Starting phenix.real_space_refine on Sat Aug 8 19:05:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e7v_47692/08_2026/9e7v_47692.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e7v_47692/08_2026/9e7v_47692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e7v_47692/08_2026/9e7v_47692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e7v_47692/08_2026/9e7v_47692.map" model { file = "/net/cci-nas-00/data/ceres_data/9e7v_47692/08_2026/9e7v_47692.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e7v_47692/08_2026/9e7v_47692.cif" } resolution = 3.4 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= 0.004 sd= 0.066 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 94 5.49 5 Mg 1 5.21 5 S 98 5.16 5 C 17956 2.51 5 N 5191 2.21 5 O 5775 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29117 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1716 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 210} Chain: "B" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1748 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 218} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 8629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8629 Classifications: {'peptide': 1114} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1051} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 9881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1265, 9881 Classifications: {'peptide': 1265} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 3, 'PTRANS': 57, 'TRANS': 1204} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 76} Chain: "F" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2501 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 308} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "J" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 857 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1241 Classifications: {'peptide': 159} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 153} Chain: "N" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1033 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain breaks: 1 Chain: "T" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 850 Classifications: {'DNA': 42} Link IDs: {'rna3p': 41} Chain breaks: 1 Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'POP': 1} Classifications: {'undetermined': 1} Chain: "D" 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 12566 SG CYS D 60 78.304 58.896 59.224 1.00124.66 S ATOM 12584 SG CYS D 62 76.987 58.947 55.696 1.00127.89 S ATOM 12693 SG CYS D 75 80.639 58.647 56.245 1.00137.81 S ATOM 12719 SG CYS D 78 78.886 61.793 56.946 1.00100.43 S ATOM 19128 SG CYS D 891 109.162 97.797 104.871 1.00 94.46 S ATOM 19695 SG CYS D 968 105.953 98.103 103.024 1.00 98.25 S ATOM 19737 SG CYS D 975 106.242 95.896 106.006 1.00 81.97 S ATOM 19755 SG CYS D 978 106.328 99.583 106.468 1.00 96.02 S Time building chain proxies: 5.17, per 1000 atoms: 0.18 Number of scatterers: 29117 At special positions: 0 Unit cell: (132.348, 162.476, 186.148, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 98 16.00 P 94 15.00 Mg 1 11.99 O 5775 8.00 N 5191 7.00 C 17956 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.84 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 60 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 968 " Number of angles added : 12 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6458 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 38 sheets defined 42.0% alpha, 13.9% beta 40 base pairs and 70 stacking pairs defined. Time for finding SS restraints: 3.64 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 203 through 224 removed outlier: 3.881A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 46 removed outlier: 4.137A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 203 through 224 Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.051A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 233 through 242 removed outlier: 4.185A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 269 through 282 removed outlier: 3.691A pdb=" N ASP C 276 " --> pdb=" O GLU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 301 removed outlier: 3.742A pdb=" N LEU C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU C 297 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 380 through 407 removed outlier: 4.376A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 444 through 452 removed outlier: 3.788A pdb=" N LYS C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 