Starting phenix.real_space_refine on Sun Aug 9 23:57:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e6x_27930/08_2026/8e6x_27930_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e6x_27930/08_2026/8e6x_27930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e6x_27930/08_2026/8e6x_27930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e6x_27930/08_2026/8e6x_27930.map" model { file = "/net/cci-nas-00/data/ceres_data/8e6x_27930/08_2026/8e6x_27930_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e6x_27930/08_2026/8e6x_27930_neut.cif" } resolution = 4.27 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 17430 2.51 5 N 4985 2.21 5 O 5665 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 11 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: 39532 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: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 577 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} 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 70 126.283 83.930 111.386 1.00 45.60 S ATOM 14329 SG CYS B 85 128.233 83.378 115.737 1.00 49.94 S ATOM 25911 SG CYS B 814 84.650 32.143 94.180 1.00 22.38 S ATOM 27048 SG CYS B 888 85.476 36.602 94.165 1.00 20.48 S ATOM 27139 SG CYS B 895 86.896 34.132 91.902 1.00 14.28 S ATOM 27176 SG CYS B 898 83.386 33.979 91.378 1.00 16.02 S Time building chain proxies: 7.12, per 1000 atoms: 0.18 Number of scatterers: 39532 At special positions: 0 Unit cell: (186.006, 157.143, 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 5665 8.00 N 4985 7.00 C 17430 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=2.27 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.94 Conformation dependent library (CDL) restraints added in 1.5 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 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6200 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 49 sheets defined 35.7% alpha, 15.2% beta 28 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 5.50 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: 3.839A pdb=" N SER A 166 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 4.132A 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: 4.147A 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: 3.626A 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: 3.694A 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: 4.192A 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: 3.652A 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: 3.744A 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: 3.893A pdb=" N PHE B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.794A 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 286 removed outlier: 3.807A pdb=" N ASP B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 308 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: 3.548A 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: 3.567A 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: 3.648A 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: 3.796A 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: 3.521A pdb=" N TYR B 899 " --> pdb=" O CYS B 895 " (cutoff:3.500A) removed outlier: 3.943A 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: 3.543A 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: 3.807A pdb=" N ASN B1350 " --> pdb=" O GLY B1346 " (cutoff:3.500A) Processing helix chain 'B' and resid 1361 through 1372 removed outlier: 4.420A pdb=" N TYR B1365 " --> pdb=" O THR B1361 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 50 removed outlier: 3.549A 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: 3.526A 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 74 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: 3.646A 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: 4.216A 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: 6.569A 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: 6.928A pdb=" N LYS A 99 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 4.763A 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: 5.617A 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: 6.575A 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: 7.194A 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: 9.206A pdb=" N ILE A1096 " --> pdb=" O ASN A 799 " (cutoff:3.500A) removed outlier: 6.444A 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: 3.559A pdb=" N LEU A 817 " --> pdb=" O VAL A1097 " (cutoff:3.500A) removed outlier: 7.536A 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: 6.411A pdb=" N ASP A 842 " --> pdb=" O VAL A1046 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL A1046 " --> pdb=" O ASP A 842 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP A 930 " --> pdb=" O TYR A1053 " (cutoff:3.500A) removed outlier: 6.653A 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: 7.409A 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: 6.519A 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: 3.618A 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: 7.345A 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: 6.341A 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: 3.522A 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: 3.836A 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: 7.041A 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 48 through 51 Processing sheet with id=AF4, first strand: chain 'F' and resid 133 through 134 removed outlier: 3.684A 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: 3.792A pdb=" N VAL F 171 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL F 162 " --> pdb=" O THR F 169 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE F 164 " --> pdb=" O ARG F 167 " (cutoff:3.500A) 1018 hydrogen bonds defined for protein. 