Starting phenix.real_space_refine on Mon Jul 6 21:30:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e5o_27916/07_2026/8e5o_27916_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e5o_27916/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8e5o_27916/07_2026/8e5o_27916_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e5o_27916/07_2026/8e5o_27916_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e5o_27916/07_2026/8e5o_27916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e5o_27916/07_2026/8e5o_27916.map" } 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-dev-6108/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: 6.63, 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: 3.88 Conformation dependent library (CDL) restraints added in 1.0 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: 5.63 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: 9.84 Time building geometry restraints manager: 5.04 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=" 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 bond pdb=" C8 G 7 33 " pdb=" H8 G 7 33 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.88e+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 1.50e+00 4.44e-01 8.62e+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=" O3' DA 6 28 " pdb=" P DT 6 29 " pdb=" O5' DT 6 29 " ideal model delta sigma weight residual 104.00 126.05 -22.05 1.50e+00 4.44e-01 2.16e+02 ... (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: 3998 0.107 - 0.215: 427 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.810 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: 0.340 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 46.150 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.700 ------------------------------------------------------------------------------- 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= 0.543 Angle : 1.195 48.337 39010 Z= 0.699 Chirality : 0.067 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 0.01003 / 0.52 (28602) covalent geometry : angle 1.17365 / 0.70 (39002) SS BOND : bond 0.23739 / 11.87 ( 1) SS BOND : angle 4.35070 / 8.29 ( 2) hydrogen bonds : bond 0.17477 / 18.94 ( 1070) hydrogen bonds : angle 7.29199 / 8.97 ( 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 : 1.342 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: A 492 MET cc_start: 0.6475 (mtm) cc_final: 0.6195 (tpp) REVERT: A 896 THR cc_start: -0.5724 (OUTLIER) cc_final: -0.5939 (m) REVERT: A 905 ILE cc_start: 0.4222 (OUTLIER) cc_final: 0.3997 (mp) REVERT: A 920 VAL cc_start: -0.0397 (OUTLIER) cc_final: -0.0786 (m) REVERT: A 990 ASP cc_start: 0.6523 (p0) cc_final: 0.5896 (t0) REVERT: A 1230 MET cc_start: 0.6084 (ttm) cc_final: 0.5475 (ttt) REVERT: A 1337 ILE cc_start: 0.4637 (tt) cc_final: 0.4346 (tt) REVERT: B 70 CYS cc_start: 0.3558 (OUTLIER) cc_final: 0.3117 (t) REVERT: B 132 LEU cc_start: 0.6321 (OUTLIER) cc_final: 0.5833 (tt) REVERT: B 154 LEU cc_start: 0.5874 (OUTLIER) cc_final: 0.5614 (mp) REVERT: B 222 LYS cc_start: 0.7186 (OUTLIER) cc_final: 0.6783 (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: 0.6711 (tt) REVERT: F 176 SER cc_start: 0.7818 (OUTLIER) cc_final: 0.6623 (p) outliers start: 121 outliers final: 37 residues processed: 456 average time/residue: 0.3325 time to fit residues: 232.2970 Evaluate side-chains 242 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 197 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 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** 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.067761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.054709 restraints weight = 642506.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.056138 restraints weight = 459967.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.057166 restraints weight = 351526.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.058017 restraints weight = 282782.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.058555 restraints weight = 236583.893| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.132 28609 Z= 0.149 Angle : 0.665 9.614 39010 Z= 0.361 Chirality : 0.044 0.224 4453 Planarity : 0.006 0.077 4803 Dihedral : 16.321 153.159 4686 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.06 % Favored : 92.67 % 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: -2.94 (0.13), residues: 3328 helix: -0.85 (0.14), residues: 1102 sheet: -1.79 (0.25), residues: 410 loop : -2.80 (0.13), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 990 TYR 0.022 0.001 TYR F 153 PHE 0.015 0.001 PHE F 65 TRP 0.013 0.002 TRP A 997 HIS 0.009 0.001 HIS F 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (28602) covalent geometry : angle 0.66127 / 0.36 (39002) SS BOND : bond 0.01767 / 0.88 ( 1) SS BOND : angle 5.44991 / 10.09 ( 2) hydrogen bonds : bond 0.05286 / 5.66 ( 1070) hydrogen bonds : angle 5.42286 / 6.61 ( 2964) metal coordination : bond 0.00408 / 0.37 ( 6) metal coordination : angle 4.76595 / 8.53 ( 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 232 