590 through 594 Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 629 through 634 removed outlier: 4.335A pdb=" N ARG C 633 " --> pdb=" O GLY C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 815 through 826 Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 954 through 959 removed outlier: 4.438A pdb=" N ARG C 958 " --> pdb=" O TRP C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 991 removed outlier: 3.690A pdb=" N CYS C 991 " --> pdb=" O GLY C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1040 Processing helix chain 'C' and resid 1069 through 1080 removed outlier: 3.526A pdb=" N GLY C1080 " --> pdb=" O MET C1076 " (cutoff:3.500A) Processing helix chain 'C' and resid 1082 through 1090 Processing helix chain 'C' and resid 1095 through 1108 removed outlier: 4.396A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1120 through 1131 Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 85 through 90 removed outlier: 3.575A pdb=" N ARG D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 removed outlier: 4.207A pdb=" N LYS D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 185 removed outlier: 4.820A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 228 removed outlier: 4.155A pdb=" N VAL D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARG D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 246 Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.560A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.746A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.725A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 339 through 361 removed outlier: 4.311A pdb=" N LEU D 343 " --> pdb=" O ASP D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 393 through 397 removed outlier: 3.717A pdb=" N ARG D 397 " --> pdb=" O PRO D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 407 Processing helix chain 'D' and resid 445 through 452 removed outlier: 4.342A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 481 through 492 removed outlier: 4.311A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 579 through 590 Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 668 through 675 Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 726 removed outlier: 3.791A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 763 removed outlier: 3.974A pdb=" N ARG D 752 " --> pdb=" O HIS D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 810 through 818 removed outlier: 3.974A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 3.867A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA D 868 " --> pdb=" O ALA D 864 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 994 through 1005 Processing helix chain 'D' and resid 1006 through 1008 No H-bonds generated for 'chain 'D' and resid 1006 through 1008' Processing helix chain 'D' and resid 1027 through 1036 Processing helix chain 'D' and resid 1117 through 1145 removed outlier: 3.658A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Proline residue: D1127 - end of helix removed outlier: 3.521A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 4.541A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1182 through 1195 removed outlier: 4.341A pdb=" N ALA D1195 " --> pdb=" O ARG D1191 " (cutoff:3.500A) Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1219 through 1227 removed outlier: 3.658A pdb=" N ALA D1223 " --> pdb=" O SER D1219 " (cutoff:3.500A) Processing helix chain 'D' and resid 1228 through 1240 Processing helix chain 'D' and resid 1249 through 1254 removed outlier: 3.547A pdb=" N ILE D1254 " --> pdb=" O GLU D1250 " (cutoff:3.500A) Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 removed outlier: 3.563A pdb=" N ASN D1269 " --> pdb=" O ASN D1265 " (cutoff:3.500A) Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.938A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN E 37 " --> pdb=" O GLY E 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 33 through 37' Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 49 through 70 Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'F' and resid 212 through 221 removed outlier: 3.577A pdb=" N LEU F 221 " --> pdb=" O LYS F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 236 Processing helix chain 'F' and resid 242 through 268 removed outlier: 3.531A pdb=" N GLU F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 308 removed outlier: 3.628A pdb=" N ASP F 289 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 316 through 334 removed outlier: 3.983A