Starting phenix.real_space_refine on Sun Aug 9 23:20:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e5o_27916/08_2026/8e5o_27916_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e5o_27916/08_2026/8e5o_27916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e5o_27916/08_2026/8e5o_27916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e5o_27916/08_2026/8e5o_27916.map" model { file = "/net/cci-nas-00/data/ceres_data/8e5o_27916/08_2026/8e5o_27916_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e5o_27916/08_2026/8e5o_27916_neut.cif" } resolution = 4.4 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 87 5.49 5 Mg 1 5.21 5 S 113 5.16 5 C 17285 2.51 5 N 4941 2.21 5 O 5571 1.98 5 H 11229 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39229 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: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 1031 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "7" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 464 Classifications: {'RNA': 17} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 15} 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: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "F" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1276 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 149} Chain breaks: 1 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 13860 SG CYS B 70 54.432 31.392 73.497 1.00 45.60 S ATOM 14119 SG CYS B 85 52.786 27.852 70.702 1.00 49.94 S ATOM 25701 SG CYS B 814 119.865 47.387 60.318 1.00 22.38 S ATOM 26838 SG CYS B 888 115.676 48.793 61.332 1.00 20.48 S ATOM 26929 SG CYS B 895 118.121 47.436 63.658 1.00 14.28 S ATOM 26966 SG CYS B 898 119.630 50.356 62.307 1.00 16.02 S Time building chain proxies: 6.83, per 1000 atoms: 0.17 Number of scatterers: 39229 At special positions: 0 Unit cell: (172.7, 139.7, 155.1, 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 87 15.00 Mg 1 11.99 O 5571 8.00 N 4941 7.00 C 17285 6.00 H 11229 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.55 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 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6182 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 46 sheets defined 35.4% alpha, 15.1% beta 29 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 5.40 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: 4.134A 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: 3.757A pdb=" N ILE A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 480 removed outlier: 4.513A 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: 4.045A 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: 3.791A 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 942 through 979 Processing helix chain 'A' and resid 987 through 991 removed outlier: 3.828A pdb=" N ASP A 990 " --> pdb=" O GLU A 987 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS A 991 " --> pdb=" O LYS A 988 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 987 through 991' Processing helix chain 'A' and resid 1005 through 1038 Processing helix chain 'A' and resid 1101 through 1106 removed outlier: 4.549A pdb=" N SER A1105 " --> pdb=" O LEU A1101 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A1106 " --> pdb=" O GLY A1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1101 through 1106' Processing helix chain 'A' and resid 1109 through 1134 removed outlier: 3.695A pdb=" N LEU A1113 " --> pdb=" O ILE A1109 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A1134 " --> pdb=" O ALA A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1151 removed outlier: 3.880A pdb=" N LEU A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) removed outlier: 3.979A 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: 3.626A 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: 3.893A 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: 3.549A pdb=" N GLY B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 404 removed outlier: 3.690A pdb=" N ALA B 397 " --> pdb=" O THR B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 417 removed outlier: 3.568A 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: 3.522A 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: 3.612A 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: 3.644A pdb=" N GLY B 636 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 670 removed outlier: 3.532A 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: 3.643A pdb=" N ARG B 838 " --> pdb=" O PRO B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 876 removed outlier: 3.797A pdb=" N ASN B 875 " --> pdb=" O LEU B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 895 through 900 removed outlier: 3.520A 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: 4.193A 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: 3.544A 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: 3.827A pdb=" N VAL B1331 " --> pdb=" O GLU B1327 " (cutoff:3.500A) Processing helix chain 'B' and resid 1346 through 1353 removed outlier: 3.806A pdb=" N ASN B1350 " --> pdb=" O GLY B1346 " (cutoff:3.500A) Processing helix chain 'B' and resid 1361 through 1372 removed outlier: 4.421A 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: 3.839A 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: 4.041A 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: 3.525A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.685A 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 77 removed outlier: 3.956A pdb=" N GLN E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 33 Processing helix chain 'F' and resid 35 through 37 No H-bonds generated for 'chain 'F' and resid 35 through 37' Processing helix chain 'F' and resid 76 through 86 Processing helix chain 'F' and resid 105 through 114 removed outlier: 3.647A pdb=" N ASP F 109 " --> pdb=" O ASP F 105 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 178 No H-bonds generated for 'chain 'F' and resid 176 through 178' Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 6.570A pdb=" N LYS A 13 " --> pdb=" O ALA A1183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.929A 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: 7.009A pdb=" N ARG A 97 " --> pdb=" O TYR A 73 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU A 75 " --> pdb=" O PRO A 95 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ALA A 94 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLU A 126 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 4.040A 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: 6.322A 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: 3.581A 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: 4.965A pdb=" N VAL A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 302 removed outlier: 7.193A pdb=" N TYR A 301 " --> pdb=" O ILE A 310 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 580 through 581 removed outlier: 3.688A 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: 5.946A 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: 3.688A 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: 4.895A pdb=" N VAL A 727 " --> pdb=" O ARG A 731 " (cutoff:3.500A) removed outlier: 6.669A 