Starting phenix.real_space_refine on Sat Mar 7 07:31:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e6x_27930/03_2026/8e6x_27930_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e6x_27930/03_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_27930/03_2026/8e6x_27930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e6x_27930/03_2026/8e6x_27930.map" model { file = "/net/cci-nas-00/data/ceres_data/8e6x_27930/03_2026/8e6x_27930_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e6x_27930/03_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-dev-5986/lib/python3.9/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: 7.45, per 1000 atoms: 0.19 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: 3.38 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1502 " pdb="ZN ZN B1502 " - pdb=" SG CYS B 70 " pdb="ZN ZN B1502 " - pdb=" SG CYS B 85 " pdb=" ZN B1503 " pdb="ZN ZN B1503 " - pdb=" SG CYS B 888 " pdb="ZN ZN B1503 " - pdb=" SG CYS B 895 " pdb="ZN ZN B1503 " - pdb=" SG CYS B 814 " pdb="ZN ZN B1503 " - pdb=" SG CYS B 898 " Number of angles added : 6 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: 4.71 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: 10.49 Time building geometry restraints manager: 4.60 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 1.50e+00 4.44e-01 8.61e+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=" O3' DA 6 28 " pdb=" P DT 6 29 " pdb=" O5' DT 6 29 " ideal model delta sigma weight residual 104.00 126.05 -22.05 1.50e+00 4.44e-01 2.16e+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: 4064 0.107 - 0.214: 418 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.310 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 46.280 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5917 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= 0.516 Angle : 1.212 48.380 39474 Z= 0.688 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 covalent geometry : bond 0.00995 (28916) covalent geometry : angle 1.19089 (39466) SS BOND : bond 0.23920 ( 1) SS BOND : angle 4.32339 ( 2) hydrogen bonds : bond 0.17754 ( 1088) hydrogen bonds : angle 7.45802 ( 3005) metal coordination : bond 0.27736 ( 6) metal coordination : angle 18.03649 ( 6) Misc. bond : bond 0.23707 ( 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 : 1.237 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: symmetry clash REVERT: A 241 LEU cc_start: 0.6557 (tp) cc_final: 0.6330 (tp) REVERT: A 1279 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7646 (mt-10) REVERT: B 114 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.5882 (tp) REVERT: B 146 VAL cc_start: 0.2958 (OUTLIER) cc_final: 0.2676 (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: 0.7371 (p) REVERT: B 513 MET cc_start: 0.6633 (ttp) cc_final: 0.6392 (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: 0.6423 (ttm) REVERT: B 1256 ILE cc_start: 0.7494 (mm) cc_final: 0.7286 (mm) REVERT: D 46 ILE cc_start: 0.8188 (mt) cc_final: 0.7601 (tp) REVERT: F 123 ARG cc_start: 0.0371 (OUTLIER) cc_final: -0.1877 (mtt180) outliers start: 122 outliers final: 30 residues processed: 686 average time/residue: 0.3398 time to fit residues: 344.2040 Evaluate side-chains 330 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 296 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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: 0.0980 chunk 298 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 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 618 GLN A 761 GLN ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1157 GLN A1268 GLN A1313 HIS B 294 ASN B 424 ASN ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 817 HIS B1279 GLN C 147 GLN D 66 HIS D 117 HIS D 227 GLN ** F 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.073994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.054088 restraints weight = 389730.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.055966 restraints weight = 207763.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.057209 restraints weight = 135967.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.058037 restraints weight = 101980.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.058440 restraints weight = 84523.726| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 28924 Z= 0.137 Angle : 0.617 9.561 39474 Z= 0.333 Chirality : 0.042 0.327 4515 Planarity : 0.006 0.059 4830 Dihedral : 16.960 172.340 4862 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 23.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.38 % Favored : 93.45 % Rotamer: Outliers : 0.10 % Allowed : 1.96 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 1.43 % Twisted General : 0.03 % 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: -2.73 (0.13), residues: 3341 helix: -0.60 (0.15), residues: 1115 sheet: -1.82 (0.24), residues: 417 loop : -2.70 (0.13), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 156 TYR 0.023 0.001 TYR F 68 PHE 0.017 0.001 PHE B 141 TRP 0.012 0.001 TRP A 997 HIS 0.008 0.001 HIS B 777 Details of bonding type rmsd covalent geometry : bond 0.00303 (28916) covalent geometry : angle 0.61430 (39466) SS BOND : bond 0.00329 ( 1) SS BOND : angle 3.73672 ( 2) hydrogen bonds : bond 0.04416 ( 1088) hydrogen bonds : angle 5.14002 ( 3005) metal coordination : bond 0.01356 ( 6) metal