2859 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 73 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 11.26 Time building geometry restraints manager: 5.37 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: 346 1.23 - 1.42: 11512 1.42 - 1.62: 16899 1.62 - 1.81: 203 Bond restraints: 40155 Sorted by residual: bond pdb=" C PHE A 828 " pdb=" N THR A 829 " ideal model delta sigma weight residual 1.331 1.535 -0.204 1.43e-02 4.89e+03 2.04e+02 bond pdb=" C PRO F 102 " pdb=" N ILE F 103 " ideal model delta sigma weight residual 1.332 1.521 -0.190 1.36e-02 5.41e+03 1.94e+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 1.49e+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 8.15e+01 bond pdb=" N3 DT 6 24 " pdb=" H3 DT 6 24 " ideal model delta sigma weight residual 0.860 1.040 -0.180 2.00e-02 2.50e+03 8.11e+01 ... (remaining 40150 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.68: 65072 9.68 - 19.35: 33 19.35 - 29.03: 2 29.03 - 38.70: 1 38.70 - 48.38: 2 Bond angle restraints: 65110 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 104.00 148.02 -44.02 1.90e+00 2.77e-01 5.37e+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 75.97 33.03 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 119.70 136.24 -16.54 1.20e+00 6.94e-01 1.90e+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 65105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 20111 35.99 - 71.98: 869 71.98 - 107.97: 27 107.97 - 143.96: 2 143.96 - 179.95: 8 Dihedral angle restraints: 21017 sinusoidal: 10962 harmonic: 10055 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 -126.68 -53.32 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 43.73 156.27 1 1.50e+01 4.44e-03 8.17e+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 -138.09 -41.91 0 5.00e+00 4.00e-02 7.03e+01 ... (remaining 21014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 4056 0.107 - 0.214: 426 0.214 - 0.322: 26 0.322 - 0.429: 4 0.429 - 0.536: 3 Chirality restraints: 4515 Sorted by residual: 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 2.11 0.54 2.00e-01 2.50e+01 7.18e+00 chirality pdb=" CA LYS F 121 " pdb=" N LYS F 121 " pdb=" C LYS F 121 " pdb=" CB LYS F 121 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.06e+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 4.88e+00 ... (remaining 4512 not shown) Planarity restraints: 6148 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 9.45e+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=" CA GLU F 41 " -0.028 2.00e-02 2.50e+03 5.99e-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 delta sigma weight rms_deltas residual plane pdb=" C ILE B 61 " -0.029 2.00e-02 2.50e+03 5.75e-02 3.31e+01 pdb=" N PHE B 62 " 0.098 2.00e-02 2.50e+03 pdb=" CA PHE B 62 " -0.023 2.00e-02 2.50e+03 pdb=" H PHE B 62 " -0.046 2.00e-02 2.50e+03 ... (remaining 6145 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.75: 105 1.75 - 2.46: 14986 2.46 - 3.18: 81548 3.18 - 3.89: 122477 3.89 - 4.60: 189407 Nonbonded interactions: 408523 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 1.118 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 1.267 2.100 ... (remaining 408518 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: 5.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.330 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 50.210 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5725 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 28924 Z= 0.578 Angle : 1.215 48.380 39474 Z= 0.728 Chirality : 0.067 0.536 4515 Planarity : 0.008 0.081 4830 Dihedral : 15.972 163.690 11437 Min Nonbonded Distance : 1.038 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.65 % Favored : 90.72 % Rotamer: Outliers : 4.27 % Allowed : 4.62 % Favored : 91.12 % Cbeta Deviations : 0.19 % 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: -4.35 (0.11), residues: 3341 helix: -2.92 (0.11), residues: 1105 sheet: -2.20 (0.24), residues: 399 loop : -3.11 (0.12), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 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 0.01011 / 0.54 (28916) covalent geometry : angle 1.19378 / 0.73 (39466) SS BOND : bond 0.23920 / 11.96 ( 1) SS BOND : angle 4.32339 / 8.24 ( 2) hydrogen bonds : bond 0.17754 / 19.23 ( 1088) hydrogen bonds : angle 7.45802 / 9.17 ( 3005) metal coordination : bond 0.27736 / 17.27 ( 6) metal coordination : angle 18.03649 / 34.66 ( 6) Misc. bond : bond 0.23707 / 11.85 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 595 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 LEU cc_start: 0.6557 (tp) cc_final: 0.6333 (tp) REVERT: A 1279 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7644 (mt-10) REVERT: B 114 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.5876 (tp) REVERT: B 146 VAL cc_start: 0.2958 (OUTLIER) cc_final: 0.2679 (m) REVERT: B 273 ILE cc_start: 0.8540 (mt) cc_final: 0.8055 (mt) REVERT: B 506 VAL cc_start: 0.7574 (OUTLIER) cc_final: 0.7372 (p) REVERT: B 513 MET cc_start: 0.6633 (ttp) cc_final: 0.6391 (ttt) REVERT: B 560 ASN cc_start: 0.6592 (p0) cc_final: 0.6219 (p0) REVERT: B 581 MET cc_start: 0.6809 (mtp) cc_final: 0.6425 (ttm) REVERT: B 1256 ILE cc_start: 0.7494 (mm) cc_final: 0.7285 (mm) REVERT: D 46 ILE cc_start: 0.8188 (mt) cc_final: 0.7602 (tp) REVERT: F 123 ARG cc_start: 0.0371 (OUTLIER) cc_final: -0.1876 (mtt180) outliers start: 122 outliers final: 30 residues processed: 686 average time/residue: 0.3256 time to fit residues: 334.2288 Evaluate side-chains 331 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 297 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 HIS A 314 ASN A 327 GLN A 330 HIS ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 604 HIS A 688 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 GLN ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1268 GLN A1313 HIS ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN B 294 ASN B 792 ASN B 817 HIS C 147 GLN D 66 HIS D 117 HIS D 227 GLN ** F 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 HIS F 117 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.075160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.055273 restraints weight = 390549.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.057162 restraints weight = 210002.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.058382 restraints weight = 137578.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.059272 restraints weight = 104039.