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 229 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 LEU cc_start: 0.8271 (mm) cc_final: 0.7841 (mm) REVERT: A 230 PHE cc_start: 0.7901 (m-80) cc_final: 0.7614 (m-80) REVERT: A 369 MET cc_start: 0.6852 (ttm) cc_final: 0.6175 (ttp) REVERT: A 370 MET cc_start: 0.6000 (tpp) cc_final: 0.5724 (tpp) REVERT: A 492 MET cc_start: 0.8084 (mtm) cc_final: 0.6671 (tpp) REVERT: A 681 MET cc_start: 0.9542 (mtp) cc_final: 0.9219 (mtt) REVERT: A 951 MET cc_start: 0.9326 (mmp) cc_final: 0.9089 (mmp) REVERT: A 1230 MET cc_start: 0.7331 (ttm) cc_final: 0.7043 (ttt) REVERT: B 366 CYS cc_start: 0.8427 (p) cc_final: 0.8200 (p) REVERT: B 513 MET cc_start: 0.8144 (tmm) cc_final: 0.6946 (tmm) REVERT: B 658 GLU cc_start: 0.9600 (tt0) cc_final: 0.9381 (mm-30) REVERT: B 1099 TYR cc_start: 0.8081 (m-80) cc_final: 0.7759 (m-80) REVERT: B 1357 ILE cc_start: 0.9433 (mt) cc_final: 0.9117 (tt) REVERT: C 115 ILE cc_start: 0.7176 (tp) cc_final: 0.6870 (tp) REVERT: D 127 GLN cc_start: 0.8789 (mp10) cc_final: 0.8326 (mp10) REVERT: D 224 LEU cc_start: 0.9122 (tp) cc_final: 0.8901 (tp) REVERT: F 75 MET cc_start: 0.2747 (ttm) cc_final: 0.2309 (mtp) REVERT: F 138 ASP cc_start: 0.7434 (t0) cc_final: 0.7144 (m-30) outliers start: 3 outliers final: 1 residues processed: 231 average time/residue: 0.2900 time to fit residues: 108.2797 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 : 1.282 ------------------------------------------------------------------------------- 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: 3.9990 chunk 67 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 142 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 chunk 149 optimal weight: 7.9990 chunk 182 optimal weight: 4.9990 chunk 253 optimal weight: 10.0000 chunk 297 optimal weight: 9.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 437 ASN ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.064542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.051581 restraints weight = 653207.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.052889 restraints weight = 462136.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.053962 restraints weight = 351220.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.054689 restraints weight = 281192.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.055300 restraints weight = 236184.089| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 28609 Z= 0.168 Angle : 0.623 11.704 39010 Z= 0.335 Chirality : 0.042 0.269 4453 Planarity : 0.005 0.080 4803 Dihedral : 15.970 150.259 4686 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 22.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.64 % Favored : 93.18 % Rotamer: Outliers : 0.11 % Allowed : 1.58 % Favored : 98.32 % 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: -2.06 (0.14), residues: 3328 helix: 0.21 (0.15), residues: 1107 sheet: -1.67 (0.24), residues: 433 loop : -2.40 (0.13), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 123 TYR 0.014 0.001 TYR B 723 PHE 0.019 0.001 PHE F 39 TRP 0.030 0.002 TRP B 115 HIS 0.006 0.001 HIS B 897 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (28602) covalent geometry : angle 0.62076 / 0.33 (39002) SS BOND : bond 0.03905 / 1.95 ( 1) SS BOND : angle 3.76645 / 6.54 ( 2) hydrogen bonds : bond 0.04395 / 4.69 ( 1070) hydrogen bonds : angle 4.91593 / 5.92 ( 2964) metal coordination : bond 0.00258 / 0.19 ( 6) metal coordination : angle 3.22014 / 6.30 ( 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 211 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 208 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 VAL cc_start: 0.7677 (t) cc_final: 0.7475 (t) REVERT: A 213 LEU cc_start: 0.8740 (mm) cc_final: 0.7944 (mm) REVERT: A 370 MET cc_start: 0.6801 (tpp) cc_final: 0.6226 (tpp) REVERT: A 459 MET cc_start: 0.8756 (mmp) cc_final: 0.8540 (mmp) REVERT: A 492 MET cc_start: 0.8205 (mtm) cc_final: 0.6772 (tpp) REVERT: A 681 MET cc_start: 0.9619 (mtp) cc_final: 0.9123 (mtt) REVERT: A 951 MET cc_start: 0.9388 (mmp) cc_final: 0.9150 (mmp) REVERT: A 1329 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8045 (tt0) REVERT: B 219 LYS cc_start: 0.9007 (mtmt) cc_final: 0.8595 (tptm) REVERT: B 466 MET cc_start: 0.8252 (mtp) cc_final: 0.8008 (mtp) REVERT: B 658 GLU cc_start: 0.9597 (tt0) cc_final: 0.9372 (mm-30) REVERT: B 1099 TYR cc_start: 0.8095 (m-80) cc_final: 0.7763 (m-80) REVERT: C 205 MET cc_start: 0.8815 (pmm) cc_final: 0.8355 (pmm) REVERT: D 224 LEU cc_start: 0.9235 (tp) cc_final: 0.8990 (tp) REVERT: F 35 MET cc_start: 0.3226 (ttm) cc_final: 0.2902 (ptm) REVERT: F 90 MET cc_start: 0.8234 (mpp) cc_final: 0.7822 (mmm) outliers start: 3 outliers final: 1 residues processed: 210 average time/residue: 0.2876 time to fit residues: 98.2979 Evaluate side-chains 168 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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: 2.9990 chunk 290 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 293 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 73 optimal weight: 0.0050 chunk 69 optimal weight: 7.9990 overall best weight: 3.8002 ------------------------------------------------------------------------------- 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 343 HIS ** 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 688 GLN A 808 ASN A1136 GLN A1244 HIS ** A1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** F 76 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.058093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.045691 restraints weight = 683401.