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: 3.994A 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: 3.591A 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: 7.413A pdb=" N LEU A1098 " --> pdb=" O ARG A 801 " (cutoff:3.500A) removed outlier: 6.730A 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: 3.863A pdb=" N GLY A 846 " --> pdb=" O THR A 843 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR A 843 " --> pdb=" O GLY A 846 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR A 830 " --> pdb=" O LYS A1057 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LYS A1057 " --> pdb=" O THR A 830 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N HIS A 832 " --> pdb=" O ALA A1055 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA A1055 " --> pdb=" O HIS A 832 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLN A 834 " --> pdb=" O TYR A1053 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TYR A1053 " --> pdb=" O GLN A 834 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU A 836 " --> pdb=" O LYS A1051 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LYS A1051 " --> pdb=" O LEU A 836 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N CYS A 838 " --> pdb=" O ILE A1049 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE A1049 " --> pdb=" O CYS A 838 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER A 840 " --> pdb=" O LEU A1047 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP A 930 " --> pdb=" O TYR A1053 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA A1055 " --> pdb=" O VAL A 928 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL A 928 " --> pdb=" O ALA A1055 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LYS A1057 " --> pdb=" O GLY A 926 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N GLY A 926 " --> pdb=" O LYS A1057 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 926 " --> pdb=" O VAL A 877 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1244 through 1246 Processing sheet with id=AC2, first strand: chain 'A' and resid 1269 through 1270 Processing sheet with id=AC3, first strand: chain 'A' and resid 1335 through 1337 Processing sheet with id=AC4, first strand: chain 'B' and resid 34 through 37 removed outlier: 4.452A pdb=" N SER B 34 " --> pdb=" O MET B 102 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N HIS B 104 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY B 36 " --> pdb=" O HIS B 104 " (cutoff:3.500A) removed outlier: 7.873A 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: 6.518A pdb=" N THR B 240 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 10.939A pdb=" N SER B 109 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 10.157A pdb=" N ILE B 238 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AC6, first strand: chain 'B' and resid 253 through 254 removed outlier: 4.415A pdb=" N VAL B 253 " --> pdb=" O ALA B 261 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 526 through 527 Processing sheet with id=AC8, first strand: chain 'B' and resid 706 through 708 removed outlier: 3.686A pdb=" N GLU B 714 " --> pdb=" O ILE B 707 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 821 through 822 Processing sheet with id=AD1, 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=AD2, first strand: chain 'B' and resid 957 through 961 removed outlier: 3.802A pdb=" N THR B 980 " --> pdb=" O VAL B 997 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 965 through 967 Processing sheet with id=AD4, first strand: chain 'B' and resid 1034 through 1038 removed outlier: 3.619A pdb=" N ARG B1036 " --> pdb=" O LYS B1079 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS B1079 " --> pdb=" O ARG B1036 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1046 through 1049 removed outlier: 4.088A 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=AD6, first strand: chain 'B' and resid 1187 through 1190 Processing sheet with id=AD7, first strand: chain 'B' and resid 1279 through 1281 removed outlier: 7.344A pdb=" N THR B1301 " --> pdb=" O VAL B1267 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 12 through 13 removed outlier: 6.338A pdb=" N ASP C 199 " --> pdb=" O PRO C 30 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 202 " --> pdb=" O ASN C 186 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 52 through 53 removed outlier: 3.521A pdb=" N GLY C 53 " --> pdb=" O GLY C 149 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 115 through 116 removed outlier: 4.249A pdb=" N THR C 101 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N SER C 141 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 5.310A 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: 4.462A pdb=" N VAL C 59 " --> pdb=" O ARG C 143 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS C 145 " --> pdb=" O THR C 57 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 90 through 91 Processing sheet with id=AE3, first strand: chain 'C' and resid 108 through 111 removed outlier: 3.837A pdb=" N CYS C 131 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing sheet with id=AE4, 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: 4.349A pdb=" N ARG D 182 " --> pdb=" O GLU D 206 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 53 through 61 removed outlier: 4.074A pdb=" N ALA D 55 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LYS D 145 " --> pdb=" O THR D 57 " (cutoff:3.500A) removed outlier: 4.263A 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=AE6, first strand: chain 'D' and resid 90 through 91 Processing sheet with id=AE7, 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=AE8, first strand: chain 'D' and resid 152 through 153 removed outlier: 3.625A pdb=" N VAL D 153 " --> pdb=" O ALA D 175 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 39 through 43 removed outlier: 4.150A pdb=" N GLU F 41 " --> pdb=" O GLN F 72 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN F 72 " --> pdb=" O GLU F 41 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL F 11 " --> pdb=" O PHE F 92 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N PHE F 92 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLN F 13 " --> pdb=" O MET F 90 " (cutoff:3.500A) Processing sheet with id=AF1, 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: 7.958A pdb=" N LYS F 159 " --> pdb=" O GLU F 149 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL F 171 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL F 162 " --> pdb=" O THR F 169 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE F 164 " --> pdb=" O ARG F 167 " (cutoff:3.500A) 998 hydrogen bonds defined for protein. 