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.059849 restraints weight = 85821.801| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 28924 Z= 0.173 Angle : 0.697 10.740 39474 Z= 0.379 Chirality : 0.045 0.309 4515 Planarity : 0.007 0.186 4830 Dihedral : 17.304 168.166 4862 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 26.47 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.00 % Favored : 92.67 % Rotamer: Outliers : 0.10 % Allowed : 2.10 % Favored : 97.80 % 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: -3.03 (0.13), residues: 3341 helix: -0.98 (0.14), residues: 1122 sheet: -1.99 (0.24), residues: 411 loop : -2.79 (0.13), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 268 TYR 0.055 0.002 TYR F 68 PHE 0.033 0.002 PHE F 128 TRP 0.010 0.002 TRP F 9 HIS 0.006 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (28916) covalent geometry : angle 0.69344 / 0.38 (39466) SS BOND : bond 0.01028 / 0.51 ( 1) SS BOND : angle 4.28364 / 8.21 ( 2) hydrogen bonds : bond 0.05590 / 6.15 ( 1088) hydrogen bonds : angle 5.60877 / 7.00 ( 3005) metal coordination : bond 0.01249 / 0.85 ( 6) metal coordination : angle 5.36621 / 9.72 ( 6) Misc. bond : bond 0.01020 / 0.51 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 368 time to evaluate : 1.265 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: A 156 PHE cc_start: 0.8479 (m-10) cc_final: 0.8083 (m-80) REVERT: A 187 GLU cc_start: 0.5985 (pm20) cc_final: 0.4956 (pm20) REVERT: A 369 MET cc_start: 0.8483 (ttt) cc_final: 0.8061 (ttt) REVERT: A 395 TYR cc_start: 0.7817 (t80) cc_final: 0.7385 (t80) REVERT: A 403 MET cc_start: 0.7658 (tmm) cc_final: 0.7373 (tmm) REVERT: A 1230 MET cc_start: 0.8672 (tpp) cc_final: 0.8402 (tpt) REVERT: A 1232 MET cc_start: 0.9220 (mtp) cc_final: 0.8224 (mmm) REVERT: A 1308 ILE cc_start: 0.9699 (mm) cc_final: 0.9427 (tp) REVERT: A 1315 MET cc_start: 0.8365 (ppp) cc_final: 0.7867 (ppp) REVERT: B 298 MET cc_start: 0.9547 (mmp) cc_final: 0.9323 (mmp) REVERT: B 466 MET cc_start: 0.9056 (mtp) cc_final: 0.8722 (mtp) REVERT: B 485 MET cc_start: 0.8227 (tpp) cc_final: 0.7997 (tpp) REVERT: B 544 LEU cc_start: 0.9086 (tp) cc_final: 0.8841 (tp) REVERT: B 560 ASN cc_start: 0.8204 (p0) cc_final: 0.7828 (p0) REVERT: B 698 MET cc_start: 0.9509 (tpt) cc_final: 0.9106 (tpp) REVERT: B 1151 LYS cc_start: 0.8266 (pptt) cc_final: 0.8023 (tttt) REVERT: B 1279 GLN cc_start: 0.8876 (tt0) cc_final: 0.8661 (pm20) REVERT: C 142 MET cc_start: 0.8369 (ptp) cc_final: 0.8160 (ptp) REVERT: D 51 MET cc_start: 0.7977 (mmp) cc_final: 0.7775 (mmm) REVERT: D 174 ASP cc_start: 0.8943 (m-30) cc_final: 0.8202 (t0) REVERT: D 186 ASN cc_start: 0.8675 (m-40) cc_final: 0.8312 (m-40) REVERT: D 194 GLN cc_start: 0.9013 (tp-100) cc_final: 0.8534 (tp-100) REVERT: D 200 LYS cc_start: 0.8619 (tmtt) cc_final: 0.8304 (tptp) REVERT: E 5 THR cc_start: 0.7031 (p) cc_final: 0.6801 (p) REVERT: E 15 ASN cc_start: 0.7466 (t0) cc_final: 0.6818 (t0) REVERT: E 26 ARG cc_start: 0.8616 (tpt170) cc_final: 0.7805 (mmp-170) REVERT: F 26 LEU cc_start: 0.9558 (tp) cc_final: 0.9336 (mt) REVERT: F 65 PHE cc_start: 0.8249 (m-80) cc_final: 0.7925 (m-80) outliers start: 3 outliers final: 1 residues processed: 371 average time/residue: 0.3102 time to fit residues: 178.1672 Evaluate side-chains 262 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 261 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 56 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 304 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 178 optimal weight: 5.9990 chunk 285 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 311 optimal weight: 9.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1157 GLN ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN B 907 HIS B 910 ASN B1279 GLN D 37 HIS ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.070574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.051214 restraints weight = 399385.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.052955 restraints weight = 212651.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.054098 restraints weight = 139685.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.054858 restraints weight = 105635.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.055220 restraints weight = 87960.360| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 28924 Z= 0.206 Angle : 0.664 9.333 39474 Z= 0.357 Chirality : 0.042 0.174 4515 Planarity : 0.005 0.102 4830 Dihedral : 17.051 173.682 4862 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 26.93 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.12 % Favored : 92.67 % Rotamer: Outliers : 0.07 % Allowed : 1.64 % Favored : 98.29 % 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: -2.20 (0.14), residues: 3341 helix: 0.09 (0.15), residues: 1137 sheet: -1.75 (0.24), residues: 446 loop : -2.52 (0.13), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 267 TYR 0.059 0.002 TYR F 68 PHE 0.027 0.002 PHE F 128 TRP 0.016 0.001 TRP F 9 HIS 0.009 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.21 (28916) covalent geometry : angle 0.66261 / 0.36 (39466) SS BOND : bond 0.01089 / 0.54 ( 1) SS BOND : angle 2.00800 / 4.00 ( 2) hydrogen bonds : bond 0.04395 / 4.94 ( 1088) hydrogen bonds : angle 5.16428 / 6.41 ( 3005) metal coordination : bond 0.00487 / 0.48 ( 6) metal coordination : angle 2.92167 / 5.74 ( 6) Misc. bond : bond 0.01137 / 0.57 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 299 time to evaluate : 1.284 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: A 100 LEU cc_start: 0.9208 (mt) cc_final: 0.8987 (mt) REVERT: A 265 LYS cc_start: 0.9129 (mppt) cc_final: 0.8829 (mppt) REVERT: A 369 MET cc_start: 0.8481 (ttt) cc_final: 0.8113 (ttt) REVERT: A 403 MET cc_start: 0.7775 (tmm) cc_final: 0.7527 (tmm) REVERT: A 704 MET cc_start: 0.9385 (mmm) cc_final: 0.9074 (mmp) REVERT: A 800 MET cc_start: 0.8208 (mpp) cc_final: 0.7722 (mpp) REVERT: A 805 MET cc_start: 0.9179 (ptm) cc_final: 0.8904 (ptp) REVERT: A 1230 MET cc_start: 0.8735 (tpp) cc_final: 0.8331 (tpp) REVERT: A 1232 MET cc_start: 0.9263 (mtp) cc_final: 0.8217 (mmm) REVERT: A 1243 MET cc_start: 0.9017 (ttp) cc_final: 0.8762 (ttp) REVERT: A 1304 MET cc_start: 0.8645 (mmp) cc_final: 0.8202 (mmp) REVERT: A 1315 MET cc_start: 0.8461 (ppp) cc_final: 0.7986 (ppp) REVERT: B 267 ASP cc_start: 0.9410 (t0) cc_final: 0.9194 (t0) REVERT: B 330 MET cc_start: 0.9054 (mmt) cc_final: 0.8484 (mmt) REVERT: B 372 MET cc_start: 0.8207 (mtt) cc_final: 0.7996 (mtt) REVERT: B 513 MET cc_start: 0.9318 (ttp) cc_final: 0.8964 (ttt) REVERT: B 534 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8379 (tm-30) REVERT: B 544 LEU cc_start: 0.9101 (tp) cc_final: 0.8854 (tp) REVERT: B 560 ASN cc_start: 0.8226 (p0) cc_final: 0.7856 (p0) REVERT: B 698 MET cc_start: 0.9546 (tpt) cc_final: 0.9146 (tpp) REVERT: B 1260 MET cc_start: 0.7801 (mtp) cc_final: 0.7166 (mmm) REVERT: D 51 MET cc_start: 0.8247 (mmp) cc_final: 0.7894 (mmm) REVERT: D 186 ASN cc_start: 0.8687 (m-40) cc_final: 0.8308 (m-40) REVERT: D 194 GLN cc_start: 0.9048 (tp-100) cc_final: 0.8666 (tp-100) REVERT: D 200 LYS cc_start: 0.8883 (tmtt) cc_final: 0.8487 (tptp) REVERT: E 15 ASN cc_start: 0.7358 (t0) cc_final: 0.7001 (t0) REVERT: E 17 PHE cc_start: 0.7484 (m-10) cc_final: 0.7229 (m-80) REVERT: F 65 PHE cc_start: 0.8401 (m-80) cc_final: 0.8023 (m-80) REVERT: F 73 MET cc_start: 0.7205 (ttp) cc_final: 0.6818 (ppp) outliers start: 2 outliers final: 1 residues processed: 301 average time/residue: 0.3117 time to fit residues: 147.0676 Evaluate side-chains 241 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 240 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 26 optimal weight: 8.9990 chunk 297 optimal weight: 9.9990 chunk 240 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 125 optimal weight: 0.0000 chunk 183 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 161 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 232 optimal weight: 0.7980 overall best weight: 1.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 HIS ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 HIS ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.069664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.050270 restraints weight = 398444.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.052013 restraints weight = 210942.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.053143 restraints weight = 138394.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.053879 restraints weight = 104688.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.054248 restraints weight = 87365.300| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 28924 Z= 0.147 Angle : 0.568 9.760 39474 Z= 0.307 Chirality : 0.041 0.181 4515 Planarity : 0.005 0.150 4830 Dihedral : 16.886 174.097 4862 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 26.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.61 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.71 % 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: -1.74 (0.14), residues: 3341 helix: 0.54 (0.15), residues: 1139 sheet: -1.56 (0.25), residues: 421 loop : -2.29 (0.14), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 27 TYR 0.032 0.001 TYR F 68 PHE 0.015 0.001 PHE F 128 TRP 0.014 0.001 TRP F 9 HIS 0.008 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (28916) covalent geometry : angle 0.56624 / 0.31 (39466) SS BOND : bond 0.01369 / 0.68 ( 1) SS BOND : angle 0.56778 / 1.12 ( 2) hydrogen bonds : bond 0.03967 / 4.40 ( 1088) hydrogen bonds : angle 4.90192 / 6.13 ( 3005) metal coordination : bond 0.00574 / 0.65 ( 6) metal coordination : angle 3.81783 / 6.95 ( 6) Misc. bond : bond 0.00383 / 0.19 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 1.016 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: A 100 LEU cc_start: 0.9256 (mt) cc_final: 0.8945 (mt) REVERT: A 156 PHE cc_start: 0.8630 (m-10) cc_final: 0.8212 (m-10) REVERT: A 239 MET cc_start: 0.6972 (ttp) cc_final: 0.6632 (ttp) REVERT: A 403 MET cc_start: 0.7936 (tmm) cc_final: 0.7664 (tmm) REVERT: A 653 MET cc_start: 0.8631 (tpp) cc_final: 0.8299 (tpt) REVERT: A 704 MET cc_start: 0.9380 (mmm) cc_final: 0.9080 (mmp) REVERT: A 800 MET cc_start: 0.8181 (mpp) cc_final: 0.7529 (mpp) REVERT: A 805 MET cc_start: 0.9292 (ptm) cc_final: 0.9022 (ptp) REVERT: A 1151 LEU cc_start: 0.8337 (tp) cc_final: 0.8044 (tt) REVERT: A 1230 MET cc_start: 0.8686 (tpp) cc_final: 0.8240 (tpp) REVERT: A 1232 MET cc_start: 0.9196 (mtp) cc_final: 0.8184 (mmm) REVERT: A 1279 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8613 (mt-10) REVERT: A 1290 MET cc_start: 0.9401 (tpp) cc_final: 0.9123 (tpp) REVERT: A 1304 MET cc_start: 0.8641 (mmp) cc_final: 0.8182 (mmp) REVERT: A 1315 MET cc_start: 0.8476 (ppp) cc_final: 0.8155 (tmm) REVERT: B 239 LEU cc_start: 0.9508 (mt) cc_final: 0.9273 (tp) REVERT: B 267 ASP cc_start: 0.9382 (t0) cc_final: 0.9182 (t0) REVERT: B 330 MET cc_start: 0.9194 (mmt) cc_final: 0.8712 (mmt) REVERT: B 513 MET cc_start: 0.9334 (ttp) cc_final: 0.8951 (ttt) REVERT: B 534 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8455 (tm-30) REVERT: B 544 LEU cc_start: 0.9127 (tp) cc_final: 0.8906 (tp) REVERT: B 560 ASN cc_start: 0.8240 (p0) cc_final: 0.7814 (p0) REVERT: B 665 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7230 (mm-40) REVERT: B 698 MET cc_start: 0.9551 (tpt) cc_final: 0.9114 (tpp) REVERT: B 1260 MET cc_start: 0.8021 (mtp) cc_final: 0.7294 (mmm) REVERT: C 80 GLU cc_start: 0.9051 (tt0) cc_final: 0.8544 (tp30) REVERT: D 51 MET cc_start: 0.8319 (mmp) cc_final: 0.8002 (mmm) REVERT: D 186 ASN cc_start: 0.8674 (m-40) cc_final: 0.8289 (m-40) REVERT: D 194 GLN cc_start: 0.9030 (tp-100) cc_final: 0.8698 (tp-100) REVERT: D 200 LYS cc_start: 0.8840 (tmtt) cc_final: 0.8421 (tptp) REVERT: E 15 ASN cc_start: 0.7097 (t0) cc_final: 0.6742 (t0) REVERT: E 19 LEU cc_start: 0.8082 (pp) cc_final: 0.7858 (tt) REVERT: F 65 PHE cc_start: 0.8446 (m-80) cc_final: 0.8122 (m-80) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.2882 time to fit residues: 130.7043 Evaluate side-chains 226 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 316 optimal weight: 6.9990 chunk 266 optimal weight: 5.9990 chunk 228 optimal weight: 9.9990 chunk 286 optimal weight: 10.0000 chunk 329 optimal weight: 0.9990 chunk 139 optimal weight: 0.0770 chunk 251 optimal weight: 9.9990 chunk 323 optimal weight: 9.9990 chunk 229 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 100 optimal weight: 0.2980 overall best weight: 1.4744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 GLN ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN B 669 GLN ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.068758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.049712 restraints weight = 388914.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.051401 restraints weight = 208473.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.052510 restraints weight = 137053.