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.046910 restraints weight = 475829.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.047808 restraints weight = 359738.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.048422 restraints weight = 288912.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.048834 restraints weight = 243542.665| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 28609 Z= 0.246 Angle : 0.770 20.809 39010 Z= 0.404 Chirality : 0.045 0.316 4453 Planarity : 0.006 0.204 4803 Dihedral : 16.006 151.973 4686 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 33.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.18 % Favored : 92.64 % Rotamer: Outliers : 0.04 % Allowed : 2.07 % Favored : 97.89 % 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: -2.02 (0.14), residues: 3328 helix: 0.17 (0.15), residues: 1103 sheet: -1.69 (0.24), residues: 439 loop : -2.31 (0.13), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG F 84 TYR 0.044 0.002 TYR A 291 PHE 0.052 0.002 PHE B 116 TRP 0.024 0.002 TRP B 115 HIS 0.012 0.002 HIS A1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.25 (28602) covalent geometry : angle 0.76744 / 0.40 (39002) SS BOND : bond 0.00192 / 0.10 ( 1) SS BOND : angle 6.70632 / 11.27 ( 2) hydrogen bonds : bond 0.04874 / 5.20 ( 1070) hydrogen bonds : angle 5.10188 / 6.24 ( 2964) metal coordination : bond 0.02795 / 2.01 ( 6) metal coordination : angle 3.70206 / 6.96 ( 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 199 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 198 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 LEU cc_start: 0.8981 (mm) cc_final: 0.8207 (mm) REVERT: A 316 GLU cc_start: 0.7948 (pm20) cc_final: 0.7444 (mp0) REVERT: A 370 MET cc_start: 0.7249 (tpp) cc_final: 0.6832 (tpp) REVERT: A 459 MET cc_start: 0.9111 (mmp) cc_final: 0.8791 (mmp) REVERT: A 492 MET cc_start: 0.8335 (mtm) cc_final: 0.7886 (mtp) REVERT: A 681 MET cc_start: 0.9624 (mtp) cc_final: 0.9175 (mtt) REVERT: A 922 ASN cc_start: 0.8370 (p0) cc_final: 0.8070 (p0) REVERT: A 951 MET cc_start: 0.9359 (mmp) cc_final: 0.9065 (mmp) REVERT: A 1180 MET cc_start: 0.8805 (tmm) cc_final: 0.8563 (tmm) REVERT: A 1230 MET cc_start: 0.7912 (tpt) cc_final: 0.7525 (tpp) REVERT: A 1329 GLU cc_start: 0.9362 (mt-10) cc_final: 0.9159 (mt-10) REVERT: B 219 LYS cc_start: 0.9129 (mtmt) cc_final: 0.8675 (tptt) REVERT: B 466 MET cc_start: 0.8459 (mtp) cc_final: 0.7374 (ttm) REVERT: B 485 MET cc_start: 0.8615 (tpp) cc_final: 0.8387 (tpp) REVERT: B 513 MET cc_start: 0.8388 (tmm) cc_final: 0.7624 (tmm) REVERT: B 658 GLU cc_start: 0.9632 (tt0) cc_final: 0.9402 (mm-30) REVERT: B 1099 TYR cc_start: 0.7949 (m-80) cc_final: 0.7692 (m-80) REVERT: B 1357 ILE cc_start: 0.9629 (mt) cc_final: 0.9369 (pt) REVERT: C 142 MET cc_start: 0.8153 (pmm) cc_final: 0.7858 (pmm) REVERT: C 205 MET cc_start: 0.9209 (pmm) cc_final: 0.8976 (pmm) REVERT: D 174 ASP cc_start: 0.7800 (m-30) cc_final: 0.7029 (t0) REVERT: D 224 LEU cc_start: 0.9472 (tp) cc_final: 0.9262 (tp) REVERT: F 35 MET cc_start: 0.4264 (ttm) cc_final: 0.3943 (ttm) REVERT: F 73 MET cc_start: 0.3702 (tpt) cc_final: 0.3336 (tpp) REVERT: F 138 ASP cc_start: 0.7541 (t0) cc_final: 0.7210 (m-30) outliers start: 1 outliers final: 0 residues processed: 199 average time/residue: 0.2766 time to fit residues: 90.3865 Evaluate side-chains 155 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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: 5.9990 chunk 256 optimal weight: 3.9990 chunk 334 optimal weight: 0.7980 chunk 148 optimal weight: 7.9990 chunk 275 optimal weight: 0.9990 chunk 281 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 chunk 142 optimal weight: 0.0970 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 343 HIS ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1244 HIS A1256 GLN E 15 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.058738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.046226 restraints weight = 673656.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.047480 restraints weight = 468846.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.048392 restraints weight = 352861.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.049028 restraints weight = 282377.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.049569 restraints weight = 238687.492| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 28609 Z= 0.102 Angle : 0.523 15.147 39010 Z= 0.280 Chirality : 0.041 0.149 4453 Planarity : 0.004 0.062 4803 Dihedral : 15.845 151.442 4686 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 27.