2814 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 75 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 10.84 Time building geometry restraints manager: 4.81 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: 11214 1.03 - 1.23: 262 1.23 - 1.42: 11425 1.42 - 1.62: 16727 1.62 - 1.81: 203 Bond restraints: 39831 Sorted by residual: bond pdb=" CA THR B 93 " pdb=" C THR B 93 " ideal model delta sigma weight residual 1.523 1.687 -0.164 1.34e-02 5.57e+03 1.50e+02 bond pdb=" N1 G 7 33 " pdb=" H1 G 7 33 " ideal model delta sigma weight residual 0.860 1.039 -0.179 2.00e-02 2.50e+03 8.03e+01 bond pdb=" CA CYS B 70 " pdb=" CB CYS B 70 " ideal model delta sigma weight residual 1.527 1.405 0.122 1.38e-02 5.25e+03 7.84e+01 bond pdb=" O3' DT 5 109 " pdb=" P DA 5 110 " ideal model delta sigma weight residual 1.607 1.712 -0.105 1.20e-02 6.94e+03 7.60e+01 bond pdb=" C1' DG 6 10 " pdb=" N9 DG 6 10 " ideal model delta sigma weight residual 1.468 1.354 0.114 1.40e-02 5.10e+03 6.63e+01 ... (remaining 39826 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.67: 64596 9.67 - 19.33: 26 19.33 - 29.00: 3 29.00 - 38.67: 1 38.67 - 48.34: 2 Bond angle restraints: 64628 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 104.00 148.03 -44.03 1.90e+00 2.77e-01 5.37e+02 angle pdb=" H2' DA 5 110 " pdb=" C2' DA 5 110 " pdb="H2'' DA 5 110 " ideal model delta sigma weight residual 109.00 76.06 32.94 1.50e+00 4.44e-01 4.82e+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 59.66 48.34 3.00e+00 1.11e-01 2.60e+02 angle pdb=" C VAL A 920 " pdb=" N PRO A 921 " pdb=" CA PRO A 921 " ideal model delta sigma weight residual 119.84 139.49 -19.65 1.25e+00 6.40e-01 2.47e+02 angle pdb=" C3' DA 6 28 " pdb=" O3' DA 6 28 " pdb=" P DT 6 29 " ideal model delta sigma weight residual 119.70 136.23 -16.53 1.20e+00 6.94e-01 1.90e+02 ... (remaining 64623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 19935 35.99 - 71.98: 830 71.98 - 107.97: 18 107.97 - 143.96: 1 143.96 - 179.95: 7 Dihedral angle restraints: 20791 sinusoidal: 10766 harmonic: 10025 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 -126.71 -53.29 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" O4' U 7 27 " pdb=" C1' U 7 27 " pdb=" N1 U 7 27 " pdb=" C2 U 7 27 " ideal model delta sinusoidal sigma weight residual 200.00 43.60 156.40 1 1.50e+01 4.44e-03 8.18e+01 dihedral pdb=" CA GLN B1326 " pdb=" C GLN B1326 " pdb=" N GLU B1327 " pdb=" CA GLU B1327 " ideal model delta harmonic sigma weight residual -180.00 -138.14 -41.86 0 5.00e+00 4.00e-02 7.01e+01 ... (remaining 20788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 4010 0.107 - 0.215: 415 0.215 - 0.322: 24 0.322 - 0.430: 2 0.430 - 0.537: 2 Chirality restraints: 4453 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 7.21e+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 chirality pdb=" CB ILE A 765 " pdb=" CA ILE A 765 " pdb=" CG1 ILE A 765 " pdb=" CG2 ILE A 765 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 4450 not shown) Planarity restraints: 6121 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 232 " 0.210 2.00e-02 2.50e+03 2.51e-01 9.43e+02 pdb=" CG ASN B 232 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN B 232 " -0.203 2.00e-02 2.50e+03 pdb=" ND2 ASN B 232 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN B 232 " 0.385 2.00e-02 2.50e+03 pdb="HD22 ASN B 232 " -0.379 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 61 " 0.029 2.00e-02 2.50e+03 5.72e-02 3.27e+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 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 69 " 0.025 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C GLU B 69 " -0.085 2.00e-02 2.50e+03 pdb=" O GLU B 69 " 0.032 2.00e-02 2.50e+03 pdb=" N CYS B 70 " 0.029 2.00e-02 2.50e+03 ... (remaining 6118 not shown) Histogram of nonbonded interaction distances: 1.21 - 1.89: 253 1.89 - 2.57: 22968 2.57 - 3.24: 82378 3.24 - 3.92: 118929 3.92 - 4.60: 180864 Nonbonded interactions: 405392 Sorted by model distance: nonbonded pdb=" O3' DA 5 103 " pdb=" NH2 ARG A 473 " model vdw 1.211 2.950 nonbonded pdb=" H42 DC 6 18 " pdb=" H1 G 7 38 " model vdw 1.266 2.100 nonbonded pdb=" HA LYS B 222 " pdb=" HD2 LYS B 222 " model vdw 1.325 2.440 nonbonded pdb=" OE2 GLU A 641 " pdb=" HZ3 LYS B 749 " model vdw 1.339 2.450 nonbonded pdb=" HG2 ARG B 202 " pdb="HH11 ARG B 202 " model vdw 1.347 2.270 ... (remaining 405387 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: 3.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.300 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 47.440 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4077 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 0.499 28609 Z= 0.546 Angle : 1.195 48.337 39010 Z= 0.694 Chirality : 0.066 0.537 4453 Planarity : 0.007 0.081 4803 Dihedral : 15.493 156.396 11233 Min Nonbonded Distance : 1.211 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.69 % Allowed : 8.77 % Favored : 90.53 % Rotamer: Outliers : 4.25 % Allowed : 4.35 % Favored : 91.40 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % 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: 3328 helix: -2.91 (0.11), residues: 1100 sheet: -2.01 (0.24), residues: 401 loop : -3.17 (0.12), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 8 TYR 0.038 0.003 TYR A1229 PHE 0.035 0.003 PHE B 620 TRP 0.043 0.004 TRP A 183 HIS 0.018 0.002 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.01004 / 0.52 (28602) covalent geometry : angle 1.17313 / 0.69 (39002) SS BOND : bond 0.23739 / 11.87 ( 1) SS BOND : angle 4.35070 / 8.29 ( 2) hydrogen bonds : bond 0.17477 / 19.12 ( 1070) hydrogen bonds : angle 7.29199 / 9.06 ( 2964) metal coordination : bond 0.27793 / 17.32 ( 6) metal coordination : angle 18.03293 / 34.65 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 347 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 MET cc_start: 0.6475 (mtm) cc_final: 0.6196 (tpp) REVERT: A 896 THR cc_start: -0.5724 (OUTLIER) cc_final: -0.5936 (m) REVERT: A 905 ILE cc_start: 0.4222 (OUTLIER) cc_final: 0.3991 (mp) REVERT: A 920 VAL cc_start: -0.0397 (OUTLIER) cc_final: -0.0801 (m) REVERT: A 990 ASP cc_start: 0.6523 (p0) cc_final: 0.5898 (t0) REVERT: A 1230 MET cc_start: 0.6084 (ttm) cc_final: 0.5473 (ttt) REVERT: A 1337 ILE cc_start: 0.4637 (tt) cc_final: 0.4342 (tt) REVERT: B 70 CYS cc_start: 0.3558 (OUTLIER) cc_final: 0.3124 (t) REVERT: B 132 LEU cc_start: 0.6321 (OUTLIER) cc_final: 0.5832 (tt) REVERT: B 154 LEU cc_start: 0.5874 (OUTLIER) cc_final: 0.5615 (mp) REVERT: B 222 LYS cc_start: 0.7186 (OUTLIER) cc_final: 0.6785 (tppt) REVERT: C 142 MET cc_start: 0.3837 (ptp) cc_final: 0.3224 (ptm) REVERT: D 82 LEU cc_start: 0.7032 (mt) cc_final: 0.6712 (tt) REVERT: F 176 SER cc_start: 0.7818 (OUTLIER) cc_final: 0.6623 (p) outliers start: 121 outliers final: 38 residues processed: 456 average time/residue: 0.3289 time to fit residues: 230.5509 Evaluate side-chains 243 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 197 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.0770 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 3.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 HIS ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN A 330 HIS ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 658 GLN A 688 GLN ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1268 GLN A1313 HIS B 294 ASN B1279 GLN C 37 HIS C 147 GLN D 66 HIS ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 HIS D 127 GLN D 227 GLN E 70 GLN F 33 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.067721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.054692 restraints weight = 646922.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.056113 restraints weight = 462463.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.057186 restraints weight = 353481.