coordination : angle 4.16368 ( 6) Misc. bond : bond 0.00204 ( 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 373 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 370 time to evaluate : 1.178 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: A 156 PHE cc_start: 0.8645 (m-10) cc_final: 0.8285 (m-80) REVERT: A 369 MET cc_start: 0.8602 (ttt) cc_final: 0.8325 (ttp) REVERT: A 395 TYR cc_start: 0.7809 (t80) cc_final: 0.7316 (t80) REVERT: A 403 MET cc_start: 0.7948 (tmm) cc_final: 0.7600 (tmm) REVERT: A 492 MET cc_start: 0.6761 (ttm) cc_final: 0.6356 (ttt) REVERT: A 800 MET cc_start: 0.8162 (mpp) cc_final: 0.7939 (mpp) REVERT: A 929 ILE cc_start: 0.9628 (pt) cc_final: 0.9307 (mm) REVERT: A 1232 MET cc_start: 0.9316 (mtp) cc_final: 0.8525 (mmm) REVERT: A 1308 ILE cc_start: 0.9696 (mm) cc_final: 0.9439 (tp) REVERT: A 1315 MET cc_start: 0.8346 (ppp) cc_final: 0.7890 (ppp) REVERT: B 237 MET cc_start: 0.8658 (mmp) cc_final: 0.8327 (mmp) REVERT: B 239 LEU cc_start: 0.9425 (mt) cc_final: 0.9080 (tp) REVERT: B 484 MET cc_start: 0.8885 (mtm) cc_final: 0.8616 (mtm) REVERT: B 534 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8310 (tm-30) REVERT: B 544 LEU cc_start: 0.9069 (tp) cc_final: 0.8814 (tp) REVERT: B 560 ASN cc_start: 0.8190 (p0) cc_final: 0.7771 (p0) REVERT: B 698 MET cc_start: 0.9536 (tpt) cc_final: 0.9108 (tpp) REVERT: B 724 MET cc_start: 0.9182 (mtm) cc_final: 0.8900 (mtm) REVERT: B 1151 LYS cc_start: 0.8271 (pptt) cc_final: 0.7962 (tttt) REVERT: C 142 MET cc_start: 0.8474 (ptp) cc_final: 0.8256 (ptp) REVERT: D 51 MET cc_start: 0.8245 (mmp) cc_final: 0.7986 (mmm) REVERT: D 186 ASN cc_start: 0.8671 (m-40) cc_final: 0.8273 (m-40) REVERT: D 194 GLN cc_start: 0.9051 (tp-100) cc_final: 0.8632 (tp-100) REVERT: E 5 THR cc_start: 0.7181 (p) cc_final: 0.6971 (p) REVERT: E 15 ASN cc_start: 0.7650 (t0) cc_final: 0.7112 (t0) REVERT: E 19 LEU cc_start: 0.7973 (pp) cc_final: 0.7726 (tt) REVERT: E 26 ARG cc_start: 0.8653 (tpt170) cc_final: 0.7906 (mmp-170) outliers start: 3 outliers final: 1 residues processed: 373 average time/residue: 0.3012 time to fit residues: 172.9887 Evaluate side-chains 257 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 256 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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: 9.9990 chunk 80 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 304 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 285 optimal weight: 0.0970 chunk 152 optimal weight: 2.9990 chunk 311 optimal weight: 7.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 HIS ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN ** A 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN A 628 HIS ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 A1135 GLN A1136 GLN ** 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** B 951 GLN B1244 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.063736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.045343 restraints weight = 403982.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.046833 restraints weight = 214995.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.047821 restraints weight = 142456.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.048384 restraints weight = 108635.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.048882 restraints weight = 92473.101| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.5865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 28924 Z= 0.272 Angle : 0.761 13.895 39474 Z= 0.405 Chirality : 0.045 0.355 4515 Planarity : 0.006 0.087 4830 Dihedral : 16.952 178.730 4862 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 38.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.32 % Favored : 91.53 % Rotamer: Outliers : 0.10 % Allowed : 2.41 % Favored : 97.48 % 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: -2.07 (0.14), residues: 3341 helix: 0.14 (0.15), residues: 1147 sheet: -1.83 (0.23), residues: 473 loop : -2.36 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.001 ARG F 114 TYR 0.024 0.002 TYR A1305 PHE 0.032 0.003 PHE D 35 TRP 0.026 0.002 TRP F 9 HIS 0.011 0.002 HIS B 450 Details of bonding type rmsd covalent geometry : bond 0.00568 (28916) covalent geometry : angle 0.75993 (39466) SS BOND : bond 0.00612 ( 1) SS BOND : angle 2.26236 ( 2) hydrogen bonds : bond 0.04724 ( 1088) hydrogen bonds : angle 5.20605 ( 3005) metal coordination : bond 0.00775 ( 6) metal coordination : angle 2.50169 ( 6) Misc. bond : bond 0.00741 ( 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 266 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 263 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 PHE cc_start: 0.8789 (m-10) cc_final: 0.8503 (m-80) REVERT: A 239 MET cc_start: 0.7064 (ttp) cc_final: 0.6816 (ttp) REVERT: A 403 MET cc_start: 0.8486 (tmm) cc_final: 0.8217 (tmm) REVERT: A 429 MET cc_start: 0.9572 (mtm) cc_final: 0.9364 (mtt) REVERT: A 704 MET cc_start: 0.9399 (mmm) cc_final: 0.9125 (mmp) REVERT: A 800 MET cc_start: 0.7728 (mpp) cc_final: 0.7309 (mpp) REVERT: A 805 MET cc_start: 0.9308 (ptm) cc_final: 0.9037 (ptp) REVERT: A 1243 MET cc_start: 0.9095 (ttp) cc_final: 0.8772 (ttp) REVERT: A 1279 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8735 (mt-10) REVERT: A 1304 MET cc_start: 0.8659 (mmp) cc_final: 0.8189 (mmp) REVERT: A 1315 MET cc_start: 0.8539 (ppp) cc_final: 0.8005 (ppp) REVERT: B 115 TRP cc_start: 0.9293 (m-10) cc_final: 0.8894 (m100) REVERT: B 237 MET cc_start: 0.9326 (mmp) cc_final: 0.9034 (mmp) REVERT: B 330 MET cc_start: 0.9297 (mmt) cc_final: 0.8768 (mmt) REVERT: B 454 CYS cc_start: 0.8488 (m) cc_final: 0.8252 (m) REVERT: B 484 MET cc_start: 0.9230 (mtm) cc_final: 0.9012 (mtm) REVERT: B 513 MET cc_start: 0.9449 (ttp) cc_final: 0.9114 (ttt) REVERT: B 544 LEU cc_start: 0.9275 (tp) cc_final: 0.9071 (tp) REVERT: B 560 ASN cc_start: 0.8547 (p0) cc_final: 0.8058 (p0) REVERT: B 698 MET cc_start: 0.9581 (tpt) cc_final: 0.9141 (tpp) REVERT: B 724 MET cc_start: 0.9135 (mtm) cc_final: 0.8805 (mtt) REVERT: B 1194 ARG cc_start: 0.7494 (mtt90) cc_final: 0.7279 (mtp180) REVERT: B 1260 MET cc_start: 0.8970 (mtp) cc_final: 0.8320 (mmm) REVERT: D 51 MET cc_start: 0.8540 (mmp) cc_final: 0.8180 (mmm) REVERT: D 186 ASN cc_start: 0.8929 (m-40) cc_final: 0.8694 (m-40) REVERT: D 194 GLN cc_start: 0.9214 (tp-100) cc_final: 0.8933 (tp-100) REVERT: E 15 ASN cc_start: 0.7903 (t0) cc_final: 0.7538 (t0) REVERT: E 17 PHE cc_start: 0.7839 (m-10) cc_final: 0.7542 (m-10) REVERT: E 30 MET cc_start: 0.9162 (tpt) cc_final: 0.8834 (tpt) REVERT: E 53 GLU cc_start: 0.8030 (tp30) cc_final: 0.7781 (tp30) REVERT: F 28 GLU cc_start: 0.9374 (mm-30) cc_final: 0.8911 (pt0) REVERT: F 73 MET cc_start: 0.7491 (ttp) cc_final: 0.7168 (ppp) outliers start: 3 outliers final: 0 residues processed: 266 average time/residue: 0.3076 time to fit residues: 125.8612 Evaluate side-chains 208 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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: 10.0000 chunk 297 optimal weight: 5.9990 chunk 240 optimal weight: 9.9990 chunk 86 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 HIS ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 GLN ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.062480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.043927 restraints weight = 402765.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.045388 restraints weight = 211738.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.046343 restraints weight = 139635.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.046972 restraints weight = 106763.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.047388 restraints weight = 89945.055| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.6509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 28924 Z= 0.174 Angle : 0.564 7.767 39474 Z= 0.306 Chirality : 0.041 0.202 4515 Planarity : 0.005 0.068 4830 Dihedral : 16.653 178.504 4862 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 34.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.79 % Favored : 93.09 % Rotamer: Outliers : 0.03 % Allowed : 1.33 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.71 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.14), residues: 3341 helix: 0.83 (0.15), residues: 1145 sheet: -1.46 (0.24), residues: 459 loop : -2.20 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG F 114 TYR 0.014 0.001 TYR A1305 PHE 0.026 0.001 PHE F 128 TRP 0.014 0.001 TRP F 9 HIS 0.006 0.001 HIS B 865 Details of bonding type rmsd covalent geometry : bond 0.00360 (28916) covalent geometry : angle 0.56275 (39466) SS BOND : bond 0.02046 ( 1) SS BOND : angle 1.41118 ( 2) hydrogen bonds : bond 0.03569 ( 1088) hydrogen bonds : angle 4.76270 ( 3005) metal coordination : bond 0.00383 ( 6) metal coordination : angle 2.65757 ( 6) Misc. bond : bond 0.00647 ( 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 246 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 245 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 PHE cc_start: 0.8828 (m-10) cc_final: 0.8555 (m-80) REVERT: A 239 MET cc_start: 0.7408 (ttp) cc_final: 0.7177 (ttp) REVERT: A 311 CYS cc_start: 0.8976 (p) cc_final: 0.8275 (p) REVERT: A 403 MET cc_start: 0.9073 (tmm) cc_final: 0.8827 (tmm) REVERT: A 429 MET cc_start: 0.9550 (mtm) cc_final: 0.9321 (mtt) REVERT: A 681 MET cc_start: 0.9439 (mtm) cc_final: 0.9119 (mtm) REVERT: A 686 GLN cc_start: 0.9498 (tt0) cc_final: 0.9290 (tt0) REVERT: A 704 MET cc_start: 0.9427 (mmm) cc_final: 0.9151 (mmp) REVERT: A 800 MET cc_start: 0.7867 (mpp) cc_final: 0.7415 (mpp) REVERT: A 805 MET cc_start: 0.9308 (ptm) cc_final: 0.9095 (ptp) REVERT: A 1066 MET cc_start: 0.9005 (mtp) cc_final: 0.8733 (mtp) REVERT: A 1230 MET cc_start: 0.8597 (ttt) cc_final: 0.8353 (ttt) REVERT: A 1243 MET cc_start: 0.8910 (ttp) cc_final: 0.8667 (ttp) REVERT: A 1279 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8598 (mt-10) REVERT: A 1290 MET cc_start: 0.9327 (tpp) cc_final: 0.9018 (mmm) REVERT: A 1304 MET cc_start: 0.8693 (mmp) cc_final: 0.8178 (mmp) REVERT: A 1315 MET cc_start: 0.8450 (ppp) cc_final: 0.8121 (ppp) REVERT: B 46 TYR cc_start: 0.7736 (t80) cc_final: 0.7511 (t80) REVERT: B 130 MET cc_start: 0.8684 (tpp) cc_final: 0.8169 (mmm) REVERT: B 237 MET cc_start: 0.9281 (mmp) cc_final: 0.8922 (mmp) REVERT: B 298 MET cc_start: 0.9570 (mmp) cc_final: 0.9304 (mmp) REVERT: B 454 CYS cc_start: 0.8556 (m) cc_final: 0.8336 (m) REVERT: B 484 MET cc_start: 0.9185 (mtm) cc_final: 0.8929 (mtm) REVERT: B 534 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8434 (tm-30) REVERT: B 560 ASN cc_start: 0.8519 (p0) cc_final: 0.8029 (p0) REVERT: B 698 