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.053249 restraints weight = 103467.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.053721 restraints weight = 86020.671| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 28924 Z= 0.130 Angle : 0.529 12.941 39474 Z= 0.287 Chirality : 0.040 0.159 4515 Planarity : 0.005 0.184 4830 Dihedral : 16.750 174.325 4862 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 27.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.06 % Favored : 92.76 % 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 : 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: -1.42 (0.14), residues: 3341 helix: 0.86 (0.16), residues: 1140 sheet: -1.44 (0.25), residues: 419 loop : -2.11 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 8 TYR 0.025 0.001 TYR F 68 PHE 0.011 0.001 PHE A 53 TRP 0.008 0.001 TRP F 9 HIS 0.007 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (28916) covalent geometry : angle 0.52796 / 0.29 (39466) SS BOND : bond 0.01960 / 0.98 ( 1) SS BOND : angle 1.97999 / 3.46 ( 2) hydrogen bonds : bond 0.03675 / 4.09 ( 1088) hydrogen bonds : angle 4.76130 / 6.02 ( 3005) metal coordination : bond 0.00590 / 0.72 ( 6) metal coordination : angle 2.78792 / 5.05 ( 6) Misc. bond : bond 0.02664 / 1.33 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 PHE cc_start: 0.8669 (m-10) cc_final: 0.8256 (m-10) REVERT: A 239 MET cc_start: 0.6851 (ttp) cc_final: 0.6489 (ttp) REVERT: A 403 MET cc_start: 0.8100 (tmm) cc_final: 0.7789 (tmm) REVERT: A 653 MET cc_start: 0.8768 (tpp) cc_final: 0.8456 (tpp) REVERT: A 704 MET cc_start: 0.9396 (mmm) cc_final: 0.9111 (mmp) REVERT: A 800 MET cc_start: 0.8187 (mpp) cc_final: 0.7572 (mpp) REVERT: A 805 MET cc_start: 0.9358 (ptm) cc_final: 0.9109 (ptp) REVERT: A 1151 LEU cc_start: 0.8434 (tp) cc_final: 0.8099 (tt) REVERT: A 1230 MET cc_start: 0.8667 (tpp) cc_final: 0.8224 (tpp) REVERT: A 1279 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8626 (mt-10) REVERT: A 1290 MET cc_start: 0.9398 (tpp) cc_final: 0.9066 (tpp) REVERT: A 1304 MET cc_start: 0.8615 (mmp) cc_final: 0.8166 (mmp) REVERT: A 1315 MET cc_start: 0.8503 (ppp) cc_final: 0.8207 (tmm) REVERT: B 135 ILE cc_start: 0.9141 (mm) cc_final: 0.8894 (mt) REVERT: B 239 LEU cc_start: 0.9531 (mt) cc_final: 0.9313 (tp) REVERT: B 330 MET cc_start: 0.9217 (mmt) cc_final: 0.8705 (mmt) REVERT: B 484 MET cc_start: 0.8678 (mtm) cc_final: 0.8401 (mtm) REVERT: B 513 MET cc_start: 0.9350 (ttp) cc_final: 0.8996 (ttt) REVERT: B 534 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8469 (tm-30) REVERT: B 544 LEU cc_start: 0.9126 (tp) cc_final: 0.8912 (tp) REVERT: B 560 ASN cc_start: 0.8386 (p0) cc_final: 0.7987 (p0) REVERT: B 698 MET cc_start: 0.9624 (tpt) cc_final: 0.9132 (tpp) REVERT: B 724 MET cc_start: 0.9293 (mtm) cc_final: 0.8707 (mtt) REVERT: B 1260 MET cc_start: 0.8137 (mtp) cc_final: 0.7382 (mmm) REVERT: C 80 GLU cc_start: 0.9100 (tt0) cc_final: 0.8460 (tp30) REVERT: D 51 MET cc_start: 0.8258 (mmp) cc_final: 0.7905 (mmm) REVERT: D 186 ASN cc_start: 0.8696 (m-40) cc_final: 0.8303 (m-40) REVERT: D 194 GLN cc_start: 0.9068 (tp-100) cc_final: 0.8727 (tp-100) REVERT: D 200 LYS cc_start: 0.8816 (tmtt) cc_final: 0.8604 (tmtt) REVERT: E 15 ASN cc_start: 0.7412 (t0) cc_final: 0.6981 (t0) REVERT: F 65 PHE cc_start: 0.8479 (m-80) cc_final: 0.8126 (m-80) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.2850 time to fit residues: 123.4963 Evaluate side-chains 212 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 161 optimal weight: 9.9990 chunk 127 optimal weight: 0.2980 chunk 205 optimal weight: 5.9990 chunk 334 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 332 optimal weight: 8.9990 chunk 285 optimal weight: 6.9990 chunk 304 optimal weight: 4.9990 chunk 214 optimal weight: 4.9990 chunk 293 optimal weight: 9.9990 chunk 254 optimal weight: 10.0000 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN A 437 ASN ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 688 GLN A 737 ASN ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 ASN ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 HIS A1136 GLN ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 ASN B 907 HIS B 910 ASN B 951 GLN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN F 33 HIS ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.063299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.044718 restraints weight = 406504.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.046214 restraints weight = 218621.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.047180 restraints weight = 145167.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.047806 restraints weight = 111112.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.048161 restraints weight = 93535.799| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.5992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 28924 Z= 0.286 Angle : 0.774 11.606 39474 Z= 0.404 Chirality : 0.044 0.274 4515 Planarity : 0.006 0.115 4830 Dihedral : 16.951 177.583 4862 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 40.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.50 % Favored : 91.35 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: -1.99 (0.14), residues: 3341 helix: 0.13 (0.15), residues: 1148 sheet: -1.68 (0.24), residues: 451 loop : -2.30 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 758 TYR 0.022 0.002 TYR A1305 PHE 0.031 0.003 PHE B 116 TRP 0.011 0.002 TRP A 807 HIS 0.011 0.002 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.29 (28916) covalent geometry : angle 0.77368 / 0.40 (39466) SS BOND : bond 0.00567 / 0.28 ( 1) SS BOND : angle 1.29370 / 2.18 ( 2) hydrogen bonds : bond 0.04636 / 5.21 ( 1088) hydrogen bonds : angle 5.23883 / 6.63 ( 3005) metal coordination : bond 0.00873 / 0.98 ( 6) metal coordination : angle 2.34029 / 4.38 ( 6) Misc. bond : bond 0.00908 / 0.45 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 1.317 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 156 PHE cc_start: 0.8835 (m-10) cc_final: 0.8446 (m-10) REVERT: A 239 MET cc_start: 0.6869 (ttp) cc_final: 0.6456 (ttp) REVERT: A 403 MET cc_start: 0.8439 (tmm) cc_final: 0.8140 (tmm) REVERT: A 429 MET cc_start: 0.9575 (mtm) cc_final: 0.9371 (mtt) REVERT: A 653 MET cc_start: 0.8311 (tpp) cc_final: 0.7845 (tpt) REVERT: A 