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.057954 restraints weight = 284071.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.058601 restraints weight = 238083.323| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6100 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 28609 Z= 0.156 Angle : 0.673 9.549 39010 Z= 0.363 Chirality : 0.044 0.235 4453 Planarity : 0.006 0.058 4803 Dihedral : 16.266 153.054 4686 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.09 % Favored : 92.64 % Rotamer: Outliers : 0.11 % Allowed : 1.93 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % 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: -2.95 (0.13), residues: 3328 helix: -0.86 (0.14), residues: 1102 sheet: -1.82 (0.24), residues: 412 loop : -2.80 (0.13), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 990 TYR 0.022 0.002 TYR F 153 PHE 0.020 0.002 PHE F 15 TRP 0.009 0.002 TRP B 580 HIS 0.009 0.001 HIS F 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (28602) covalent geometry : angle 0.66888 / 0.36 (39002) SS BOND : bond 0.01535 / 0.77 ( 1) SS BOND : angle 6.27233 / 11.61 ( 2) hydrogen bonds : bond 0.05313 / 5.74 ( 1070) hydrogen bonds : angle 5.42146 / 6.68 ( 2964) metal coordination : bond 0.01173 / 1.05 ( 6) metal coordination : angle 4.69401 / 8.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 230 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 LEU cc_start: 0.8266 (mm) cc_final: 0.7831 (mm) REVERT: A 230 PHE cc_start: 0.7909 (m-80) cc_final: 0.7613 (m-80) REVERT: A 369 MET cc_start: 0.6847 (ttm) cc_final: 0.6177 (ttp) REVERT: A 370 MET cc_start: 0.6019 (tpp) cc_final: 0.5740 (tpp) REVERT: A 492 MET cc_start: 0.8087 (mtm) cc_final: 0.6649 (tpp) REVERT: A 681 MET cc_start: 0.9539 (mtp) cc_final: 0.9218 (mtt) REVERT: A 951 MET cc_start: 0.9324 (mmp) cc_final: 0.9085 (mmp) REVERT: A 1230 MET cc_start: 0.7324 (ttm) cc_final: 0.7022 (ttt) REVERT: B 366 CYS cc_start: 0.8430 (p) cc_final: 0.8201 (p) REVERT: B 513 MET cc_start: 0.8133 (tmm) cc_final: 0.6929 (tmm) REVERT: B 658 GLU cc_start: 0.9600 (tt0) cc_final: 0.9380 (mm-30) REVERT: B 1099 TYR cc_start: 0.8193 (m-80) cc_final: 0.7830 (m-80) REVERT: B 1357 ILE cc_start: 0.9435 (mt) cc_final: 0.9119 (tt) REVERT: C 115 ILE cc_start: 0.7183 (tp) cc_final: 0.6876 (tp) REVERT: D 127 GLN cc_start: 0.8780 (mp10) cc_final: 0.8314 (mp10) REVERT: D 224 LEU cc_start: 0.9123 (tp) cc_final: 0.8902 (tp) REVERT: F 112 MET cc_start: 0.8545 (mpp) cc_final: 0.7575 (mmp) REVERT: F 138 ASP cc_start: 0.7426 (t0) cc_final: 0.7118 (m-30) outliers start: 3 outliers final: 1 residues processed: 232 average time/residue: 0.2751 time to fit residues: 102.6590 Evaluate side-chains 178 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 201 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 142 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 182 optimal weight: 5.9990 chunk 253 optimal weight: 10.0000 chunk 297 optimal weight: 9.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 618 GLN A 628 HIS A 658 GLN ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 HIS C 132 HIS C 147 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.062346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.049572 restraints weight = 662199.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.050871 restraints weight = 466206.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.051872 restraints weight = 353644.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.052564 restraints weight = 282400.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.053146 restraints weight = 237110.637| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.180 28609 Z= 0.225 Angle : 0.707 15.286 39010 Z= 0.378 Chirality : 0.044 0.361 4453 Planarity : 0.005 0.053 4803 Dihedral : 16.010 150.782 4686 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 26.31 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.03 % Favored : 92.79 % Rotamer: Outliers : 0.11 % Allowed : 2.07 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % 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: -2.19 (0.14), residues: 3328 helix: 0.04 (0.15), residues: 1111 sheet: -1.77 (0.23), residues: 452 loop : -2.44 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.070 0.001 ARG F 84 TYR 0.018 0.002 TYR D 177 PHE 0.027 0.002 PHE F 92 TRP 0.032 0.002 TRP B 115 HIS 0.007 0.002 HIS B 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.22 (28602) covalent geometry : angle 0.70547 / 0.38 (39002) SS BOND : bond 0.04253 / 2.13 ( 1) SS BOND : angle 2.40032 / 4.22 ( 2) hydrogen bonds : bond 0.04785 / 5.14 ( 1070) hydrogen bonds : angle 5.06547 / 6.14 ( 2964) metal coordination : bond 0.00631 / 0.34 ( 6) metal coordination : angle 3.74597 / 7.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 207 time to evaluate : 1.275 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: A 213 LEU cc_start: 0.8833 (mm) cc_final: 0.8243 (mm) REVERT: A 370 MET cc_start: 0.7037 (tpp) cc_final: 0.6492 (tpp) REVERT: A 492 MET cc_start: 0.8403 (mtm) cc_final: 0.8120 (mtp) REVERT: A 681 MET cc_start: 0.9634 (mtp) cc_final: 0.9126 (mtt) REVERT: A 951 MET cc_start: 0.9384 (mmp) cc_final: 0.9129 (mmp) REVERT: A 962 GLU cc_start: 0.9309 (mm-30) cc_final: 0.8992 (tm-30) REVERT: A 966 ILE cc_start: 0.6785 (mp) cc_final: 0.6477 (mp) REVERT: A 1230 MET cc_start: 0.8031 (ttm) cc_final: 0.7784 (mmm) REVERT: A 1329 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8159 (tt0) REVERT: B 113 HIS cc_start: 0.8186 (t-90) cc_final: 0.7921 (t-90) REVERT: B 116 PHE cc_start: 0.8392 (m-80) cc_final: 0.7837 (m-10) REVERT: B 658 GLU cc_start: 0.9614 (tt0) cc_final: 0.9395 (mm-30) REVERT: B 725 MET cc_start: 0.9166 (mtt) cc_final: 0.8904 (mtt) REVERT: B 1099 TYR cc_start: 0.8107 (m-80) cc_final: 0.7779 (m-80) REVERT: C 80 GLU cc_start: 0.9158 (tt0) cc_final: 0.8942 (tp30) REVERT: C 205 MET cc_start: 0.8923 (pmm) cc_final: 0.8466 (pmm) REVERT: D 127 GLN cc_start: 0.8738 (mp10) cc_final: 0.8330 (mp10) REVERT: D 224 LEU cc_start: 0.9335 (tp) cc_final: 0.9107 (tp) REVERT: E 43 ASN cc_start: 0.9352 (m-40) cc_final: 0.9129 (t0) REVERT: F 35 MET cc_start: 0.3770 (ttm) cc_final: 0.3350 (ptm) outliers start: 3 outliers final: 2 residues processed: 209 average time/residue: 0.2771 time to fit residues: 94.7761 Evaluate side-chains 169 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 167 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 10 optimal weight: 3.9990 chunk 290 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 293 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 204 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 688 GLN A 808 ASN A1136 GLN A1244 HIS ** A1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1307 ASN B 277 ASN B 300 GLN B 951 GLN B1259 GLN ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS ** D 75 GLN ** 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 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.053102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.041084 restraints weight = 709966.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.042128 restraints weight = 485432.