509 (m-80) cc_final: 0.6856 (m-80) REVERT: C 199 ASP cc_start: 0.8012 (m-30) cc_final: 0.7749 (m-30) REVERT: D 25 LYS cc_start: 0.9075 (tmtt) cc_final: 0.8873 (tmmt) REVERT: D 144 ILE cc_start: 0.9575 (tt) cc_final: 0.9288 (tt) REVERT: E 5 THR cc_start: 0.8579 (m) cc_final: 0.8223 (m) REVERT: E 7 GLN cc_start: 0.7545 (tp40) cc_final: 0.7301 (tt0) REVERT: E 8 ASP cc_start: 0.9131 (m-30) cc_final: 0.8785 (p0) REVERT: F 35 MET cc_start: 0.8305 (mmp) cc_final: 0.8063 (mmm) REVERT: F 73 MET cc_start: 0.8282 (ppp) cc_final: 0.7739 (ppp) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.2941 time to fit residues: 108.2365 Evaluate side-chains 195 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 141 optimal weight: 0.0980 chunk 299 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 241 optimal weight: 8.9990 chunk 307 optimal weight: 10.0000 chunk 236 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 305 optimal weight: 0.0770 chunk 254 optimal weight: 9.9990 overall best weight: 2.8344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 ASN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 HIS ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.060649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.041791 restraints weight = 388556.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.043210 restraints weight = 197270.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.044156 restraints weight = 130577.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.044649 restraints weight = 100323.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.045055 restraints weight = 87034.538| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.7057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 28896 Z= 0.203 Angle : 0.592 15.312 39438 Z= 0.310 Chirality : 0.040 0.170 4512 Planarity : 0.004 0.090 4824 Dihedral : 16.619 172.371 4859 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 37.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.82 % Favored : 92.03 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.71 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.15), residues: 3338 helix: 1.17 (0.16), residues: 1129 sheet: -1.31 (0.25), residues: 442 loop : -1.64 (0.15), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 62 TYR 0.015 0.001 TYR A1305 PHE 0.044 0.002 PHE F 65 TRP 0.009 0.001 TRP F 9 HIS 0.007 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.20 (28889) covalent geometry : angle 0.58968 / 0.31 (39430) SS BOND : bond 0.00879 / 0.44 ( 1) SS BOND : angle 2.60162 / 4.35 ( 2) hydrogen bonds : bond 0.03679 / 4.08 ( 1079) hydrogen bonds : angle 4.48448 / 5.74 ( 2981) metal coordination : bond 0.00912 / 0.90 ( 6) metal coordination : angle 4.45206 / 8.83 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7514.60 seconds wall clock time: 129 minutes 37.76 seconds (7777.76 seconds total)