pdb=" N LEU F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 362 removed outlier: 3.890A pdb=" N TYR F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 390 Processing helix chain 'F' and resid 395 through 404 Processing helix chain 'F' and resid 406 through 417 Processing helix chain 'F' and resid 434 through 438 Processing helix chain 'F' and resid 448 through 466 Processing helix chain 'F' and resid 470 through 479 Processing helix chain 'F' and resid 488 through 497 Processing helix chain 'F' and resid 500 through 515 removed outlier: 3.549A pdb=" N LYS F 513 " --> pdb=" O LYS F 509 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG F 515 " --> pdb=" O MET F 511 " (cutoff:3.500A) Processing helix chain 'F' and resid 516 through 522 removed outlier: 4.345A pdb=" N VAL F 522 " --> pdb=" O SER F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 527 Processing helix chain 'J' and resid 80 through 89 removed outlier: 3.651A pdb=" N ARG J 88 " --> pdb=" O MET J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 110 Processing helix chain 'M' and resid 64 through 75 Processing helix chain 'M' and resid 84 through 99 removed outlier: 3.520A pdb=" N ARG M 88 " --> pdb=" O ASN M 84 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY M 99 " --> pdb=" O LYS M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 118 removed outlier: 4.223A pdb=" N GLU M 117 " --> pdb=" O ARG M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 143 Processing helix chain 'M' and resid 146 through 160 removed outlier: 3.873A pdb=" N ALA M 159 " --> pdb=" O ASP M 155 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA M 160 " --> pdb=" O GLU M 156 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 3.579A pdb=" N GLU A 24 " --> pdb=" O THR A 8 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.488A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 141 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.721A pdb=" N GLY A 103 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 126 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 15 removed outlier: 6.736A pdb=" N ARG B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ARG B 18 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N THR B 198 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N GLN B 20 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL B 196 " --> pdb=" O GLN B 20 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N VAL B 22 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU B 194 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N GLU B 24 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU B 192 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N PHE B 189 " --> pdb=" O ALA B 180 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA B 180 " --> pdb=" O PHE B 189 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LYS B 191 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL B 178 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE B 193 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR B 176 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASP B 195 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL B 174 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU B 197 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 105 removed outlier: 3.624A pdb=" N GLY B 132 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N GLY B 103 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASP B 130 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL B 105 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU B 128 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU B 141 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA B 50 " --> pdb=" O GLU B 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 147 removed outlier: 3.539A pdb=" N VAL B 147 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.289A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY C 627 " --> pdb=" O VAL C 972 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 96 through 97 removed outlier: 5.109A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU C 133 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 96 through 97 removed outlier: 5.109A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU C 146 " --> pdb=" O ASN C 141 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE C 147 " --> pdb=" O ARG M 47 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG M 47 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER C 149 " --> pdb=" O THR M 45 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR M 45 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL M 36 " --> pdb=" O GLU M 20 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB4, first strand: chain 'C' and resid 376 through 379 removed outlier: 6.471A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 187 through 191 removed outlier: 4.387A pdb=" N HIS C 200 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE C 214 " --> pdb=" O VAL C 202 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AB7, first strand: chain 'C' and resid 505 through 506 removed outlier: 3.508A pdb=" N LYS C 518 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AB9, first strand: chain 'C' and resid 559 through 562 removed outlier: 3.502A pdb=" N VAL C 571 " --> pdb=" O VAL C 559 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.677A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 667 through 671 removed outlier: 6.618A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC4, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 3.673A pdb=" N ALA C 886 " --> pdb=" O MET C1031 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE C 735 " --> pdb=" O LYS C 897 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N LEU C 899 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU C 737 " --> pdb=" O LEU C 899 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 748 through 760 removed outlier: 3.890A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC7, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.610A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 3.766A pdb=" N GLN D 510 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N CYS D 441 " --> pdb=" O MET D 515 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL D 517 " --> pdb=" O CYS D 441 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 7.422A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1067 through 1068 Processing sheet with id=AD2, first strand: chain 'C' and resid 1136 through 1138 removed outlier: 3.512A pdb=" N GLU D 9 " --> pdb=" O LEU C1138 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 93 through 102 removed outlier: 10.298A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.853A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 234 through 235 removed outlier: 6.556A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 336 through 337 Processing sheet with id=AD6, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AD7, first strand: chain 'D' and resid 897 through 899 Processing sheet with id=AD8, first strand: chain 'D' and resid 1053 through 1054 Processing sheet with id=AD9, first strand: chain 'D' and resid 1180 through 1181 removed outlier: 6.724A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 1271 through 1274 removed outlier: 3.592A pdb=" N GLN D1273 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 39 through 42 1181 hydrogen bonds defined for protein. 3363 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 100 hydrogen bonds 200 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 70 stacking parallelities Total time for adding SS restraints: 5.74 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8550 1.33 - 1.46: 5784 1.46 - 1.58: 15098 1.58 - 1.70: 184 1.70 - 1.83: 173 Bond restraints: 29789 Sorted by residual: bond pdb=" C3' DG N 54 " pdb=" C2' DG N 54 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.63e+01 bond pdb=" C1' DT N 59 " pdb=" N1 DT N 59 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.44e+01 bond pdb=" C1' DC T 38 " pdb=" N1 DC T 38 " ideal model delta sigma weight residual 1.468 1.517 -0.049 1.40e-02 5.10e+03 1.21e+01 bond pdb=" C3' DT N 51 " pdb=" C2' DT N 51 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DA N 76 " pdb=" C2' DA N 76 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 ... (remaining 29784 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.51: 40573 4.51 - 9.01: 147 9.01 - 13.52: 13 13.52 - 18.03: 0 18.03 - 22.54: 2 Bond angle restraints: 40735 Sorted by residual: angle pdb=" CA LEU D 244 " pdb=" CB LEU D 244 " pdb=" CG LEU D 244 " ideal model delta sigma weight residual 116.30 138.84 -22.54 3.50e+00 8.16e-02 4.15e+01 angle pdb=" CA LYS B 131 " pdb=" CB LYS B 131 " pdb=" CG LYS B 131 " ideal model delta sigma weight residual 114.10 126.97 -12.87 2.00e+00 2.50e-01 4.14e+01 angle pdb=" P1 POP C2000 " pdb=" O POP C2000 " pdb=" P2 POP C2000 " ideal model delta sigma weight residual 