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.042988 restraints weight = 366003.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.043587 restraints weight = 294011.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.043969 restraints weight = 247317.135| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.6315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.163 28609 Z= 0.352 Angle : 0.978 27.464 39010 Z= 0.522 Chirality : 0.051 0.412 4453 Planarity : 0.009 0.269 4803 Dihedral : 16.311 156.158 4686 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 48.85 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.41 % Favored : 90.26 % Rotamer: Outliers : 0.25 % Allowed : 2.60 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.13), residues: 3328 helix: -0.72 (0.14), residues: 1122 sheet: -2.01 (0.23), residues: 462 loop : -2.58 (0.13), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.002 ARG E 69 TYR 0.037 0.003 TYR A 215 PHE 0.046 0.003 PHE F 65 TRP 0.047 0.004 TRP B 115 HIS 0.023 0.003 HIS A1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00724 / 0.35 (28602) covalent geometry : angle 0.97463 / 0.52 (39002) SS BOND : bond 0.00040 / 0.02 ( 1) SS BOND : angle 8.37847 / 14.12 ( 2) hydrogen bonds : bond 0.05964 / 6.45 ( 1070) hydrogen bonds : angle 5.70677 / 6.91 ( 2964) metal coordination : bond 0.03123 / 1.81 ( 6) metal coordination : angle 4.58830 / 8.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 183 time to evaluate : 1.323 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 321 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7405 (tt) REVERT: A 370 MET cc_start: 0.7460 (tpp) cc_final: 0.7177 (tpp) REVERT: A 425 ILE cc_start: 0.9045 (mt) cc_final: 0.8830 (tp) REVERT: A 429 MET cc_start: 0.9336 (mtp) cc_final: 0.9070 (mtp) REVERT: A 492 MET cc_start: 0.8375 (mtm) cc_final: 0.7474 (ttm) REVERT: A 515 MET cc_start: 0.8258 (ptm) cc_final: 0.7975 (tmm) REVERT: A 805 MET cc_start: 0.8988 (ttp) cc_final: 0.8216 (ttp) REVERT: A 951 MET cc_start: 0.9130 (mmp) cc_final: 0.8792 (mmp) REVERT: A 1180 MET cc_start: 0.9116 (tmm) cc_final: 0.8793 (tmm) REVERT: A 1230 MET cc_start: 0.8770 (ttm) cc_final: 0.8552 (ttt) REVERT: A 1232 MET cc_start: 0.7858 (mmp) cc_final: 0.7440 (mmm) REVERT: A 1273 MET cc_start: 0.7424 (ptp) cc_final: 0.6738 (ptp) REVERT: A 1290 MET cc_start: 0.9632 (ttm) cc_final: 0.9359 (ttt) REVERT: A 1304 MET cc_start: 0.9067 (mmp) cc_final: 0.8748 (mmp) REVERT: A 1319 MET cc_start: 0.7236 (tmm) cc_final: 0.6861 (tmm) REVERT: A 1329 GLU cc_start: 0.9498 (mt-10) cc_final: 0.9175 (mt-10) REVERT: B 115 TRP cc_start: 0.9166 (m-10) cc_final: 0.8941 (m-10) REVERT: B 219 LYS cc_start: 0.9207 (mtmt) cc_final: 0.8861 (tmtt) REVERT: B 289 ASP cc_start: 0.9159 (OUTLIER) cc_final: 0.8861 (p0) REVERT: B 485 MET cc_start: 0.9133 (tpp) cc_final: 0.8843 (tpp) REVERT: B 513 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7846 (tmm) REVERT: B 747 MET cc_start: 0.8221 (mmp) cc_final: 0.7842 (mmp) REVERT: B 1099 TYR cc_start: 0.7995 (m-80) cc_final: 0.7726 (m-80) REVERT: D 205 MET cc_start: 0.7581 (ppp) cc_final: 0.7031 (ppp) REVERT: F 32 LEU cc_start: 0.8310 (mt) cc_final: 0.7824 (pp) REVERT: F 35 MET cc_start: 0.4940 (ttm) cc_final: 0.4649 (ttm) REVERT: F 63 LYS cc_start: 0.6101 (tttt) cc_final: 0.5778 (tmtt) REVERT: F 73 MET cc_start: 0.5365 (tpt) cc_final: 0.4971 (tpp) REVERT: F 90 MET cc_start: 0.8576 (mpp) cc_final: 0.7812 (mpp) REVERT: F 138 ASP cc_start: 0.7606 (t0) cc_final: 0.7258 (m-30) outliers start: 7 outliers final: 1 residues processed: 188 average time/residue: 0.2555 time to fit residues: 82.0178 Evaluate side-chains 145 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 282 optimal weight: 0.7980 chunk 256 optimal weight: 4.9990 chunk 334 optimal weight: 6.9990 chunk 148 optimal weight: 8.9990 chunk 275 optimal weight: 6.9990 chunk 281 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 60 optimal weight: 0.0170 chunk 149 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 overall best weight: 2.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 HIS ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A1256 GLN A1307 ASN ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.053559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.041316 restraints weight = 698922.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.042459 restraints weight = 475251.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.043237 restraints weight = 354278.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.043917 restraints weight = 284201.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.044302 restraints weight = 238386.607| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.6534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28609 Z= 0.137 Angle : 0.593 21.366 39010 Z= 0.316 Chirality : 0.042 0.186 4453 Planarity : 0.005 0.075 4803 Dihedral : 16.067 154.830 4686 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 33.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.85 % Favored : 93.03 % Rotamer: Outliers : 0.04 % Allowed : 1.05 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % 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: -2.10 (0.14), residues: 3328 helix: 0.08 (0.15), residues: 1127 sheet: -1.82 (0.23), residues: 446 loop : -2.36 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 69 TYR 0.012 0.001 TYR B 723 PHE 0.040 0.002 PHE A 230 TRP 0.017 0.002 TRP F 80 HIS 0.007 0.001 HIS B1227 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (28602) covalent geometry : angle 0.58985 / 0.32 (39002) SS BOND : bond 0.00444 / 0.22 ( 1) SS BOND : angle 3.78549 / 6.31 ( 2) hydrogen bonds : bond 0.04355 / 4.72 ( 1070) hydrogen bonds : angle 4.97539 / 6.08 ( 2964) metal coordination : bond 0.01173 / 0.97 ( 6) metal coordination : angle 4.05645 / 7.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 0.978 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: A 230 PHE cc_start: 0.8122 (t80) cc_final: 0.6867 (t80) REVERT: A 369 MET cc_start: 0.7670 (ttm) cc_final: 0.7360 (tmm) REVERT: A 370 MET cc_start: 0.7777 (tpp) cc_final: 0.7502 (tpp) REVERT: A 459 MET cc_start: 0.9263 (mmp) cc_final: 0.8728 (mmp) REVERT: A 492 MET cc_start: 0.8241 (mtm) cc_final: 0.7283 (ttm) REVERT: A 805 MET cc_start: 0.9001 (ttp) cc_final: 0.8208 (ttp) REVERT: A 951 MET cc_start: 0.9258 (mmp) cc_final: 0.8842 (mmp) REVERT: A 1180 MET cc_start: 0.9165 (tmm) cc_final: 0.8514 (tmm) REVERT: A 1230 MET cc_start: 0.9025 (ttm) cc_final: 0.8560 (ttt) REVERT: A 1273 MET cc_start: 0.7527 (ptp) cc_final: 0.6873 (ptp) REVERT: A 1290 MET cc_start: 0.9630 (ttm) cc_final: 0.9404 (ttm) REVERT: A 1329 GLU cc_start: 0.9506 (mt-10) cc_final: 0.9083 (mt-10) REVERT: B 485 MET cc_start: 0.9164 (tpp) cc_final: 0.8794 (tpp) REVERT: B 513 MET cc_start: 0.8732 (tmm) cc_final: 0.8316 (tmm) REVERT: B 747 MET cc_start: 0.8133 (mmp) cc_final: 0.7685 (mmp) REVERT: B 1099 TYR cc_start: 0.7989 (m-80) cc_final: 0.7711 (m-80) REVERT: B 1357 ILE cc_start: 0.9594 (mt) cc_final: 0.9368 (pt) REVERT: C 142 MET cc_start: 0.8337 (pmm) cc_final: 0.8058 (pmm) REVERT: D 115 ILE cc_start: 0.8021 (mt) cc_final: 0.7658 (mt) REVERT: D 174 ASP cc_start: 0.8215 (m-30) cc_final: 0.7973 (m-30) REVERT: D 205 MET cc_start: 0.7788 (ppp) cc_final: 0.7558 (ppp) REVERT: F 35 MET cc_start: 0.5176 (ttm) cc_final: 0.4460 (ttm) REVERT: F 63 LYS cc_start: 0.6417 (tttt) cc_final: 0.6101 (tmtt) REVERT: F 73 MET cc_start: 0.5072 (tpt) cc_final: 0.4813 (tpp) REVERT: F 90 MET cc_start: 0.8468 (mpp) cc_final: 0.7827 (mpp) REVERT: F 138 ASP cc_start: 0.7784 (t0) cc_final: 0.7483 (m-30) outliers start: 1 outliers final: 1 residues processed: 169 average time/residue: 0.2442 time to fit residues: 69.9881 Evaluate side-chains 141 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 303 optimal weight: 0.9990 chunk 248 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 chunk 240 optimal weight: 7.9990 chunk 247 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 271 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 291 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 239 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1235 ASN B1244 GLN C 84 ASN C 117 HIS ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.050645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.038705 restraints weight = 715713.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.039743 restraints weight = 482737.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.040524 restraints weight = 361175.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.040967 restraints weight = 289688.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.041497 restraints weight = 247480.588| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.7521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 28609 Z= 0.223 Angle : 0.690 19.364 39010 Z= 0.362 Chirality : 0.043 0.311 4453 Planarity : 0.005 0.056 4803 Dihedral : 15.989 155.552 4686 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 42.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.28 % Favored : 90.53 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % 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: -1.98 (0.14), residues: 3328 helix: 0.18 (0.15), residues: 1124 sheet: -1.84 (0.24), residues: 431 loop : -2.24 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.001 ARG E 69 TYR 0.022 0.002 TYR B 269 PHE 0.028 0.002 PHE F 65 TRP 0.016 0.002 TRP F 80 HIS 0.009 0.002 HIS B 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.22 (28602) covalent geometry : angle 0.68893 / 0.36 (39002) SS BOND : bond 0.00804 / 0.40 ( 1) SS BOND : angle 2.64085 / 4.41 ( 2) hydrogen bonds : bond 0.04468 / 4.85 ( 1070) hydrogen bonds : angle 4.99715 / 6.18 ( 2964) metal coordination : bond 0.00386 / 0.29 ( 6) metal coordination : angle 3.33996 / 6.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.017 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 239 MET cc_start: 0.6742 (mmm) cc_final: 0.6527 (mmt) REVERT: A 291 TYR cc_start: 0.8313 (t80) cc_final: 0.8085 (t80) REVERT: A 370 MET cc_start: 0.7700 (tpp) cc_final: 0.7433 (tpp) REVERT: A 429 MET cc_start: 0.9401 (mtm) cc_final: 0.9105 (mtp) REVERT: A 459 MET cc_start: 0.9300 (mmp) cc_final: 0.8754 (mmp) REVERT: A 492 MET cc_start: 0.8119 (mtm) cc_final: 0.7300 (ttm) REVERT: A 805 MET cc_start: 0.9047 (ttp) cc_final: 0.8842 (ttp) REVERT: A 951 MET cc_start: 0.9160 (mmp) cc_final: 0.8803 (mmp) REVERT: A 1151 LEU cc_start: 0.8623 (tp) cc_final: 0.8064 (tp) REVERT: A 1230 MET cc_start: 0.8998 (ttm) cc_final: 0.8562 (ttt) REVERT: A 1232 MET cc_start: 0.8082 (mmp) cc_final: 0.7869 (mmp) REVERT: A 1273 MET cc_start: 0.7592 (ptp) cc_final: 0.7013 (ptp) REVERT: A 1290 MET cc_start: 0.9671 (ttm) cc_final: 0.9418 (ttm) REVERT: B 485 MET cc_start: 0.9339 (tpp) cc_final: 0.8898 (tpp) REVERT: B 513 MET cc_start: 0.8551 (tmm) cc_final: 0.8350 (tmm) REVERT: B 747 MET cc_start: 0.8313 (mmp) cc_final: 0.7926 (mmp) REVERT: B 1099 TYR cc_start: 0.8048 (m-80) cc_final: 0.7735 (m-80) REVERT: B 1357 ILE cc_start: 0.9603 (mt) cc_final: 0.9370 (pt) REVERT: C 51 MET cc_start: 0.8795 (tpp) cc_final: 0.8469 (tpp) REVERT: D 174 ASP cc_start: 0.8353 (m-30) cc_final: 0.8150 (m-30) REVERT: D 205 MET cc_start: 0.8210 (ppp) cc_final: 0.7996 (ppp) REVERT: F 35 MET cc_start: 0.6424 (ttm) cc_final: 0.5316 (ttm) REVERT: F 90 MET cc_start: 0.8950 (mpp) cc_final: 0.8597 (mpp) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2284 time to fit residues: 60.6406 Evaluate side-chains 135 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 88 optimal weight: 9.9990 chunk 228 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 252 optimal weight: 6.9990 chunk 303 optimal weight: 1.9990 chunk 211 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 318 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 295 optimal weight: 3.9990 chunk 329 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 HIS ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** 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 = 0.3571 r_free = 0.3571 target = 0.049116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.037255 restraints weight = 714609.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.038296 restraints weight = 475907.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.039005 restraints weight = 352139.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.039585 restraints weight = 282232.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.040018 restraints weight = 237914.687| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.8282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.166 28609 Z= 0.187 Angle : 0.626 18.183 39010 Z= 0.336 Chirality : 0.042 0.234 4453 Planarity : 0.005 0.075 4803 Dihedral : 16.010 156.349 4686 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 38.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.18 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % 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: -1.81 (0.14), residues: 3328 helix: 0.33 (0.15), residues: 1131 sheet: -1.75 (0.24), residues: 447 loop : -2.15 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 12 TYR 0.032 0.001 TYR B 269 PHE 0.021 0.002 PHE B 141 TRP 0.019 0.002 TRP F 80 HIS 0.008 0.001 HIS B1227 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 (28602) covalent geometry : angle 0.62423 / 0.34 (39002) SS BOND : bond 0.00801 / 0.40 ( 1) SS BOND : angle 2.30960 / 4.05 ( 2) hydrogen bonds : bond 0.04303 / 4.68 ( 1070) hydrogen bonds : angle 4.84881 / 5.91 ( 2964) metal coordination : bond 0.00292 / 0.26 ( 6) metal coordination : angle 3.18951 / 6.