MET cc_start: 0.9604 (tpt) cc_final: 0.9028 (tpp) REVERT: B 1189 MET cc_start: 0.8066 (tpt) cc_final: 0.7696 (tpt) REVERT: C 80 GLU cc_start: 0.9101 (tt0) cc_final: 0.8887 (tt0) REVERT: D 186 ASN cc_start: 0.8846 (m-40) cc_final: 0.8635 (m-40) REVERT: D 194 GLN cc_start: 0.9155 (tp-100) cc_final: 0.8841 (tp-100) REVERT: E 15 ASN cc_start: 0.8389 (t0) cc_final: 0.8015 (t0) REVERT: E 53 GLU cc_start: 0.8012 (tp30) cc_final: 0.7747 (tp30) outliers start: 1 outliers final: 0 residues processed: 246 average time/residue: 0.3103 time to fit residues: 118.0855 Evaluate side-chains 206 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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: 9.9990 chunk 266 optimal weight: 5.9990 chunk 228 optimal weight: 10.0000 chunk 286 optimal weight: 5.9990 chunk 329 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 chunk 251 optimal weight: 0.9980 chunk 323 optimal weight: 7.9990 chunk 229 optimal weight: 4.9990 chunk 186 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 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 613 ASN A 658 GLN ** 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 186 GLN B 488 ASN B 951 GLN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 HIS ** F 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.058134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.040524 restraints weight = 413666.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.041880 restraints weight = 218250.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.042742 restraints weight = 144484.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.043313 restraints weight = 111063.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.043663 restraints weight = 93988.696| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.7815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 28924 Z= 0.282 Angle : 0.709 8.733 39474 Z= 0.380 Chirality : 0.043 0.165 4515 Planarity : 0.006 0.126 4830 Dihedral : 16.846 177.893 4862 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 45.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.37 % Favored : 90.45 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.00 % 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: -1.84 (0.14), residues: 3341 helix: 0.34 (0.15), residues: 1158 sheet: -1.70 (0.24), residues: 456 loop : -2.26 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1034 TYR 0.026 0.002 TYR A1305 PHE 0.021 0.002 PHE A 390 TRP 0.011 0.002 TRP A1276 HIS 0.009 0.002 HIS B 450 Details of bonding type rmsd covalent geometry : bond 0.00574 (28916) covalent geometry : angle 0.70811 (39466) SS BOND : bond 0.02622 ( 1) SS BOND : angle 0.64499 ( 2) hydrogen bonds : bond 0.04394 ( 1088) hydrogen bonds : angle 5.24320 ( 3005) metal coordination : bond 0.00934 ( 6) metal coordination : angle 2.72170 ( 6) Misc. bond : bond 0.00462 ( 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 210 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.155 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: 0.8910 (m-10) cc_final: 0.8532 (m-10) REVERT: A 311 CYS cc_start: 0.8956 (p) cc_final: 0.7854 (p) REVERT: A 429 MET cc_start: 0.9527 (mtm) cc_final: 0.9307 (mtt) REVERT: A 681 MET cc_start: 0.9464 (mtm) cc_final: 0.9173 (mtm) REVERT: A 800 MET cc_start: 0.7841 (mpp) cc_final: 0.7186 (mpp) REVERT: A 805 MET cc_start: 0.9370 (ptm) cc_final: 0.9155 (ptp) REVERT: A 1230 MET cc_start: 0.8736 (ttt) cc_final: 0.8382 (ttt) REVERT: A 1232 MET cc_start: 0.9085 (mtp) cc_final: 0.8763 (mtp) REVERT: A 1287 LEU cc_start: 0.9845 (tt) cc_final: 0.9476 (tt) REVERT: A 1319 MET cc_start: 0.8686 (tpp) cc_final: 0.8395 (tpp) REVERT: B 130 MET cc_start: 0.8591 (tpp) cc_final: 0.8308 (mmm) REVERT: B 237 MET cc_start: 0.9425 (mmp) cc_final: 0.9048 (mmp) REVERT: B 484 MET cc_start: 0.9183 (mtm) cc_final: 0.8800 (mtm) REVERT: B 560 ASN cc_start: 0.8654 (p0) cc_final: 0.8137 (p0) REVERT: B 698 MET cc_start: 0.9591 (tpt) cc_final: 0.9019 (tpp) REVERT: D 194 GLN cc_start: 0.9169 (tp-100) cc_final: 0.8951 (tp-100) REVERT: E 53 GLU cc_start: 0.8076 (tp30) cc_final: 0.7843 (tp30) REVERT: F 13 GLN cc_start: 0.7926 (tm-30) cc_final: 0.7673 (tm-30) REVERT: F 73 MET cc_start: 0.8752 (ppp) cc_final: 0.8487 (ppp) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.2955 time to fit residues: 97.3126 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 : 1.211 ------------------------------------------------------------------------------- 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: 8.9990 chunk 127 optimal weight: 0.8980 chunk 205 optimal weight: 1.9990 chunk 334 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 332 optimal weight: 7.9990 chunk 285 optimal weight: 8.9990 chunk 304 optimal weight: 2.9990 chunk 214 optimal weight: 0.7980 chunk 293 optimal weight: 8.9990 chunk 254 optimal weight: 20.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 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 604 HIS ** 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.058381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.040424 restraints weight = 415911.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.041820 restraints weight = 215200.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.042705 restraints weight = 141389.