139.66 121.11 18.55 3.00e+00 1.11e-01 3.82e+01 angle pdb=" C ASP F 280 " pdb=" N MET F 281 " pdb=" CA MET F 281 " ideal model delta sigma weight residual 122.06 111.29 10.77 1.86e+00 2.89e-01 3.35e+01 angle pdb=" CA LEU D 579 " pdb=" C LEU D 579 " pdb=" N ASP D 580 " ideal model delta sigma weight residual 119.98 115.07 4.91 8.50e-01 1.38e+00 3.34e+01 ... (remaining 40730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 17162 35.30 - 70.60: 808 70.60 - 105.91: 32 105.91 - 141.21: 0 141.21 - 176.51: 1 Dihedral angle restraints: 18003 sinusoidal: 7966 harmonic: 10037 Sorted by residual: dihedral pdb=" CA THR D1173 " pdb=" C THR D1173 " pdb=" N GLU D1174 " pdb=" CA GLU D1174 " ideal model delta harmonic sigma weight residual 180.00 150.37 29.63 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA THR M 145 " pdb=" C THR M 145 " pdb=" N ASP M 146 " pdb=" CA ASP M 146 " ideal model delta harmonic sigma weight residual 180.00 154.22 25.78 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA MET F 281 " pdb=" C MET F 281 " pdb=" N MET F 282 " pdb=" CA MET F 282 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 18000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 4239 0.087 - 0.174: 385 0.174 - 0.261: 11 0.261 - 0.347: 2 0.347 - 0.434: 3 Chirality restraints: 4640 Sorted by residual: chirality pdb=" CB ILE B 56 " pdb=" CA ILE B 56 " pdb=" CG1 ILE B 56 " pdb=" CG2 ILE B 56 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CB VAL C 571 " pdb=" CA VAL C 571 " pdb=" CG1 VAL C 571 " pdb=" CG2 VAL C 571 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CG LEU B 138 " pdb=" CB LEU B 138 " pdb=" CD1 LEU B 138 " pdb=" CD2 LEU B 138 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 4637 not shown) Planarity restraints: 5037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 232 " 0.105 5.00e-02 4.00e+02 1.55e-01 3.86e+01 pdb=" N PRO C 233 " -0.268 5.00e-02 4.00e+02 pdb=" CA PRO C 233 " 0.084 5.00e-02 4.00e+02 pdb=" CD PRO C 233 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 349 " 0.043 2.00e-02 2.50e+03 3.68e-02 3.38e+01 pdb=" CG TRP F 349 " -0.099 2.00e-02 2.50e+03 pdb=" CD1 TRP F 349 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TRP F 349 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 349 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP F 349 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP F 349 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 349 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 349 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP F 349 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 88 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.03e+01 pdb=" CD GLU C 88 " 0.056 2.00e-02 2.50e+03 pdb=" OE1 GLU C 88 " -0.020 2.00e-02 2.50e+03 pdb=" OE2 GLU C 88 " -0.020 2.00e-02 2.50e+03 ... (remaining 5034 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 892 2.70 - 3.25: 28902 3.25 - 3.80: 47574 3.80 - 4.35: 59551 4.35 - 4.90: 97196 Nonbonded interactions: 234115 Sorted by model distance: nonbonded pdb=" N MET B 1 " pdb=" O GLY B 231 " model vdw 2.149 3.120 nonbonded pdb=" OG1 THR D 924 " pdb=" O THR D 977 " model vdw 2.166 3.040 nonbonded pdb=" O GLN C1086 " pdb=" OG1 THR C1090 " model vdw 2.186 3.040 nonbonded pdb=" O SER C 182 " pdb=" OH TYR C 186 " model vdw 2.198 3.040 nonbonded pdb=" OG1 THR J 34 " pdb=" OE1 GLU J 38 " model vdw 2.198 3.040 ... (remaining 234110 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 'A' and (resid 2 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 223 o \ r (resid 224 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 25 through 226)) selection = (chain 'B' and resid 2 through 226) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.160 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 28.150 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 : 0.005 0.121 29797 Z= 0.269 Angle : 0.844 22.537 40747 Z= 0.491 Chirality : 0.050 0.434 4640 Planarity : 0.007 0.155 5037 Dihedral : 17.711 176.509 11545 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.94 % Favored : 94.00 % Rotamer: Outliers : 0.34 % Allowed : 20.36 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.64 (0.14), residues: 3483 helix: -0.09 (0.13), residues: 1372 sheet: -1.46 (0.26), residues: 385 loop : -1.83 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 762 TYR 0.041 0.002 TYR A 146 PHE 0.040 0.002 PHE M 71 TRP 0.099 0.003 TRP F 349 HIS 0.008 0.001 HIS E 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.27 (29789) covalent geometry : angle 0.84452 / 0.49 (40735) hydrogen bonds : bond 0.13879 / 9.53 ( 1271) hydrogen bonds : angle 6.20195 / 4.40 ( 3563) metal coordination : bond 0.07052 / 3.95 ( 8) metal coordination : angle 0.06078 / 0.