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.01 % Favored : 93.87 % Rotamer: Outliers : 0.04 % Allowed : 0.49 % Favored : 99.47 % 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: -1.45 (0.14), residues: 3328 helix: 0.91 (0.16), residues: 1101 sheet: -1.52 (0.24), residues: 442 loop : -2.12 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 417 TYR 0.016 0.001 TYR A 215 PHE 0.018 0.001 PHE B 116 TRP 0.012 0.001 TRP A 183 HIS 0.005 0.001 HIS B 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (28602) covalent geometry : angle 0.52036 / 0.28 (39002) SS BOND : bond 0.00801 / 0.40 ( 1) SS BOND : angle 3.85022 / 6.53 ( 2) hydrogen bonds : bond 0.03790 / 4.07 ( 1070) hydrogen bonds : angle 4.55182 / 5.53 ( 2964) metal coordination : bond 0.00689 / 0.55 ( 6) metal coordination : angle 3.32891 / 6.19 ( 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 188 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 MET cc_start: 0.7380 (tpp) cc_final: 0.6921 (tpp) REVERT: A 459 MET cc_start: 0.9100 (mmp) cc_final: 0.8808 (mmp) REVERT: A 951 MET cc_start: 0.9399 (mmp) cc_final: 0.9037 (mmp) REVERT: A 1180 MET cc_start: 0.8654 (tmm) cc_final: 0.8032 (tmm) REVERT: A 1230 MET cc_start: 0.7867 (tpt) cc_final: 0.7452 (tpp) REVERT: A 1290 MET cc_start: 0.9221 (ttp) cc_final: 0.8930 (ttp) REVERT: A 1329 GLU cc_start: 0.9413 (mt-10) cc_final: 0.8987 (mt-10) REVERT: B 115 TRP cc_start: 0.8399 (m-10) cc_final: 0.8055 (m100) REVERT: B 219 LYS cc_start: 0.9099 (mtmt) cc_final: 0.8659 (tptt) REVERT: B 485 MET cc_start: 0.8603 (tpp) cc_final: 0.8307 (tpp) REVERT: B 513 MET cc_start: 0.8054 (tmm) cc_final: 0.7645 (tmm) REVERT: B 658 GLU cc_start: 0.9628 (tt0) cc_final: 0.9388 (mm-30) REVERT: B 1099 TYR cc_start: 0.8133 (m-80) cc_final: 0.7785 (m-80) REVERT: B 1357 ILE cc_start: 0.9584 (mt) cc_final: 0.9309 (pt) REVERT: C 205 MET cc_start: 0.9299 (pmm) cc_final: 0.9070 (pmm) REVERT: D 174 ASP cc_start: 0.7708 (m-30) cc_final: 0.7361 (m-30) REVERT: D 224 LEU cc_start: 0.9399 (tp) cc_final: 0.9173 (tp) REVERT: D 231 PHE cc_start: 0.7391 (m-10) cc_final: 0.7013 (m-80) REVERT: E 43 ASN cc_start: 0.8737 (t0) cc_final: 0.8508 (t0) REVERT: F 35 MET cc_start: 0.4216 (ttm) cc_final: 0.3708 (ptm) REVERT: F 90 MET cc_start: 0.7940 (mmt) cc_final: 0.7057 (mmt) REVERT: F 138 ASP cc_start: 0.7509 (t0) cc_final: 0.7173 (m-30) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.2782 time to fit residues: 86.6249 Evaluate side-chains 158 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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: 9.9990 chunk 248 optimal weight: 0.9990 chunk 176 optimal weight: 7.9990 chunk 240 optimal weight: 8.9990 chunk 247 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 271 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 291 optimal weight: 7.9990 chunk 100 optimal weight: 0.3980 chunk 239 optimal weight: 20.0000 overall best weight: 2.8788 ------------------------------------------------------------------------------- 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 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 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 HIS ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1324 ASN B 277 ASN B 300 GLN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1244 GLN ** D 23 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 = 0.3723 r_free = 0.3723 target = 0.054249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.042102 restraints weight = 694161.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.043254 restraints weight = 475374.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.044064 restraints weight = 356573.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.044696 restraints weight = 286691.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.045079 restraints weight = 241746.533| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.6320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 28609 Z= 0.210 Angle : 0.689 16.802 39010 Z= 0.360 Chirality : 0.042 0.181 4453 Planarity : 0.005 0.062 4803 Dihedral : 15.790 152.150 4686 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 36.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.35 % Favored : 91.50 % Rotamer: Outliers : 0.04 % Allowed : 1.23 % Favored : 98.74 % 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: -1.54 (0.14), residues: 3328 helix: 0.70 (0.15), residues: 1121 sheet: -1.60 (0.24), residues: 456 loop : -2.08 (0.14), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG F 123 TYR 0.022 0.002 TYR D 177 PHE 0.025 0.002 PHE F 65 TRP 0.015 0.002 TRP F 80 HIS 0.007 0.002 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.21 (28602) covalent geometry : angle 0.68744 / 0.36 (39002) SS BOND : bond 0.02000 / 1.00 ( 1) SS BOND : angle 3.28459 / 5.90 ( 2) hydrogen bonds : bond 0.04398 / 4.79 ( 1070) hydrogen bonds : angle 4.66971 / 5.71 ( 2964) metal coordination : bond 0.00509 / 0.34 ( 6) metal coordination : angle 2.74681 / 5.29 ( 