704 MET cc_start: 0.9422 (mmm) cc_final: 0.9212 (mmp) REVERT: A 800 MET cc_start: 0.8212 (mpp) cc_final: 0.7455 (mpp) REVERT: A 805 MET cc_start: 0.9312 (ptm) cc_final: 0.9001 (ptp) REVERT: A 978 VAL cc_start: 0.5116 (t) cc_final: 0.4912 (t) REVERT: A 1279 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8728 (mt-10) REVERT: A 1304 MET cc_start: 0.8638 (mmp) cc_final: 0.8186 (mmp) REVERT: A 1315 MET cc_start: 0.8496 (ppp) cc_final: 0.8224 (ppp) REVERT: B 237 MET cc_start: 0.9396 (mmp) cc_final: 0.9146 (mmp) REVERT: B 298 MET cc_start: 0.9602 (mmp) cc_final: 0.9401 (mmp) REVERT: B 330 MET cc_start: 0.9328 (mmt) cc_final: 0.9065 (mmm) REVERT: B 484 MET cc_start: 0.9020 (mtm) cc_final: 0.8797 (mtm) REVERT: B 513 MET cc_start: 0.9482 (ttp) cc_final: 0.9105 (ttt) REVERT: B 534 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8639 (tm-30) REVERT: B 544 LEU cc_start: 0.9286 (tp) cc_final: 0.9081 (tp) REVERT: B 560 ASN cc_start: 0.8490 (p0) cc_final: 0.8032 (p0) REVERT: B 698 MET cc_start: 0.9629 (tpt) cc_final: 0.9148 (tpp) REVERT: B 724 MET cc_start: 0.9402 (mtm) cc_final: 0.9104 (mtm) REVERT: B 1260 MET cc_start: 0.8841 (mtp) cc_final: 0.8081 (mmm) REVERT: D 186 ASN cc_start: 0.8931 (m-40) cc_final: 0.8723 (m-40) REVERT: D 194 GLN cc_start: 0.9109 (tp-100) cc_final: 0.8854 (tp-100) REVERT: E 15 ASN cc_start: 0.7555 (t0) cc_final: 0.7124 (t0) REVERT: F 65 PHE cc_start: 0.8633 (m-80) cc_final: 0.8186 (m-80) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.3128 time to fit residues: 114.4111 Evaluate side-chains 188 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 250 optimal weight: 20.0000 chunk 322 optimal weight: 9.9990 chunk 316 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 70 optimal weight: 0.1980 chunk 98 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 271 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 315 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN ** 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 = 0.3477 r_free = 0.3477 target = 0.061627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.042723 restraints weight = 416620.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.044227 restraints weight = 219534.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.045180 restraints weight = 145301.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.045825 restraints weight = 112202.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.046233 restraints weight = 94945.067| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.6710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 28924 Z= 0.243 Angle : 0.657 9.273 39474 Z= 0.356 Chirality : 0.042 0.187 4515 Planarity : 0.006 0.133 4830 Dihedral : 16.970 179.534 4862 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 38.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.84 % Favored : 92.01 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.71 % 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: -1.92 (0.14), residues: 3341 helix: 0.16 (0.15), residues: 1151 sheet: -1.48 (0.24), residues: 427 loop : -2.27 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 478 TYR 0.031 0.002 TYR A 123 PHE 0.017 0.002 PHE A 337 TRP 0.011 0.002 TRP B 409 HIS 0.009 0.002 HIS B 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.24 (28916) covalent geometry : angle 0.65519 / 0.36 (39466) SS BOND : bond 0.01033 / 0.52 ( 1) SS BOND : angle 2.36087 / 3.97 ( 2) hydrogen bonds : bond 0.04078 / 4.56 ( 1088) hydrogen bonds : angle 5.20083 / 6.55 ( 3005) metal coordination : bond 0.00907 / 0.99 ( 6) metal coordination : angle 3.64141 / 6.52 ( 6) Misc. bond : bond 0.01950 / 0.97 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 1.341 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: A 239 MET cc_start: 0.7418 (ttp) cc_final: 0.6988 (ttp) REVERT: A 311 CYS cc_start: 0.8925 (p) cc_final: 0.8249 (p) REVERT: A 403 MET cc_start: 0.9114 (tmm) cc_final: 0.8884 (tmm) REVERT: A 492 MET cc_start: 0.7277 (ttt) cc_final: 0.7064 (ttt) REVERT: A 653 MET cc_start: 0.8286 (tpp) cc_final: 0.7802 (tpt) REVERT: A 800 MET cc_start: 0.8036 (mpp) cc_final: 0.7275 (mpp) REVERT: A 805 MET cc_start: 0.9414 (ptm) cc_final: 0.9144 (ptp) REVERT: A 1232 MET cc_start: 0.9098 (mmm) cc_final: 0.8711 (mmm) REVERT: A 1287 LEU cc_start: 0.9817 (tt) cc_final: 0.9460 (tt) REVERT: A 1304 MET cc_start: 0.8721 (mmp) cc_final: 0.8260 (mmp) REVERT: A 1315 MET cc_start: 0.8457 (ppp) cc_final: 0.8043 (ppp) REVERT: A 1319 MET cc_start: 0.8671 (tpp) cc_final: 0.8407 (tpp) REVERT: B 115 TRP cc_start: 0.9279 (m-10) cc_final: 0.8859 (m100) REVERT: B 237 MET cc_start: 0.9446 (mmp) cc_final: 0.9173 (mmp) REVERT: B 298 MET cc_start: 0.9602 (mmp) cc_final: 0.9385 (mmp) REVERT: B 454 CYS cc_start: 0.8848 (m) cc_final: 0.8625 (m) REVERT: B 484 MET cc_start: 0.9073 (mtm) cc_final: 0.8863 (mtm) REVERT: B 485 MET cc_start: 0.9138 (tpp) cc_final: 0.8934 (tpp) REVERT: B 513 MET cc_start: 0.9495 (ttp) cc_final: 0.9152 (ttt) REVERT: B 534 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8636 (tm-30) REVERT: B 560 ASN cc_start: 0.8536 (p0) cc_final: 0.8062 (p0) REVERT: B 698 MET cc_start: 0.9632 (tpt) cc_final: 0.9107 (tpp) REVERT: D 194 GLN cc_start: 0.9183 (tp-100) cc_final: 0.8922 (tp-100) REVERT: E 15 ASN cc_start: 0.7870 (t160) cc_final: 0.7560 (t0) REVERT: E 30 MET cc_start: 0.9220 (tpt) cc_final: 0.9018 (tpt) REVERT: F 65 PHE cc_start: 0.8832 (m-80) cc_final: 0.8324 (m-80) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.3138 time to fit residues: 115.1775 Evaluate side-chains 182 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 73 optimal weight: 3.9990 chunk 236 optimal weight: 7.9990 chunk 1 optimal weight: 30.0000 chunk 50 optimal weight: 0.7980 chunk 266 optimal weight: 3.9990 chunk 298 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 261 optimal weight: 0.8980 chunk 197 optimal weight: 6.9990 chunk 99 optimal weight: 0.5980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 HIS ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.062064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.043575 restraints weight = 398850.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.045061 restraints weight = 211434.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.046033 restraints weight = 139577.