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.043306 restraints weight = 108644.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.043582 restraints weight = 91874.652| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.8178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 28924 Z= 0.178 Angle : 0.554 6.505 39474 Z= 0.302 Chirality : 0.041 0.162 4515 Planarity : 0.004 0.056 4830 Dihedral : 16.679 177.686 4862 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 39.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.30 % Favored : 92.58 % Rotamer: Outliers : 0.03 % Allowed : 0.66 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.71 % Twisted General : 0.03 % 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: -1.51 (0.14), residues: 3341 helix: 0.69 (0.15), residues: 1167 sheet: -1.53 (0.23), residues: 465 loop : -2.13 (0.14), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 322 TYR 0.017 0.001 TYR A1305 PHE 0.013 0.001 PHE B 141 TRP 0.010 0.001 TRP A1276 HIS 0.006 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00364 (28916) covalent geometry : angle 0.55288 (39466) SS BOND : bond 0.00969 ( 1) SS BOND : angle 1.47210 ( 2) hydrogen bonds : bond 0.03549 ( 1088) hydrogen bonds : angle 4.84330 ( 3005) metal coordination : bond 0.00406 ( 6) metal coordination : angle 2.40422 ( 6) Misc. bond : bond 0.00098 ( 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 209 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.968 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: A 156 PHE cc_start: 0.8884 (m-10) cc_final: 0.8506 (m-10) REVERT: A 311 CYS cc_start: 0.8740 (p) cc_final: 0.7470 (p) REVERT: A 492 MET cc_start: 0.7775 (ttt) cc_final: 0.7461 (ttt) REVERT: A 681 MET cc_start: 0.9451 (mtm) cc_final: 0.9143 (mtm) REVERT: A 800 MET cc_start: 0.7903 (mpp) cc_final: 0.7187 (mpp) REVERT: A 1007 LYS cc_start: 0.6981 (mmtt) cc_final: 0.6643 (mmtt) REVERT: A 1066 MET cc_start: 0.8989 (mtp) cc_final: 0.8755 (mtp) REVERT: A 1230 MET cc_start: 0.8605 (ttt) cc_final: 0.8296 (ttp) REVERT: A 1272 GLU cc_start: 0.8636 (pp20) cc_final: 0.8436 (pp20) REVERT: A 1319 MET cc_start: 0.8678 (tpp) cc_final: 0.8385 (tpp) REVERT: B 237 MET cc_start: 0.9401 (mmp) cc_final: 0.9028 (mmp) REVERT: B 298 MET cc_start: 0.9536 (mmp) cc_final: 0.9276 (mmp) REVERT: B 454 CYS cc_start: 0.8697 (m) cc_final: 0.8450 (m) REVERT: B 466 MET cc_start: 0.9116 (mtp) cc_final: 0.8467 (mtp) REVERT: B 484 MET cc_start: 0.9216 (mtm) cc_final: 0.8761 (mtm) REVERT: B 485 MET cc_start: 0.9484 (tpp) cc_final: 0.9166 (tpp) REVERT: B 497 GLU cc_start: 0.8506 (mp0) cc_final: 0.8177 (mp0) REVERT: B 560 ASN cc_start: 0.8712 (p0) cc_final: 0.8311 (p0) REVERT: B 698 MET cc_start: 0.9591 (tpt) cc_final: 0.9040 (tpp) REVERT: B 747 MET cc_start: 0.8455 (mmm) cc_final: 0.7681 (mmm) REVERT: B 1284 ARG cc_start: 0.9374 (tpt90) cc_final: 0.9067 (tpp-160) REVERT: B 1325 PHE cc_start: 0.8794 (t80) cc_final: 0.8154 (t80) REVERT: D 194 GLN cc_start: 0.9119 (tp-100) cc_final: 0.8910 (tp-100) REVERT: E 53 GLU cc_start: 0.8110 (tp30) cc_final: 0.7797 (tp30) REVERT: F 13 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7704 (tm-30) REVERT: F 73 MET cc_start: 0.8820 (ppp) cc_final: 0.8611 (ppp) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.2952 time to fit residues: 96.5427 Evaluate side-chains 181 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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: 0.7980 chunk 316 optimal weight: 9.9990 chunk 184 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 271 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 315 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1175 ASN ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.055972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.038429 restraints weight = 433729.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.039735 restraints weight = 225903.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.040552 restraints weight = 150366.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.040957 restraints weight = 117127.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.041350 restraints weight = 102133.288| |-----------------------------------------------------------------------------| r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.9076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 28924 Z= 0.273 Angle : 0.681 8.561 39474 Z= 0.365 Chirality : 0.043 0.181 4515 Planarity : 0.005 0.055 4830 Dihedral : 16.892 179.471 4862 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 49.