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 179 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 1.150 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 215 TYR cc_start: 0.6261 (m-80) cc_final: 0.6015 (m-80) REVERT: A 316 GLU cc_start: 0.8059 (pm20) cc_final: 0.7506 (mp0) REVERT: A 370 MET cc_start: 0.7501 (tpp) cc_final: 0.7096 (tpp) REVERT: A 429 MET cc_start: 0.9197 (mtm) cc_final: 0.8967 (mtp) REVERT: A 492 MET cc_start: 0.9010 (mmp) cc_final: 0.6438 (tpt) REVERT: A 515 MET cc_start: 0.8351 (ptm) cc_final: 0.8053 (tmm) REVERT: A 951 MET cc_start: 0.9254 (mmp) cc_final: 0.8906 (mmp) REVERT: A 1329 GLU cc_start: 0.9517 (mt-10) cc_final: 0.9020 (mt-10) REVERT: B 219 LYS cc_start: 0.9217 (mtmt) cc_final: 0.8924 (tmtt) REVERT: B 485 MET cc_start: 0.8936 (tpp) cc_final: 0.8559 (tpp) REVERT: B 513 MET cc_start: 0.8454 (tmm) cc_final: 0.8058 (tmm) REVERT: B 644 MET cc_start: 0.8464 (mtm) cc_final: 0.7572 (mpp) REVERT: B 821 MET cc_start: 0.5337 (tpt) cc_final: 0.4918 (tpt) REVERT: B 1099 TYR cc_start: 0.7994 (m-80) cc_final: 0.7700 (m-80) REVERT: D 174 ASP cc_start: 0.8122 (m-30) cc_final: 0.7883 (m-30) REVERT: D 205 MET cc_start: 0.7784 (ppp) cc_final: 0.7505 (ppp) REVERT: D 224 LEU cc_start: 0.9571 (tp) cc_final: 0.9357 (tp) REVERT: E 43 ASN cc_start: 0.8757 (t0) cc_final: 0.8499 (t0) REVERT: F 35 MET cc_start: 0.5092 (ttm) cc_final: 0.4708 (ttm) REVERT: F 90 MET cc_start: 0.8397 (mmt) cc_final: 0.7512 (mmt) REVERT: F 138 ASP cc_start: 0.7691 (t0) cc_final: 0.7354 (m-30) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.2269 time to fit residues: 68.8013 Evaluate side-chains 145 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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: 10.0000 chunk 228 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 chunk 252 optimal weight: 5.9990 chunk 303 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 96 optimal weight: 0.0970 chunk 318 optimal weight: 10.0000 chunk 156 optimal weight: 0.8980 chunk 295 optimal weight: 3.9990 chunk 329 optimal weight: 10.0000 overall best weight: 1.9982 ------------------------------------------------------------------------------- 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 327 GLN ** 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 618 GLN ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1244 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** ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.054053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.041897 restraints weight = 691599.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.043040 restraints weight = 470926.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.043884 restraints weight = 352500.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.044423 restraints weight = 282131.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.044955 restraints weight = 239466.358| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.6575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 28609 Z= 0.121 Angle : 0.521 14.081 39010 Z= 0.281 Chirality : 0.040 0.149 4453 Planarity : 0.004 0.054 4803 Dihedral : 15.745 152.155 4686 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 32.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.10 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -1.24 (0.14), residues: 3328 helix: 0.98 (0.16), residues: 1123 sheet: -1.46 (0.24), residues: 446 loop : -1.93 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 69 TYR 0.013 0.001 TYR A 291 PHE 0.012 0.001 PHE F 65 TRP 0.012 0.001 TRP F 80 HIS 0.005 0.001 HIS B 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (28602) covalent geometry : angle 0.51996 / 0.28 (39002) SS BOND : bond 0.00239 / 0.12 ( 1) SS BOND : angle 2.36315 / 4.15 ( 2) hydrogen bonds : bond 0.03689 / 4.00 ( 1070) hydrogen bonds : angle 4.43944 / 5.40 ( 2964) metal coordination : bond 0.00312 / 0.29 ( 6) metal coordination : angle 2.62210 / 5.04 ( 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 174 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 PHE cc_start: 0.8554 (m-80) cc_final: 0.8259 (t80) REVERT: A 370 MET cc_start: 0.7688 (tpp) cc_final: 0.7324 (tpp) REVERT: A 429 MET cc_start: 0.9254 (mtm) cc_final: 0.9005 (mtp) REVERT: A 459 MET cc_start: 0.9209 (mmp) cc_final: 0.8829 (mmp) REVERT: A 492 MET cc_start: 0.8634 (mmp) cc_final: 0.6231 (tpt) REVERT: A 515 MET cc_start: 0.8313 (ptm) cc_final: 0.8080 (tmm) REVERT: A 903 ARG cc_start: 0.8700 (pmt170) cc_final: 0.8276 (tpm170) REVERT: A 951 MET cc_start: 0.9312 (mmp) cc_final: 0.8905 (mmp) REVERT: A 1151 LEU cc_start: 0.8385 (tp) cc_final: 0.7949 (tp) REVERT: A 1180 MET cc_start: 0.9049 (tmm) cc_final: 0.8463 (tmm) REVERT: A 1232 MET cc_start: 0.8450 (mmp) cc_final: 0.8231 (mmp) REVERT: A 1290 MET cc_start: 0.9605 (ttt) cc_final: 0.9143 (tmm) REVERT: A 1329 GLU cc_start: 0.9512 (mt-10) cc_final: 0.8998 (mt-10) REVERT: B 219 LYS cc_start: 0.9210 (mtmt) cc_final: 0.8918 (tmtt) REVERT: B 485 MET cc_start: 0.9043 (tpp) cc_final: 0.8679 (tpp) REVERT: B 513 MET cc_start: 0.8411 (tmm) cc_final: 0.8079 (tmm) REVERT: B 644 MET cc_start: 0.8557 (mtm) cc_final: 0.7661 (mpp) REVERT: B 821 MET cc_start: 0.5117 (tpt) cc_final: 0.4778 (mmm) REVERT: B 1099 TYR cc_start: 0.8067 (m-80) cc_final: 0.7750 (m-80) REVERT: B 1357 ILE cc_start: 0.9554 (mt) cc_final: 0.9277 (pt) REVERT: C 142 MET cc_start: 0.7403 (pmm) cc_final: 0.7128 (pmm) REVERT: D 174 ASP cc_start: 0.8072 (m-30) cc_final: 0.7844 (m-30) REVERT: D 205 MET cc_start: 0.7732 (ppp) cc_final: 0.7463 (ppp) REVERT: D 224 LEU cc_start: 0.9549 (tp) cc_final: 0.9339 (tp) REVERT: E 43 ASN cc_start: 0.8768 (t0) cc_final: 0.8516 (t0) REVERT: F 35 MET cc_start: 0.5051 (ttm) cc_final: 0.4338 (ttm) REVERT: F 90 MET cc_start: 0.8346 (mmt) cc_final: 0.7452 (mmt) REVERT: F 138 ASP cc_start: 0.7758 (t0) cc_final: 0.7453 (m-30) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2633 time to fit residues: 76.4666 Evaluate side-chains 145 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.352 ------------------------------------------------------------------------------- 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: 0.0270 chunk 320 optimal weight: 0.8980 chunk 303 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 184 optimal weight: 10.0000 chunk 291 optimal weight: 9.9990 chunk 331 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 329 optimal weight: 2.9990 chunk 185 optimal weight: 10.0000 overall best weight: 1.9844 ------------------------------------------------------------------------------- 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 327 GLN ** 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** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 HIS ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.053048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.040939 restraints weight = 695194.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.042071 restraints weight = 472558.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.042888 restraints weight = 352877.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.043495 restraints weight = 282731.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.043894 restraints weight = 237755.696| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.6974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 28609 Z= 0.133 Angle : 0.522 12.180 39010 Z= 0.281 Chirality : 0.040 0.227 4453 Planarity : 0.004 0.052 4803 Dihedral : 15.677 152.117 4686 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 33.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.33 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -1.09 (0.15), residues: 3328 helix: 1.11 (0.16), residues: 1132 sheet: -1.37 (0.24), residues: 448 loop : -1.85 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 417 TYR 0.034 0.001 TYR A 742 PHE 0.015 0.001 PHE F 39 TRP 0.012 0.001 TRP F 80 HIS 0.005 0.001 HIS B 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (28602) covalent geometry : angle 0.52146 / 0.28 (39002) SS BOND : bond 0.00528 / 0.26 ( 1) SS BOND : angle 2.04401 / 3.68 ( 2) hydrogen bonds : bond 0.03610 / 3.93 ( 1070) hydrogen bonds : angle 4.36647 / 5.30 ( 2964) metal coordination : bond 0.00249 / 0.20 ( 6) metal coordination : angle 2.27204 / 4.37 ( 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 163 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.6982 (ppp) cc_final: 0.6530 (ttm) REVERT: A 230 PHE cc_start: 0.8595 (m-80) cc_final: 0.8186 (t80) REVERT: A 369 MET cc_start: 0.7705 (ttm) cc_final: 0.7237 (tmm) REVERT: A 370 MET cc_start: 0.7730 (tpp) cc_final: 0.7358 (tpp) REVERT: A 429 MET cc_start: 0.9282 (mtm) cc_final: 0.9051 (mtp) REVERT: A 515 MET cc_start: 0.8394 (ptm) cc_final: 0.8156 (tmm) REVERT: A 951 MET cc_start: 0.9330 (mmp) cc_final: 0.8917 (mmp) REVERT: A 1151 LEU cc_start: 0.8524 (tp) cc_final: 0.8147 (tp) REVERT: A 1329 GLU cc_start: 0.9515 (mt-10) cc_final: 0.9031 (mt-10) REVERT: B 372 MET cc_start: 0.8207 (mtp) cc_final: 0.7928 (ttt) REVERT: B 485 MET cc_start: 0.9081 (tpp) cc_final: 0.8647 (tpp) REVERT: B 513 MET cc_start: 0.8998 (tmm) cc_final: 0.8443 (tmm) REVERT: B 644 MET cc_start: 0.8607 (mtm) cc_final: 0.7724 (mpp) REVERT: B 747 MET cc_start: 0.8052 (mmp) cc_final: 0.7647 (mmp) REVERT: B 821 MET cc_start: 0.5354 (tpt) cc_final: 0.5013 (mmm) REVERT: B 1099 TYR cc_start: 0.7955 (m-80) cc_final: 0.7670 (m-80) REVERT: B 1357 ILE cc_start: 0.9552 (mt) cc_final: 0.9269 (pt) REVERT: C 142 MET cc_start: 0.7545 (pmm) cc_final: 0.7263 (pmm) REVERT: D 115 ILE cc_start: 0.8098 (mt) cc_final: 0.7750 (mt) REVERT: D 174 ASP cc_start: 0.8129 (m-30) cc_final: 0.7874 (m-30) REVERT: D 205 MET cc_start: 0.8065 (ppp) cc_final: 0.7813 (ppp) REVERT: E 43 ASN cc_start: 0.8781 (t0) cc_final: 0.8559 (t0) REVERT: F 35 MET cc_start: 0.5599 (ttm) cc_final: 0.4804 (ptm) REVERT: F 138 ASP cc_start: 0.7731 (t0) cc_final: 0.7434 (m-30) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2417 time to fit residues: 68.3514 Evaluate side-chains 141 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.270 ------------------------------------------------------------------------------- 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: 0.0060 chunk 206 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 270 optimal weight: 10.0000 chunk 198 optimal weight: 6.9990 chunk 320 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 318 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 overall best weight: 1.