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.046622 restraints weight = 106578.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.047045 restraints weight = 90044.719| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.6820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28924 Z= 0.124 Angle : 0.534 9.297 39474 Z= 0.291 Chirality : 0.041 0.164 4515 Planarity : 0.005 0.141 4830 Dihedral : 16.797 179.077 4862 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 34.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.30 % Favored : 92.58 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.71 % 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: -1.45 (0.14), residues: 3341 helix: 0.72 (0.15), residues: 1156 sheet: -1.38 (0.24), residues: 438 loop : -2.09 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 473 TYR 0.011 0.001 TYR A1305 PHE 0.014 0.001 PHE B 172 TRP 0.008 0.001 TRP F 9 HIS 0.006 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (28916) covalent geometry : angle 0.53306 / 0.29 (39466) SS BOND : bond 0.00723 / 0.36 ( 1) SS BOND : angle 1.93223 / 3.26 ( 2) hydrogen bonds : bond 0.03681 / 4.14 ( 1088) hydrogen bonds : angle 4.85732 / 6.07 ( 3005) metal coordination : bond 0.01032 / 0.67 ( 6) metal coordination : angle 2.54283 / 4.64 ( 6) Misc. bond : bond 0.00085 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 1.377 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 156 PHE cc_start: 0.8863 (m-10) cc_final: 0.8489 (m-10) REVERT: A 239 MET cc_start: 0.7310 (ttp) cc_final: 0.6857 (ttp) REVERT: A 311 CYS cc_start: 0.8750 (p) cc_final: 0.8060 (p) REVERT: A 403 MET cc_start: 0.9162 (tmm) cc_final: 0.8891 (tmm) REVERT: A 653 MET cc_start: 0.8317 (tpp) cc_final: 0.7897 (tpt) REVERT: A 681 MET cc_start: 0.9362 (mtm) cc_final: 0.9148 (mtm) REVERT: A 800 MET cc_start: 0.8081 (mpp) cc_final: 0.7231 (mpp) REVERT: A 805 MET cc_start: 0.9432 (ptm) cc_final: 0.9213 (ptp) REVERT: A 1304 MET cc_start: 0.8649 (mmp) cc_final: 0.8196 (mmp) REVERT: A 1315 MET cc_start: 0.8487 (ppp) cc_final: 0.8061 (ppp) REVERT: B 237 MET cc_start: 0.9372 (mmp) cc_final: 0.9067 (mmp) REVERT: B 298 MET cc_start: 0.9591 (mmp) cc_final: 0.9369 (mmp) REVERT: B 454 CYS cc_start: 0.8741 (m) cc_final: 0.8523 (m) REVERT: B 484 MET cc_start: 0.9064 (mtm) cc_final: 0.8762 (mtm) REVERT: B 485 MET cc_start: 0.9092 (tpp) cc_final: 0.8874 (tpp) REVERT: B 534 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8523 (tm-30) REVERT: B 560 ASN cc_start: 0.8595 (p0) cc_final: 0.8151 (p0) REVERT: B 698 MET cc_start: 0.9611 (tpt) cc_final: 0.9052 (tpp) REVERT: D 51 MET cc_start: 0.9192 (tpt) cc_final: 0.8969 (tpp) REVERT: D 194 GLN cc_start: 0.9149 (tp-100) cc_final: 0.8867 (tp-100) REVERT: E 15 ASN cc_start: 0.7786 (t160) cc_final: 0.7546 (t0) REVERT: F 65 PHE cc_start: 0.8705 (m-80) cc_final: 0.8153 (m-80) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.2776 time to fit residues: 97.7608 Evaluate side-chains 178 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 141 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 126 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 341 optimal weight: 3.9990 chunk 266 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.060948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.042337 restraints weight = 410346.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.043815 restraints weight = 215186.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.044760 restraints weight = 142156.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.045394 restraints weight = 109053.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.045670 restraints weight = 91992.506| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.7118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 28924 Z= 0.177 Angle : 0.571 7.650 39474 Z= 0.307 Chirality : 0.040 0.160 4515 Planarity : 0.005 0.120 4830 Dihedral : 16.741 179.066 4862 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 37.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.41 % Favored : 91.47 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.71 % 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: -1.42 (0.14), residues: 3341 helix: 0.77 (0.15), residues: 1151 sheet: -1.38 (0.24), residues: 456 loop : -2.09 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 403 TYR 0.015 0.001 TYR A1305 PHE 0.012 0.002 PHE A 337 TRP 0.009 0.001 TRP A1276 HIS 0.007 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 (28916) covalent geometry : angle 0.56986 / 0.31 (39466) SS BOND : bond 0.01015 / 0.51 ( 1) SS BOND : angle 1.50831 / 2.58 ( 2) hydrogen bonds : bond 0.03682 / 4.15 ( 1088) hydrogen bonds : angle 4.88203 / 6.08 ( 3005) metal coordination : bond 0.00679 / 0.61 ( 6) metal coordination : angle 2.59607 / 4.93 ( 6) Misc. bond : bond 0.00175 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 1.267 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: A 156 PHE cc_start: 0.8908 (m-10) cc_final: 0.8329 (m-10) REVERT: A 239 MET cc_start: 0.7459 (ttp) cc_final: 0.7065 (ttp) REVERT: A 311 CYS cc_start: 0.8871 (p) cc_final: 0.8191 (p) REVERT: A 370 MET cc_start: 0.9109 (mmp) cc_final: 0.8851 (mmp) REVERT: A 403 MET cc_start: 0.9193 (tmm) cc_final: 0.8960 (tmm) REVERT: A 653 MET cc_start: 0.8300 (tpp) cc_final: 0.7823 (tpt) REVERT: A 681 MET cc_start: 0.9408 (mtm) cc_final: 0.9143 (mtm) REVERT: A 800 MET cc_start: 0.8012 (mpp) cc_final: 0.7255 (mpp) REVERT: A 805 MET cc_start: 0.9399 (ptm) cc_final: 0.9174 (ptp) REVERT: A 1304 MET cc_start: 0.8681 (mmp) cc_final: 0.8224 (mmp) REVERT: A 1315 MET cc_start: 0.8488 (ppp) cc_final: 0.8237 (ppp) REVERT: A 1319 MET cc_start: 0.8644 (tpp) cc_final: 0.8378 (tpp) REVERT: B 87 LYS cc_start: 0.8812 (ptpt) cc_final: 0.8382 (pttp) REVERT: B 237 MET cc_start: 0.9374 (mmp) cc_final: 0.9074 (mmp) REVERT: B 298 MET cc_start: 0.9619 (mmp) cc_final: 0.9397 (mmp) REVERT: B 454 CYS cc_start: 0.8735 (m) cc_final: 0.8531 (m) REVERT: B 485 MET cc_start: 0.9107 (tpp) cc_final: 0.8895 (tpp) REVERT: B 534 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8598 (tm-30) REVERT: B 560 ASN cc_start: 0.8689 (p0) cc_final: 0.8234 (p0) REVERT: B 698 MET cc_start: 0.9605 (tpt) cc_final: 0.9030 (tpp) REVERT: D 194 GLN cc_start: 0.9139 (tp-100) cc_final: 0.8889 (tp-100) REVERT: E 15 ASN cc_start: 0.7754 (t160) cc_final: 0.7498 (t0) REVERT: E 30 MET cc_start: 0.9207 (tpp) cc_final: 0.8959 (tpp) REVERT: F 65 PHE cc_start: 0.8733 (m-80) cc_final: 0.8186 (m-80) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.2850 time to fit residues: 97.9126 Evaluate side-chains 177 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 11 optimal weight: 0.4980 chunk 271 optimal weight: 0.6980 chunk 219 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 209 optimal weight: 8.9990 chunk 175 optimal weight: 4.9990 chunk 334 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 77 optimal weight: 0.0970 chunk 158 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.061793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.042922 restraints weight = 406548.