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.66 % Favored : 89.19 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.00 % 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: -1.87 (0.14), residues: 3341 helix: 0.28 (0.15), residues: 1165 sheet: -1.50 (0.24), residues: 442 loop : -2.32 (0.13), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 297 TYR 0.025 0.002 TYR A1305 PHE 0.022 0.002 PHE F 128 TRP 0.017 0.002 TRP A1276 HIS 0.007 0.002 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00554 (28916) covalent geometry : angle 0.67970 (39466) SS BOND : bond 0.00838 ( 1) SS BOND : angle 1.59767 ( 2) hydrogen bonds : bond 0.04310 ( 1088) hydrogen bonds : angle 5.24599 ( 3005) metal coordination : bond 0.00704 ( 6) metal coordination : angle 2.76820 ( 6) Misc. bond : bond 0.00232 ( 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 193 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.190 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: A 156 PHE cc_start: 0.8785 (m-10) cc_final: 0.8513 (m-10) REVERT: A 311 CYS cc_start: 0.8827 (p) cc_final: 0.8579 (p) REVERT: A 320 ASP cc_start: 0.9115 (t70) cc_final: 0.8827 (p0) REVERT: A 429 MET cc_start: 0.9351 (mtm) cc_final: 0.9084 (mtt) REVERT: A 459 MET cc_start: 0.9362 (mmp) cc_final: 0.9137 (mmm) REVERT: A 681 MET cc_start: 0.9461 (mtm) cc_final: 0.9113 (mtm) REVERT: A 800 MET cc_start: 0.7813 (mpp) cc_final: 0.7025 (mpp) REVERT: A 1010 GLN cc_start: 0.6988 (mt0) cc_final: 0.6725 (mt0) REVERT: A 1230 MET cc_start: 0.8691 (ttt) cc_final: 0.8328 (ttt) REVERT: A 1290 MET cc_start: 0.9492 (tpp) cc_final: 0.9109 (tpp) REVERT: A 1319 MET cc_start: 0.8729 (tpp) cc_final: 0.8384 (tpp) REVERT: B 237 MET cc_start: 0.9459 (mmp) cc_final: 0.9103 (mmp) REVERT: B 330 MET cc_start: 0.9433 (mmt) cc_final: 0.9189 (mmm) REVERT: B 454 CYS cc_start: 0.8759 (m) cc_final: 0.8540 (m) REVERT: B 485 MET cc_start: 0.9454 (tpp) cc_final: 0.9229 (tpp) REVERT: B 560 ASN cc_start: 0.8839 (p0) cc_final: 0.8394 (p0) REVERT: B 698 MET cc_start: 0.9554 (tpt) cc_final: 0.8982 (tpp) REVERT: B 747 MET cc_start: 0.8457 (mmm) cc_final: 0.7466 (mmm) REVERT: B 1325 PHE cc_start: 0.8758 (t80) cc_final: 0.8189 (t80) REVERT: E 53 GLU cc_start: 0.8201 (tp30) cc_final: 0.7888 (tp30) REVERT: F 73 MET cc_start: 0.9024 (ppp) cc_final: 0.8728 (ppp) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.2917 time to fit residues: 88.5289 Evaluate side-chains 162 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.109 ------------------------------------------------------------------------------- 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: 1.9990 chunk 236 optimal weight: 0.1980 chunk 1 optimal weight: 10.0000 chunk 50 optimal weight: 0.4980 chunk 266 optimal weight: 4.9990 chunk 298 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 261 optimal weight: 0.7980 chunk 197 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 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** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 HIS ** 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 = 0.3391 r_free = 0.3391 target = 0.057640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.040161 restraints weight = 408260.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.041486 restraints weight = 213029.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.042353 restraints weight = 141199.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.042897 restraints weight = 108735.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.043156 restraints weight = 92568.736| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.9033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 28924 Z= 0.099 Angle : 0.496 5.268 39474 Z= 0.269 Chirality : 0.040 0.164 4515 Planarity : 0.004 0.045 4830 Dihedral : 16.553 179.752 4862 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 36.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.99 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.10 (0.14), residues: 3341 helix: 1.15 (0.16), residues: 1158 sheet: -1.29 (0.24), residues: 455 loop : -1.97 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1171 TYR 0.012 0.001 TYR B 795 PHE 0.013 0.001 PHE B 620 TRP 0.008 0.001 TRP B 409 HIS 0.005 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00214 (28916) covalent geometry : angle 0.49527 (39466) SS BOND : bond 0.00556 ( 1) SS BOND : angle 1.34442 ( 2) hydrogen bonds : bond 0.03295 ( 1088) hydrogen bonds : angle 4.53532 ( 3005) metal coordination : bond 0.00248 ( 6) metal coordination : angle 2.07318 ( 6) Misc. bond : bond 0.00108 ( 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 197 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 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: A 156 PHE cc_start: 0.8759 (m-10) cc_final: 0.8469 (m-10) REVERT: A 311 CYS cc_start: 0.8621 (p) cc_final: 0.7230 (p) REVERT: A 320 ASP cc_start: 0.9134 (t70) cc_final: 0.8881 (p0) REVERT: A 681 MET cc_start: 0.9358 (mtm) cc_final: 0.9075 (mtm) REVERT: A 800 MET cc_start: 0.7820 (mpp) cc_final: 0.7059 (mpp) REVERT: A 825 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8911 (mt-10) REVERT: A 1230 MET cc_start: 0.8557 (ttt) cc_final: 0.8201 (ttp) REVERT: A 1319 MET cc_start: 0.8715 (tpp) cc_final: 0.8385 (tpp) REVERT: B 219 LYS cc_start: 0.9354 (mtmt) cc_final: 0.9145 (ptpp) REVERT: B 223 LEU cc_start: 0.9005 (mm) cc_final: 0.8638 (tt) REVERT: B 237 MET cc_start: 0.9416 (mmp) cc_final: 0.9073 (mmp) REVERT: B 298 MET cc_start: 0.9434 (mmp) cc_final: 0.9208 (mmp) REVERT: B 330 MET cc_start: 0.9388 (mmt) cc_final: 0.8989 (mmm) REVERT: B 454 CYS cc_start: 0.8623 (m) cc_final: 0.8404 (m) REVERT: B 560 ASN cc_start: 0.8807 (p0) cc_final: 0.8373 (p0) REVERT: B 698 MET cc_start: 0.9542 (tpt) cc_final: 0.8982 (tpp) REVERT: B 747 MET cc_start: 0.8334 (mmm) cc_final: 0.7278 (mmm) REVERT: B 1325 PHE cc_start: 0.8607 (t80) cc_final: 0.8057 (t80) REVERT: C 95 LYS cc_start: 0.8959 (mppt) cc_final: 0.8752 (mtmm) REVERT: E 53 GLU cc_start: 0.8379 (tp30) cc_final: 0.7984 (tp30) REVERT: F 13 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7667 (tm-30) REVERT: F 70 LEU cc_start: 0.9179 (tp) cc_final: 0.8728 (tp) REVERT: F 73 MET cc_start: 0.8846 (ppp) cc_final: 0.8633 (ppp) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2900 time to fit residues: 89.8662 Evaluate side-chains 166 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.109 ------------------------------------------------------------------------------- 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: 3.9990 chunk 207 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 341 optimal weight: 10.0000 chunk 266 optimal weight: 6.9990 chunk 84 optimal weight: 0.0980 chunk 88 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 437 ASN ** A 517 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** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 HIS ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 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 = 0.3376 r_free = 0.3376 target = 0.056990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.039615 restraints weight = 412403.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.040930 restraints weight = 216973.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.041772 restraints weight = 144031.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.042337 restraints weight = 111366.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.042593 restraints weight = 94530.770| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.9230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28924 Z= 0.132 Angle : 0.506 5.344 39474 Z= 0.274 Chirality : 0.040 0.151 4515 Planarity : 0.004 0.044 4830 Dihedral : 16.433 179.443 4862 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 39.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.47 % Favored : 91.44 % 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 : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.15), residues: 3341 helix: 1.23 (0.16), residues: 1165 sheet: -1.12 (0.25), residues: 442 loop : -1.88 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 250 TYR 0.022 0.001 TYR D 68 PHE 0.015 0.001 PHE B 620 TRP 0.007 0.001 TRP A1276 HIS 0.004 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00275 (28916) covalent geometry : angle 0.50454 (39466) SS BOND : bond 0.00715 ( 1) SS BOND : angle 1.15937 ( 2) hydrogen bonds : bond 0.03305 ( 1088) hydrogen bonds : angle 4.57531 ( 3005) metal coordination : bond 0.00418 ( 6) metal coordination : angle 2.56735 ( 6) Misc. bond : bond 0.00157 ( 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 194 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.139 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: A 156 PHE cc_start: 0.8722 (m-10) cc_final: 0.8441 (m-10) REVERT: A 311 CYS cc_start: 0.8706 (p) cc_final: 0.8453 (p) REVERT: A 320 ASP cc_start: 0.9098 (t70) cc_final: 0.8839 (p0) REVERT: A 681 MET cc_start: 0.9385 (mtm) cc_final: 0.9070 (mtm) REVERT: A 800 MET cc_start: 0.7823 (mpp) cc_final: 0.7078 (mpp) REVERT: A 1066 MET cc_start: 0.8963 (mtp) cc_final: 0.8723 (mtp) REVERT: A 1230 MET cc_start: 0.8650 (ttt) cc_final: 0.8203 (ttt) REVERT: A 1232 MET cc_start: 0.9025 (mtp) cc_final: 0.8707 (mtp) REVERT: A 1319 MET cc_start: 0.8780 (tpp) cc_final: 0.8420 (tpp) REVERT: B 223 LEU cc_start: 0.9033 (mm) cc_final: 0.8669 (tt) REVERT: B 237 MET cc_start: 0.9452 (mmp) cc_final: 0.9128 (mmp) REVERT: B 298 MET cc_start: 0.9396 (mmp) cc_final: 0.9117 (mmp) REVERT: B 484 MET cc_start: 0.8757 (mtm) cc_final: 0.8326 (mtm) REVERT: B 485 MET cc_start: 0.9444 (tpp) cc_final: 0.9155 (tpp) REVERT: B 513 MET cc_start: 0.9448 (ttp) cc_final: 0.9176 (ttt) REVERT: B 560 ASN cc_start: 0.8813 (p0) cc_final: 0.8505 (p0) REVERT: B 698 MET cc_start: 0.9539 (tpt) cc_final: 0.8980 (tpp) REVERT: B 747 MET cc_start: 0.8353 (mmm) cc_final: 0.7314 (mmm) REVERT: B 1325 PHE cc_start: 0.8608 (t80) cc_final: 0.8077 (t80) REVERT: E 29 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8538 (tm-30) REVERT: E 53 GLU cc_start: 0.8431 (tp30) cc_final: 0.8040 (tp30) REVERT: F 70 LEU cc_start: 0.9106 (tp) cc_final: 0.8714 (tp) REVERT: F 73 MET cc_start: 0.8868 (ppp) cc_final: 0.8628 (ppp) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.2884 time to fit residues: 88.4934 Evaluate side-chains 165 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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: 2.9990 chunk 271 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 193 optimal weight: 0.7980 chunk 209 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 334 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 GLN B1367 GLN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.055736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.038647 restraints weight = 418592.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.039895 restraints weight = 219535.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.040707 restraints weight = 146784.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.041240 restraints weight = 113605.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.041513 restraints weight = 96714.876| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.9614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.766 28924 Z= 0.392 Angle : 0.617 30.175 39474 Z= 0.335 Chirality : 0.041 0.363 4515 Planarity : 0.004 0.044 4830 Dihedral : 16.545 179.982 4862 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 45.