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 GLN ** 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** A 613 ASN ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1367 GLN ** 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** ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.051936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.039872 restraints weight = 703969.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.040994 restraints weight = 475195.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.041814 restraints weight = 351876.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.042397 restraints weight = 281045.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.042743 restraints weight = 236917.606| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.7510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 28609 Z= 0.125 Angle : 0.517 9.942 39010 Z= 0.278 Chirality : 0.040 0.182 4453 Planarity : 0.004 0.052 4803 Dihedral : 15.650 152.112 4686 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 32.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.41 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -0.91 (0.15), residues: 3328 helix: 1.25 (0.16), residues: 1131 sheet: -1.24 (0.25), residues: 445 loop : -1.75 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 114 TYR 0.036 0.001 TYR A 215 PHE 0.010 0.001 PHE F 65 TRP 0.012 0.001 TRP F 80 HIS 0.005 0.001 HIS B 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 (28602) covalent geometry : angle 0.51581 / 0.28 (39002) SS BOND : bond 0.00551 / 0.28 ( 1) SS BOND : angle 1.55017 / 2.71 ( 2) hydrogen bonds : bond 0.03517 / 3.84 ( 1070) hydrogen bonds : angle 4.28520 / 5.21 ( 2964) metal coordination : bond 0.00276 / 0.22 ( 6) metal coordination : angle 2.26461 / 4.34 ( 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 164 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.865 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: A 230 PHE cc_start: 0.8512 (m-80) cc_final: 0.8184 (t80) REVERT: A 369 MET cc_start: 0.7848 (ttm) cc_final: 0.7291 (tmm) REVERT: A 370 MET cc_start: 0.7807 (tpp) cc_final: 0.7470 (tpp) REVERT: A 429 MET cc_start: 0.9327 (mtm) cc_final: 0.9063 (mtp) REVERT: A 459 MET cc_start: 0.9294 (mmp) cc_final: 0.9081 (mmp) REVERT: A 515 MET cc_start: 0.8453 (ptm) cc_final: 0.8101 (tmm) REVERT: A 903 ARG cc_start: 0.8711 (pmt170) cc_final: 0.8248 (tpm170) REVERT: A 951 MET cc_start: 0.9330 (mmp) cc_final: 0.8923 (mmp) REVERT: A 1151 LEU cc_start: 0.8685 (tp) cc_final: 0.8295 (tp) REVERT: A 1180 MET cc_start: 0.9150 (tmm) cc_final: 0.8602 (tmm) REVERT: A 1329 GLU cc_start: 0.9520 (mt-10) cc_final: 0.8949 (mt-10) REVERT: B 513 MET cc_start: 0.9234 (tmm) cc_final: 0.9000 (tmm) REVERT: B 644 MET cc_start: 0.8697 (mtm) cc_final: 0.7853 (mpp) REVERT: B 747 MET cc_start: 0.8095 (mmp) cc_final: 0.7657 (mmp) REVERT: B 821 MET cc_start: 0.5742 (tpt) cc_final: 0.5402 (mmm) REVERT: B 1099 TYR cc_start: 0.7998 (m-80) cc_final: 0.7698 (m-80) REVERT: B 1357 ILE cc_start: 0.9539 (mt) cc_final: 0.9252 (pt) REVERT: C 205 MET cc_start: 0.9320 (pmm) cc_final: 0.9104 (pmm) REVERT: D 174 ASP cc_start: 0.8144 (m-30) cc_final: 0.7884 (m-30) REVERT: D 205 MET cc_start: 0.8356 (ppp) cc_final: 0.8082 (ppp) REVERT: E 43 ASN cc_start: 0.8900 (t0) cc_final: 0.8620 (t0) REVERT: F 35 MET cc_start: 0.5919 (ttm) cc_final: 0.5594 (ptm) REVERT: F 75 MET cc_start: 0.8695 (ppp) cc_final: 0.8364 (ppp) REVERT: F 90 MET cc_start: 0.8542 (mmt) cc_final: 0.7198 (mpp) REVERT: F 138 ASP cc_start: 0.7772 (t0) cc_final: 0.7448 (m-30) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2224 time to fit residues: 62.5824 Evaluate side-chains 138 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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: 0.1980 chunk 43 optimal weight: 4.9990 chunk 295 optimal weight: 0.9980 chunk 316 optimal weight: 7.9990 chunk 302 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 chunk 299 optimal weight: 4.9990 chunk 281 optimal weight: 0.6980 chunk 96 optimal weight: 9.9990 chunk 238 optimal weight: 20.0000 overall best weight: 2.3784 ------------------------------------------------------------------------------- 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** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.050397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.038448 restraints weight = 710392.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.039513 restraints weight = 477531.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.040258 restraints weight = 354490.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.040864 restraints weight = 285036.