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.044443 restraints weight = 212114.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.045420 restraints weight = 139822.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.046073 restraints weight = 107258.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.046370 restraints weight = 90641.692| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.7142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 28924 Z= 0.100 Angle : 0.500 7.142 39474 Z= 0.271 Chirality : 0.040 0.167 4515 Planarity : 0.004 0.135 4830 Dihedral : 16.613 178.452 4862 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 34.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.67 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.71 % 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: -1.03 (0.15), residues: 3341 helix: 1.19 (0.16), residues: 1152 sheet: -1.21 (0.24), residues: 458 loop : -1.91 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 114 TYR 0.009 0.001 TYR A1305 PHE 0.013 0.001 PHE B 620 TRP 0.008 0.001 TRP B1193 HIS 0.006 0.001 HIS B 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (28916) covalent geometry : angle 0.49873 / 0.27 (39466) SS BOND : bond 0.00663 / 0.33 ( 1) SS BOND : angle 1.64998 / 2.88 ( 2) hydrogen bonds : bond 0.03396 / 3.81 ( 1088) hydrogen bonds : angle 4.61087 / 5.75 ( 3005) metal coordination : bond 0.00286 / 0.34 ( 6) metal coordination : angle 2.37838 / 4.54 ( 6) Misc. bond : bond 0.00188 / 0.09 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.288 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: A 156 PHE cc_start: 0.8932 (m-10) cc_final: 0.8332 (m-10) REVERT: A 239 MET cc_start: 0.7453 (ttp) cc_final: 0.7058 (ttp) REVERT: A 370 MET cc_start: 0.9124 (mmp) cc_final: 0.8882 (mmp) REVERT: A 403 MET cc_start: 0.9208 (tmm) cc_final: 0.8958 (tmm) REVERT: A 653 MET cc_start: 0.8393 (tpp) cc_final: 0.7972 (tpt) REVERT: A 681 MET cc_start: 0.9359 (mtm) cc_final: 0.9144 (mtm) REVERT: A 686 GLN cc_start: 0.9441 (tm-30) cc_final: 0.9160 (tm-30) REVERT: A 800 MET cc_start: 0.8085 (mpp) cc_final: 0.7300 (mpp) REVERT: A 1151 LEU cc_start: 0.8358 (tp) cc_final: 0.8073 (tt) REVERT: A 1230 MET cc_start: 0.8593 (ttt) cc_final: 0.7805 (ttt) REVERT: A 1288 GLN cc_start: 0.9603 (tt0) cc_final: 0.9234 (tm-30) REVERT: A 1315 MET cc_start: 0.8456 (ppp) cc_final: 0.7766 (ppp) REVERT: A 1319 MET cc_start: 0.8623 (tpp) cc_final: 0.8352 (tpp) REVERT: B 237 MET cc_start: 0.9342 (mmp) cc_final: 0.9047 (mmp) REVERT: B 298 MET cc_start: 0.9610 (mmp) cc_final: 0.9386 (mmp) REVERT: B 454 CYS cc_start: 0.8699 (m) cc_final: 0.8454 (m) REVERT: B 484 MET cc_start: 0.9029 (mtm) cc_final: 0.8461 (mtm) REVERT: B 534 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8517 (tm-30) REVERT: B 560 ASN cc_start: 0.8673 (p0) cc_final: 0.8230 (p0) REVERT: B 698 MET cc_start: 0.9608 (tpt) cc_final: 0.9035 (tpp) REVERT: D 194 GLN cc_start: 0.9169 (tp-100) cc_final: 0.8862 (tp-100) REVERT: E 15 ASN cc_start: 0.7758 (t160) cc_final: 0.7515 (t0) REVERT: E 30 MET cc_start: 0.9201 (tpp) cc_final: 0.8987 (tpp) REVERT: F 65 PHE cc_start: 0.8624 (m-80) cc_final: 0.8048 (m-80) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.2864 time to fit residues: 100.8674 Evaluate side-chains 180 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 210 optimal weight: 1.9990 chunk 184 optimal weight: 4.9990 chunk 266 optimal weight: 3.9990 chunk 293 optimal weight: 7.9990 chunk 133 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 299 optimal weight: 0.0570 chunk 145 optimal weight: 2.9990 chunk 294 optimal weight: 0.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS E 15 ASN E 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.060942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.042661 restraints weight = 404356.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.044108 restraints weight = 212657.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.045040 restraints weight = 140620.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.045673 restraints weight = 107729.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.045959 restraints weight = 90542.936| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.7320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 28924 Z= 0.137 Angle : 0.519 8.570 39474 Z= 0.280 Chirality : 0.040 0.157 4515 Planarity : 0.004 0.124 4830 Dihedral : 16.558 178.428 4862 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 36.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.57 % Favored : 92.31 % Rotamer: Outliers : 0.03 % Allowed : 0.14 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.71 % 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: -1.01 (0.15), residues: 3341 helix: 1.17 (0.16), residues: 1161 sheet: -1.19 (0.24), residues: 456 loop : -1.89 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 25 TYR 0.012 0.001 TYR A1305 PHE 0.011 0.001 PHE B 620 TRP 0.008 0.001 TRP A 997 HIS 0.006 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (28916) covalent geometry : angle 0.51821 / 0.28 (39466) SS BOND : bond 0.00754 / 0.38 ( 1) SS BOND : angle 1.54215 / 2.68 ( 2) hydrogen bonds : bond 0.03432 / 3.85 ( 1088) hydrogen bonds : angle 4.61022 / 5.74 ( 3005) metal coordination : bond 0.00346 / 0.41 ( 6) metal coordination : angle 2.35546 / 4.53 ( 6) Misc. bond : bond 0.00173 / 0.09 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7481.19 seconds wall clock time: 129 minutes 1.77 seconds (7741.77 seconds total)