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 PHE cc_start: 0.8603 (t80) cc_final: 0.7075 (t80) REVERT: A 239 MET cc_start: 0.6537 (mmm) cc_final: 0.4911 (mmm) REVERT: A 291 TYR cc_start: 0.8427 (t80) cc_final: 0.8140 (t80) REVERT: A 369 MET cc_start: 0.7800 (ttm) cc_final: 0.7597 (tmm) REVERT: A 370 MET cc_start: 0.7952 (tpp) cc_final: 0.7717 (tpp) REVERT: A 429 MET cc_start: 0.9337 (mtm) cc_final: 0.9045 (mtp) REVERT: A 459 MET cc_start: 0.9362 (mmp) cc_final: 0.8751 (mmp) REVERT: A 492 MET cc_start: 0.8258 (mtm) cc_final: 0.7366 (ttp) REVERT: A 951 MET cc_start: 0.9079 (mmp) cc_final: 0.8749 (mmt) REVERT: A 1151 LEU cc_start: 0.8727 (tp) cc_final: 0.8389 (tp) REVERT: A 1230 MET cc_start: 0.8908 (ttm) cc_final: 0.8616 (ttt) REVERT: A 1290 MET cc_start: 0.9672 (ttm) cc_final: 0.9445 (ttm) REVERT: A 1329 GLU cc_start: 0.9548 (mt-10) cc_final: 0.9070 (mt-10) REVERT: B 747 MET cc_start: 0.8374 (mmp) cc_final: 0.7994 (mmp) REVERT: B 1099 TYR cc_start: 0.8077 (m-80) cc_final: 0.7764 (m-80) REVERT: B 1357 ILE cc_start: 0.9596 (mt) cc_final: 0.9370 (pt) REVERT: C 51 MET cc_start: 0.8856 (tpp) cc_final: 0.8597 (tpp) REVERT: D 115 ILE cc_start: 0.8887 (mt) cc_final: 0.8656 (tp) REVERT: D 118 ASP cc_start: 0.5586 (t0) cc_final: 0.5361 (m-30) REVERT: D 174 ASP cc_start: 0.8331 (m-30) cc_final: 0.8111 (m-30) REVERT: F 35 MET cc_start: 0.6511 (ttm) cc_final: 0.6194 (ttm) REVERT: F 90 MET cc_start: 0.9011 (mpp) cc_final: 0.8752 (mpp) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2547 time to fit residues: 64.2821 Evaluate side-chains 130 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 91 optimal weight: 1.9990 chunk 320 optimal weight: 0.7980 chunk 303 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 184 optimal weight: 7.9990 chunk 291 optimal weight: 1.9990 chunk 331 optimal weight: 3.9990 chunk 186 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 329 optimal weight: 9.9990 chunk 185 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 HIS ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.049347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.037346 restraints weight = 706258.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.038432 restraints weight = 468880.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.039212 restraints weight = 344890.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.039625 restraints weight = 274965.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.040136 restraints weight = 235879.203| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.8412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 28609 Z= 0.111 Angle : 0.520 15.620 39010 Z= 0.280 Chirality : 0.040 0.152 4453 Planarity : 0.004 0.049 4803 Dihedral : 15.896 155.842 4686 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 35.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.36 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % 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: -1.48 (0.14), residues: 3328 helix: 0.75 (0.16), residues: 1133 sheet: -1.70 (0.24), residues: 462 loop : -2.03 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 114 TYR 0.015 0.001 TYR A 215 PHE 0.019 0.001 PHE B 141 TRP 0.012 0.001 TRP F 80 HIS 0.005 0.001 HIS B 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (28602) covalent geometry : angle 0.51861 / 0.28 (39002) SS BOND : bond 0.00852 / 0.43 ( 1) SS BOND : angle 1.96501 / 3.37 ( 2) hydrogen bonds : bond 0.03790 / 4.13 ( 1070) hydrogen bonds : angle 4.57975 / 5.60 ( 2964) metal coordination : bond 0.00283 / 0.28 ( 6) metal coordination : angle 2.92700 / 5.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.204 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 230 PHE cc_start: 0.8569 (t80) cc_final: 0.7201 (t80) REVERT: A 239 MET cc_start: 0.6422 (mmm) cc_final: 0.5420 (mmm) REVERT: A 291 TYR cc_start: 0.8399 (t80) cc_final: 0.8095 (t80) REVERT: A 369 MET cc_start: 0.7866 (ttm) cc_final: 0.7629 (tmm) REVERT: A 370 MET cc_start: 0.8014 (tpp) cc_final: 0.7742 (tpp) REVERT: A 429 MET cc_start: 0.9345 (mtm) cc_final: 0.9039 (mtp) REVERT: A 459 MET cc_start: 0.9380 (mmp) cc_final: 0.8752 (mmp) REVERT: A 488 MET cc_start: 0.8534 (mmp) cc_final: 0.8254 (mmm) REVERT: A 492 MET cc_start: 0.8382 (mtm) cc_final: 0.7430 (ttp) REVERT: A 951 MET cc_start: 0.9173 (mmp) cc_final: 0.8800 (mmp) REVERT: A 1119 MET cc_start: 0.8441 (ptp) cc_final: 0.8062 (ptt) REVERT: A 1151 LEU cc_start: 0.8748 (tp) cc_final: 0.8411 (tp) REVERT: A 1180 MET cc_start: 0.9080 (tmm) cc_final: 0.8655 (tmm) REVERT: A 1230 MET cc_start: 0.8941 (ttm) cc_final: 0.8660 (ttt) REVERT: A 1273 MET cc_start: 0.7826 (ptp) cc_final: 0.7208 (ptp) REVERT: A 1290 MET cc_start: 0.9694 (ttm) cc_final: 0.9488 (ttm) REVERT: A 1329 GLU cc_start: 0.9548 (mt-10) cc_final: 0.9082 (mt-10) REVERT: B 747 MET cc_start: 0.8388 (mmp) cc_final: 0.7985 (mmp) REVERT: B 1099 TYR cc_start: 0.8060 (m-80) cc_final: 0.7743 (m-80) REVERT: B 1357 ILE cc_start: 0.9588 (mt) cc_final: 0.9327 (pt) REVERT: C 51 MET cc_start: 0.8648 (tpp) cc_final: 0.8406 (tpp) REVERT: D 115 ILE cc_start: 0.8867 (mt) cc_final: 0.8636 (tp) REVERT: D 118 ASP cc_start: 0.5701 (t0) cc_final: 0.5479 (m-30) REVERT: F 35 MET cc_start: 0.6392 (ttm) cc_final: 0.4852 (ppp) REVERT: F 90 MET cc_start: 0.9057 (mpp) cc_final: 0.8778 (mpp) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2341 time to fit residues: 58.7912 Evaluate side-chains 129 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 147 optimal weight: 9.9990 chunk 206 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 270 optimal weight: 7.9990 chunk 198 optimal weight: 5.9990 chunk 320 optimal weight: 9.9990 chunk 160 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 318 optimal weight: 9.9990 chunk 186 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1367 GLN ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** 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 = 0.3516 r_free = 0.3516 target = 0.047192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.035504 restraints weight = 732976.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.036505 restraints weight = 483142.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.037259 restraints weight = 355993.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.037793 restraints weight = 283401.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.038093 restraints weight = 239975.555| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.9175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28609 Z= 0.179 Angle : 0.609 16.862 39010 Z= 0.323 Chirality : 0.041 0.162 4453 Planarity : 0.004 0.057 4803 Dihedral : 15.902 156.604 4686 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 41.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.19 % Favored : 90.69 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % 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: -1.53 (0.14), residues: 3328 helix: 0.58 (0.15), residues: 1143 sheet: -1.69 (0.24), residues: 435 loop : -1.98 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 114 TYR 0.016 0.002 TYR D 177 PHE 0.020 0.002 PHE B 141 TRP 0.013 0.002 TRP B 868 HIS 0.007 0.001 HIS B1227 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 (28602) covalent geometry : angle 0.60752 / 0.32 (39002) SS BOND : bond 0.00959 / 0.48 ( 1) SS BOND : angle 1.64232 / 2.74 ( 2) hydrogen bonds : bond 0.04186 / 4.63 ( 1070) hydrogen bonds : angle 4.69486 / 5.76 ( 2964) metal coordination : bond 0.00307 / 0.32 ( 6) metal coordination : angle 2.78632 / 5.