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.58 % Favored : 90.30 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.71 % Twisted General : 0.03 % 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: -1.23 (0.14), residues: 3341 helix: 0.91 (0.15), residues: 1172 sheet: -1.28 (0.25), residues: 432 loop : -1.98 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 202 TYR 0.021 0.002 TYR A1305 PHE 0.050 0.002 PHE F 175 TRP 0.009 0.001 TRP B1193 HIS 0.006 0.001 HIS B 777 Details of bonding type rmsd covalent geometry : bond 0.00991 (28916) covalent geometry : angle 0.61639 (39466) SS BOND : bond 0.00720 ( 1) SS BOND : angle 2.00985 ( 2) hydrogen bonds : bond 0.03672 ( 1088) hydrogen bonds : angle 4.89836 ( 3005) metal coordination : bond 0.00664 ( 6) metal coordination : angle 2.68045 ( 6) Misc. bond : bond 0.00209 ( 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 181 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.215 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: A 156 PHE cc_start: 0.8731 (m-10) cc_final: 0.8430 (m-10) REVERT: A 239 MET cc_start: 0.8060 (tmm) cc_final: 0.7823 (tmm) REVERT: A 320 ASP cc_start: 0.9055 (t70) cc_final: 0.8817 (p0) REVERT: A 429 MET cc_start: 0.9375 (mtm) cc_final: 0.9143 (mtt) REVERT: A 681 MET cc_start: 0.9456 (mtm) cc_final: 0.9101 (mtm) REVERT: A 800 MET cc_start: 0.7847 (mpp) cc_final: 0.7405 (mpp) REVERT: A 1066 MET cc_start: 0.9111 (mtp) cc_final: 0.8906 (mtp) REVERT: A 1230 MET cc_start: 0.8760 (ttt) cc_final: 0.8434 (ttt) REVERT: A 1232 MET cc_start: 0.9093 (mtp) cc_final: 0.8732 (mtp) REVERT: A 1290 MET cc_start: 0.9453 (tpp) cc_final: 0.9039 (mmm) REVERT: A 1315 MET cc_start: 0.8560 (ppp) cc_final: 0.8202 (tmm) REVERT: A 1319 MET cc_start: 0.8682 (tpp) cc_final: 0.8385 (tpp) REVERT: B 223 LEU cc_start: 0.9122 (mm) cc_final: 0.8766 (tt) REVERT: B 237 MET cc_start: 0.9480 (mmp) cc_final: 0.9145 (mmp) REVERT: B 298 MET cc_start: 0.9371 (mmp) cc_final: 0.9086 (mmp) REVERT: B 330 MET cc_start: 0.9443 (mmt) cc_final: 0.9187 (mmm) REVERT: B 454 CYS cc_start: 0.8727 (m) cc_final: 0.8506 (m) REVERT: B 485 MET cc_start: 0.9441 (tpp) cc_final: 0.9149 (tpp) REVERT: B 560 ASN cc_start: 0.8831 (p0) cc_final: 0.8567 (p0) REVERT: B 698 MET cc_start: 0.9545 (tpt) cc_final: 0.8997 (tpp) REVERT: B 747 MET cc_start: 0.8351 (mmm) cc_final: 0.7284 (mmm) REVERT: B 1193 TRP cc_start: 0.8462 (t60) cc_final: 0.7872 (t60) REVERT: B 1260 MET cc_start: 0.9311 (mtp) cc_final: 0.8686 (mmm) REVERT: B 1325 PHE cc_start: 0.8652 (t80) cc_final: 0.8118 (t80) REVERT: D 205 MET cc_start: 0.8596 (ttp) cc_final: 0.8290 (ttp) REVERT: E 53 GLU cc_start: 0.8463 (tp30) cc_final: 0.8117 (tp30) REVERT: F 70 LEU cc_start: 0.9038 (tp) cc_final: 0.8586 (tp) REVERT: F 73 MET cc_start: 0.8992 (ppp) cc_final: 0.8694 (ppp) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2915 time to fit residues: 83.8077 Evaluate side-chains 161 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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: 6.9990 chunk 184 optimal weight: 3.9990 chunk 266 optimal weight: 5.9990 chunk 293 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 195 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 299 optimal weight: 5.9990 chunk 145 optimal weight: 0.3980 chunk 294 optimal weight: 6.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 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 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 GLN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.056121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.038588 restraints weight = 429405.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.039939 restraints weight = 221441.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.040792 restraints weight = 146559.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.041209 restraints weight = 113376.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.041649 restraints weight = 98906.973| |-----------------------------------------------------------------------------| r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.9810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.770 28924 Z= 0.364 Angle : 0.556 29.265 39474 Z= 0.304 Chirality : 0.040 0.293 4515 Planarity : 0.004 0.039 4830 Dihedral : 16.443 179.859 4862 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 42.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.53 % Favored : 91.38 % Rotamer: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.04 (0.15), residues: 3341 helix: 1.11 (0.16), residues: 1169 sheet: -1.22 (0.25), residues: 448 loop : -1.88 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 133 TYR 0.014 0.001 TYR A1305 PHE 0.038 0.001 PHE F 175 TRP 0.008 0.001 TRP B 409 HIS 0.005 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00952 (28916) covalent geometry : angle 0.55440 (39466) SS BOND : bond 0.00982 ( 1) SS BOND : angle 2.37978 ( 2) hydrogen bonds : bond 0.03299 ( 1088) hydrogen bonds : angle 4.68504 ( 3005) metal coordination : bond 0.00499 ( 6) metal coordination : angle 2.71079 ( 6) Misc. bond : bond 0.00170 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7080.52 seconds wall clock time: 122 minutes 12.84 seconds (7332.84 seconds total)