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.041190 restraints weight = 240034.491| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.8028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 28609 Z= 0.150 Angle : 0.551 12.022 39010 Z= 0.294 Chirality : 0.040 0.180 4453 Planarity : 0.004 0.057 4803 Dihedral : 15.627 152.407 4686 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 36.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.45 % Favored : 92.31 % 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: -0.94 (0.15), residues: 3328 helix: 1.19 (0.16), residues: 1141 sheet: -1.21 (0.25), residues: 434 loop : -1.76 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 195 TYR 0.014 0.001 TYR A 291 PHE 0.019 0.001 PHE F 65 TRP 0.012 0.001 TRP F 80 HIS 0.005 0.001 HIS B1227 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (28602) covalent geometry : angle 0.55006 / 0.29 (39002) SS BOND : bond 0.00354 / 0.18 ( 1) SS BOND : angle 1.59393 / 2.70 ( 2) hydrogen bonds : bond 0.03682 / 4.05 ( 1070) hydrogen bonds : angle 4.36516 / 5.28 ( 2964) metal coordination : bond 0.00170 / 0.19 ( 6) metal coordination : angle 2.14235 / 4.05 ( 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 155 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.370 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: A 130 MET cc_start: 0.6938 (ppp) cc_final: 0.6606 (ttm) REVERT: A 230 PHE cc_start: 0.8466 (m-80) cc_final: 0.8083 (t80) REVERT: A 369 MET cc_start: 0.7751 (ttm) cc_final: 0.6552 (tmm) REVERT: A 370 MET cc_start: 0.7861 (tpp) cc_final: 0.7567 (tpp) REVERT: A 429 MET cc_start: 0.9320 (mtm) cc_final: 0.9022 (mtp) REVERT: A 459 MET cc_start: 0.9304 (mmp) cc_final: 0.8902 (mmp) REVERT: A 492 MET cc_start: 0.7896 (mmp) cc_final: 0.6343 (ttt) REVERT: A 951 MET cc_start: 0.9318 (mmp) cc_final: 0.8937 (mmp) REVERT: A 1119 MET cc_start: 0.8456 (ptp) cc_final: 0.7954 (ptp) REVERT: A 1151 LEU cc_start: 0.8700 (tp) cc_final: 0.8335 (tp) REVERT: A 1329 GLU cc_start: 0.9568 (mt-10) cc_final: 0.9065 (mt-10) REVERT: B 644 MET cc_start: 0.8663 (mtm) cc_final: 0.7792 (mpp) REVERT: B 747 MET cc_start: 0.8242 (mmp) cc_final: 0.7832 (mmp) REVERT: B 821 MET cc_start: 0.6066 (tpt) cc_final: 0.5737 (mmm) REVERT: B 1099 TYR cc_start: 0.7900 (m-80) cc_final: 0.7629 (m-80) REVERT: B 1357 ILE cc_start: 0.9553 (mt) cc_final: 0.9266 (pt) REVERT: C 205 MET cc_start: 0.9101 (pmm) cc_final: 0.8888 (pmm) REVERT: D 174 ASP cc_start: 0.8237 (m-30) cc_final: 0.8000 (m-30) REVERT: D 205 MET cc_start: 0.8438 (ppp) cc_final: 0.8194 (ppp) REVERT: E 43 ASN cc_start: 0.8811 (t0) cc_final: 0.8484 (t0) REVERT: F 35 MET cc_start: 0.6207 (ttm) cc_final: 0.5228 (ptm) REVERT: F 75 MET cc_start: 0.8770 (ppp) cc_final: 0.8541 (ppp) REVERT: F 90 MET cc_start: 0.8696 (mmt) cc_final: 0.7423 (mpp) REVERT: F 138 ASP cc_start: 0.7692 (t0) cc_final: 0.7355 (m-30) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.2586 time to fit residues: 68.8136 Evaluate side-chains 131 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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: 0.3980 chunk 339 optimal weight: 0.0570 chunk 66 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 243 optimal weight: 9.9990 chunk 297 optimal weight: 8.9990 chunk 313 optimal weight: 10.0000 chunk 192 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 187 optimal weight: 6.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.050898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.038752 restraints weight = 696824.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.039855 restraints weight = 465870.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.040675 restraints weight = 345358.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.041161 restraints weight = 275013.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.041624 restraints weight = 234092.657| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.8056 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= 0.088 Angle : 0.471 8.533 39010 Z= 0.254 Chirality : 0.039 0.144 4453 Planarity : 0.004 0.051 4803 Dihedral : 15.577 152.006 4686 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 31.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.44 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.67 (0.15), residues: 3328 helix: 1.47 (0.16), residues: 1142 sheet: -1.09 (0.25), residues: 429 loop : -1.64 (0.15), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1345 TYR 0.018 0.001 TYR A 291 PHE 0.011 0.001 PHE B 62 TRP 0.008 0.001 TRP F 9 HIS 0.005 0.001 HIS B 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00184 / 0.09 (28602) covalent geometry : angle 0.47006 / 0.25 (39002) SS BOND : bond 0.00710 / 0.36 ( 1) SS BOND : angle 2.76441 / 4.74 ( 2) hydrogen bonds : bond 0.03324 / 3.63 ( 1070) hydrogen bonds : angle 4.14077 / 5.04 ( 2964) metal coordination : bond 0.00261 / 0.24 ( 6) metal coordination : angle 2.11824 / 4.10 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7846.67 seconds wall clock time: 135 minutes 18.38 seconds (8118.38 seconds total)