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.289 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 230 PHE cc_start: 0.8425 (t80) cc_final: 0.6872 (t80) REVERT: A 239 MET cc_start: 0.6504 (mmm) cc_final: 0.5569 (mmm) REVERT: A 291 TYR cc_start: 0.8572 (t80) cc_final: 0.8128 (t80) REVERT: A 369 MET cc_start: 0.8037 (ttm) cc_final: 0.6943 (tmm) REVERT: A 370 MET cc_start: 0.8088 (tpp) cc_final: 0.7868 (tpp) REVERT: A 429 MET cc_start: 0.9446 (mtm) cc_final: 0.9130 (mtp) REVERT: A 459 MET cc_start: 0.9396 (mmp) cc_final: 0.8831 (mmp) REVERT: A 488 MET cc_start: 0.8646 (mmp) cc_final: 0.8400 (mmm) REVERT: A 492 MET cc_start: 0.8410 (mtm) cc_final: 0.7485 (ttp) REVERT: A 515 MET cc_start: 0.9174 (tmm) cc_final: 0.8672 (tmm) REVERT: A 653 MET cc_start: 0.8342 (tpt) cc_final: 0.7682 (tpt) REVERT: A 951 MET cc_start: 0.9113 (mmp) cc_final: 0.8799 (mmm) REVERT: A 1119 MET cc_start: 0.8492 (ptp) cc_final: 0.8150 (ptt) REVERT: A 1151 LEU cc_start: 0.8841 (tp) cc_final: 0.8539 (tp) REVERT: A 1230 MET cc_start: 0.8956 (ttm) cc_final: 0.8422 (ttt) REVERT: B 724 MET cc_start: 0.9557 (mtm) cc_final: 0.8997 (mpp) REVERT: B 747 MET cc_start: 0.8473 (mmp) cc_final: 0.8090 (mmp) REVERT: B 1099 TYR cc_start: 0.8027 (m-80) cc_final: 0.7734 (m-80) REVERT: B 1357 ILE cc_start: 0.9624 (mt) cc_final: 0.9385 (pt) REVERT: C 51 MET cc_start: 0.8805 (tpp) cc_final: 0.8599 (mmm) REVERT: F 35 MET cc_start: 0.6748 (ttm) cc_final: 0.5230 (ppp) REVERT: F 90 MET cc_start: 0.9112 (mpp) cc_final: 0.8812 (mpp) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2437 time to fit residues: 60.2025 Evaluate side-chains 122 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 31 optimal weight: 0.0020 chunk 43 optimal weight: 1.9990 chunk 295 optimal weight: 0.0040 chunk 316 optimal weight: 1.9990 chunk 302 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 166 optimal weight: 7.9990 chunk 299 optimal weight: 0.0970 chunk 281 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 238 optimal weight: 20.0000 overall best weight: 0.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.047749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.035875 restraints weight = 708197.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.036929 restraints weight = 463307.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.037691 restraints weight = 339264.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.038264 restraints weight = 269857.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.038570 restraints weight = 226803.760| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.9216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 28609 Z= 0.095 Angle : 0.509 14.921 39010 Z= 0.272 Chirality : 0.040 0.145 4453 Planarity : 0.004 0.066 4803 Dihedral : 15.817 155.990 4686 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 34.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.61 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % 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: -1.21 (0.15), residues: 3328 helix: 0.98 (0.16), residues: 1144 sheet: -1.58 (0.24), residues: 423 loop : -1.89 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1194 TYR 0.011 0.001 TYR B 723 PHE 0.012 0.001 PHE B 62 TRP 0.010 0.001 TRP F 80 HIS 0.005 0.001 HIS B 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.09 (28602) covalent geometry : angle 0.50771 / 0.27 (39002) SS BOND : bond 0.00629 / 0.31 ( 1) SS BOND : angle 2.04932 / 3.60 ( 2) hydrogen bonds : bond 0.03632 / 3.98 ( 1070) hydrogen bonds : angle 4.40107 / 5.38 ( 2964) metal coordination : bond 0.00353 / 0.35 ( 6) metal coordination : angle 2.98569 / 5.80 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.183 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 230 PHE cc_start: 0.8464 (t80) cc_final: 0.6957 (t80) REVERT: A 239 MET cc_start: 0.6410 (mmm) cc_final: 0.5406 (mmm) REVERT: A 291 TYR cc_start: 0.8546 (t80) cc_final: 0.8059 (t80) REVERT: A 369 MET cc_start: 0.7971 (ttm) cc_final: 0.6930 (tmm) REVERT: A 370 MET cc_start: 0.8169 (tpp) cc_final: 0.7944 (tpp) REVERT: A 429 MET cc_start: 0.9468 (mtm) cc_final: 0.9186 (mtp) REVERT: A 459 MET cc_start: 0.9431 (mmp) cc_final: 0.8861 (mmp) REVERT: A 488 MET cc_start: 0.8573 (mmp) cc_final: 0.8322 (mmm) REVERT: A 492 MET cc_start: 0.8434 (mtm) cc_final: 0.7502 (ttp) REVERT: A 515 MET cc_start: 0.9285 (tmm) cc_final: 0.8714 (tmm) REVERT: A 951 MET cc_start: 0.9149 (mmp) cc_final: 0.8776 (mmp) REVERT: A 1119 MET cc_start: 0.8497 (ptp) cc_final: 0.8133 (ptt) REVERT: A 1151 LEU cc_start: 0.8835 (tp) cc_final: 0.8508 (tp) REVERT: A 1180 MET cc_start: 0.9077 (tmm) cc_final: 0.8678 (tmm) REVERT: A 1230 MET cc_start: 0.8973 (ttm) cc_final: 0.8616 (ttt) REVERT: A 1273 MET cc_start: 0.7900 (ptp) cc_final: 0.7269 (ptp) REVERT: A 1329 GLU cc_start: 0.9528 (mt-10) cc_final: 0.9066 (mt-10) REVERT: B 747 MET cc_start: 0.8445 (mmp) cc_final: 0.8032 (mmp) REVERT: B 1099 TYR cc_start: 0.8006 (m-80) cc_final: 0.7705 (m-80) REVERT: B 1357 ILE cc_start: 0.9585 (mt) cc_final: 0.9317 (pt) REVERT: D 174 ASP cc_start: 0.8343 (m-30) cc_final: 0.8109 (m-30) REVERT: D 205 MET cc_start: 0.8349 (ppp) cc_final: 0.8123 (ppp) REVERT: F 35 MET cc_start: 0.6865 (ttm) cc_final: 0.5758 (ppp) REVERT: F 90 MET cc_start: 0.9116 (mpp) cc_final: 0.8810 (mpp) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2406 time to fit residues: 57.6040 Evaluate side-chains 126 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 285 optimal weight: 0.0370 chunk 339 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 243 optimal weight: 9.9990 chunk 297 optimal weight: 20.0000 chunk 313 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 50 optimal weight: 0.0270 chunk 187 optimal weight: 2.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** 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 = 0.3529 r_free = 0.3529 target = 0.047585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.035748 restraints weight = 727059.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.036802 restraints weight = 472967.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.037568 restraints weight = 345925.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.038106 restraints weight = 274569.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.038431 restraints weight = 231683.902| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.9343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 28609 Z= 0.099 Angle : 0.494 12.339 39010 Z= 0.265 Chirality : 0.039 0.143 4453 Planarity : 0.004 0.054 4803 Dihedral : 15.722 155.494 4686 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 34.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.88 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % 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: -0.98 (0.15), residues: 3328 helix: 1.23 (0.16), residues: 1145 sheet: -1.49 (0.24), residues: 443 loop : -1.77 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 156 TYR 0.011 0.001 TYR B1282 PHE 0.010 0.001 PHE B 62 TRP 0.010 0.001 TRP F 80 HIS 0.004 0.001 HIS B 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 (28602) covalent geometry : angle 0.49276 / 0.26 (39002) SS BOND : bond 0.00706 / 0.35 ( 1) SS BOND : angle 1.90534 / 3.33 ( 2) hydrogen bonds : bond 0.03483 / 3.82 ( 1070) hydrogen bonds : angle 4.28380 / 5.24 ( 2964) metal coordination : bond 0.00272 / 0.27 ( 6) metal coordination : angle 2.56163 / 4.97 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7225.31 seconds wall clock time: 124 minutes 32.62 seconds (7472.62 seconds total)