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 890 time to evaluate : 0.722 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: A 12 ASP cc_start: 0.7860 (t0) cc_final: 0.6771 (p0) REVERT: A 88 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8540 (mm-30) REVERT: A 100 GLN cc_start: 0.8383 (tp-100) cc_final: 0.8179 (tp-100) REVERT: A 133 LYS cc_start: 0.8704 (tptp) cc_final: 0.8437 (tppt) REVERT: A 189 PHE cc_start: 0.8563 (p90) cc_final: 0.8329 (p90) REVERT: B 1 MET cc_start: 0.7239 (mtp) cc_final: 0.6950 (pmm) REVERT: B 3 ILE cc_start: 0.8919 (tp) cc_final: 0.8219 (pt) REVERT: B 79 ASN cc_start: 0.9324 (m-40) cc_final: 0.9002 (m-40) REVERT: B 95 MET cc_start: 0.7474 (mmp) cc_final: 0.7111 (tmm) REVERT: B 123 MET cc_start: 0.8162 (mmp) cc_final: 0.6783 (mmp) REVERT: B 176 TYR cc_start: 0.8790 (p90) cc_final: 0.8579 (p90) REVERT: B 213 LYS cc_start: 0.8423 (tmmt) cc_final: 0.7903 (mttt) REVERT: C 92 GLU cc_start: 0.7449 (pt0) cc_final: 0.7245 (pt0) REVERT: C 111 ARG cc_start: 0.7569 (ttp-110) cc_final: 0.7191 (ttp-110) REVERT: C 125 LYS cc_start: 0.8502 (mmtp) cc_final: 0.7955 (mmtt) REVERT: C 127 MET cc_start: 0.8631 (ptm) cc_final: 0.8421 (ptp) REVERT: C 154 MET cc_start: 0.8715 (tpp) cc_final: 0.8078 (mpp) REVERT: C 168 ILE cc_start: 0.8965 (mm) cc_final: 0.8710 (mm) REVERT: C 225 ARG cc_start: 0.7536 (ttm-80) cc_final: 0.6890 (ttm110) REVERT: C 307 ASP cc_start: 0.7237 (t0) cc_final: 0.6912 (t0) REVERT: C 366 GLU cc_start: 0.8544 (pt0) cc_final: 0.8213 (pm20) REVERT: C 584 ARG cc_start: 0.8391 (ptt90) cc_final: 0.8167 (ptm160) REVERT: C 607 MET cc_start: 0.8138 (mtt) cc_final: 0.7883 (mtt) REVERT: C 670 TYR cc_start: 0.8892 (m-80) cc_final: 0.8665 (m-80) REVERT: C 694 ASP cc_start: 0.7844 (t0) cc_final: 0.7444 (m-30) REVERT: C 709 ASP cc_start: 0.8288 (t70) cc_final: 0.8031 (t0) REVERT: C 712 GLU cc_start: 0.7853 (pt0) cc_final: 0.7369 (pt0) REVERT: C 743 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7971 (mp0) REVERT: D 7 PHE cc_start: 0.7801 (m-80) cc_final: 0.7440 (m-80) REVERT: D 11 ARG cc_start: 0.8240 (ttp80) cc_final: 0.7977 (ptt180) REVERT: D 37 ARG cc_start: 0.7834 (ttm170) cc_final: 0.7556 (ttm170) REVERT: D 42 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7937 (mm-30) REVERT: D 73 ILE cc_start: 0.7596 (pt) cc_final: 0.7367 (pt) REVERT: D 108 LYS cc_start: 0.8868 (tptt) cc_final: 0.8372 (tppp) REVERT: D 243 GLU cc_start: 0.8709 (pt0) cc_final: 0.7688 (tp30) REVERT: D 294 LYS cc_start: 0.8028 (mtpt) cc_final: 0.7553 (mtmm) REVERT: D 310 MET cc_start: 0.8067 (tpt) cc_final: 0.7615 (tpp) REVERT: D 329 GLN cc_start: 0.8166 (tt0) cc_final: 0.7870 (tm-30) REVERT: D 369 ASN cc_start: 0.8673 (t0) cc_final: 0.8295 (t0) REVERT: D 617 GLU cc_start: 0.8906 (tt0) cc_final: 0.8678 (tt0) REVERT: D 741 ARG cc_start: 0.7285 (ttm-80) cc_final: 0.7049 (ttm-80) REVERT: D 800 ILE cc_start: 0.9067 (tp) cc_final: 0.8627 (tp) REVERT: D 910 LEU cc_start: 0.8500 (mp) cc_final: 0.8264 (mt) REVERT: D 928 ASP cc_start: 0.7757 (m-30) cc_final: 0.7524 (m-30) REVERT: D 972 THR cc_start: 0.8449 (p) cc_final: 0.8178 (p) REVERT: D 1129 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7695 (tp30) REVERT: D 1137 GLU cc_start: 0.8105 (tp30) cc_final: 0.7675 (tp30) REVERT: D 1227 GLN cc_start: 0.7855 (tt0) cc_final: 0.7596 (tt0) REVERT: D 1268 ARG cc_start: 0.7947 (ttp-110) cc_final: 0.7623 (ttp-170) REVERT: D 1279 ARG cc_start: 0.8324 (tpt-90) cc_final: 0.7890 (tpp80) REVERT: E 79 VAL cc_start: 0.7223 (m) cc_final: 0.6686 (t) REVERT: F 229 ARG cc_start: 0.8109 (mtt90) cc_final: 0.7635 (mmt180) REVERT: F 242 ASN cc_start: 0.8037 (p0) cc_final: 0.7353 (p0) REVERT: F 249 LEU cc_start: 0.9315 (mt) cc_final: 0.8787 (mt) REVERT: F 294 HIS cc_start: 0.8751 (t70) cc_final: 0.8305 (t-90) REVERT: F 318 LEU cc_start: 0.8291 (mp) cc_final: 0.7775 (mt) REVERT: F 334 LYS cc_start: 0.8358 (tppt) cc_final: 0.6351 (mttt) REVERT: F 342 LYS cc_start: 0.8176 (tppp) cc_final: 0.7878 (tptm) REVERT: F 372 MET cc_start: 0.8267 (tpp) cc_final: 0.7951 (tpp) REVERT: F 403 MET cc_start: 0.8407 (tpt) cc_final: 0.7865 (tpp) REVERT: F 440 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7779 (mp0) REVERT: F 467 LEU cc_start: 0.8966 (mt) cc_final: 0.8597 (mt) REVERT: F 509 LYS cc_start: 0.8552 (tppp) cc_final: 0.8343 (tppp) REVERT: J 28 GLN cc_start: 0.7246 (pp30) cc_final: 0.6975 (pp30) REVERT: J 40 PHE cc_start: 0.8427 (m-80) cc_final: 0.8146 (m-80) REVERT: J 58 ASN cc_start: 0.8273 (t0) cc_final: 0.7913 (t0) REVERT: M 87 ARG cc_start: 0.9316 (mtp85) cc_final: 0.9019 (ptt180) REVERT: M 94 GLU cc_start: 0.8966 (tt0) cc_final: 0.8451 (tm-30) outliers start: 10 outliers final: 3 residues processed: 894 average time/residue: 0.2062 time to fit residues: 275.5167 Evaluate side-chains 635 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 632 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 491 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 HIS B 119 HIS ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 HIS ** C 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1066 GLN D 375 GLN D 689 HIS ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN F 353 GLN F 461 GLN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN M 133 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.188185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.116698 restraints weight = 41826.067| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.19 r_work: 0.3247 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 29797 Z= 0.166 Angle : 0.734 16.208 40747 Z= 0.384 Chirality : 0.046 0.259 4640 Planarity : 0.006 0.100 5037 Dihedral : 15.651 176.640 4870 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.37 % Favored : 94.60 % Rotamer: Outliers : 4.41 % Allowed : 20.46 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.35 (0.14), residues: 3483 helix: 0.25 (0.14), residues: 1373 sheet: -1.60 (0.25), residues: 389 loop : -1.67 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 504 TYR 0.028 0.002 TYR B 168 PHE 0.018 0.002 PHE C 139 TRP 0.018 0.002 TRP F 349 HIS 0.008 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (29789) covalent geometry : angle 0.73222 / 0.38 (40735) hydrogen bonds : bond 0.04933 / 3.33 ( 1271) hydrogen bonds : angle 5.08901 / 3.57 ( 3563) metal coordination : bond 0.01247 / 0.64 ( 8) metal coordination : angle 2.63438 / 1.26 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 655 time to evaluate : 0.951 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 27 GLU cc_start: 0.8118 (pm20) cc_final: 0.7912 (pm20) REVERT: A 100 GLN cc_start: 0.8595 (tp-100) cc_final: 0.8374 (tp-100) REVERT: A 133 LYS cc_start: 0.8734 (tptp) cc_final: 0.8487 (tppt) REVERT: A 146 TYR cc_start: 0.8735 (t80) cc_final: 0.8518 (t80) REVERT: A 189 PHE cc_start: 0.8786 (p90) cc_final: 0.8219 (p90) REVERT: B 3 ILE cc_start: 0.8849 (tp) cc_final: 0.8444 (tt) REVERT: B 45 SER cc_start: 0.8720 (OUTLIER) cc_final: 0.8285 (m) REVERT: B 72 ASP cc_start: 0.8550 (p0) cc_final: 0.7975 (p0) REVERT: B 79 ASN cc_start: 0.9483 (m-40) cc_final: 0.9136 (m-40) REVERT: B 168 TYR cc_start: 0.8859 (m-10) cc_final: 0.8595 (m-10) REVERT: B 185 GLN cc_start: 0.8747 (pm20) cc_final: 0.8086 (pm20) REVERT: B 196 VAL cc_start: 0.7536 (OUTLIER) cc_final: 0.6799 (m) REVERT: B 213 LYS cc_start: 0.8425 (tmmt) cc_final: 0.7815 (mtmm) REVERT: B 233 GLU cc_start: 0.8153 (tp30) cc_final: 0.7944 (pp20) REVERT: C 62 GLU cc_start: 0.8604 (mt-10) cc_final: 0.7891 (mm-30) REVERT: C 92 GLU cc_start: 0.7675 (pt0) cc_final: 0.7447 (pt0) REVERT: C 111 ARG cc_start: 0.7966 (ttp-110) cc_final: 0.7537 (ttp-110) REVERT: C 127 MET cc_start: 0.8808 (ptm) cc_final: 0.8508 (ptp) REVERT: C 154 MET cc_start: 0.8810 (tpp) cc_final: 0.8409 (tpp) REVERT: C 168 ILE cc_start: 0.8861 (mm) cc_final: 0.8611 (mm) REVERT: C 225 ARG cc_start: 0.7351 (ttm-80) cc_final: 0.6617 (ttm110) REVERT: C 227 ASP cc_start: 0.8595 (t0) cc_final: 0.8287 (t0) REVERT: C 232 GLN cc_start: 0.6267 (OUTLIER) cc_final: 0.5643 (tp40) REVERT: C 307 ASP cc_start: 0.7572 (t0) cc_final: 0.7312 (t0) REVERT: C 355 MET cc_start: 0.4769 (tpt) cc_final: 0.2887 (tpt) REVERT: C 366 GLU cc_start: 0.8805 (pt0) cc_final: 0.8282 (pm20) REVERT: C 440 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.7343 (tpt) REVERT: C 587 VAL cc_start: 0.9054 (OUTLIER) cc_final: 0.8835 (m) REVERT: C 670 TYR cc_start: 0.8942 (m-80) cc_final: 0.8402 (m-80) REVERT: C 709 ASP cc_start: 0.8385 (t70) cc_final: 0.8028 (t0) REVERT: C 770 THR cc_start: 0.8050 (p) cc_final: 0.7747 (t) REVERT: C 818 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7363 (tm-30) REVERT: C 978 ASP cc_start: 0.7695 (p0) cc_final: 0.7486 (p0) REVERT: C 1021 TYR cc_start: 0.9160 (m-10) cc_final: 0.8811 (m-10) REVERT: C 1037 VAL cc_start: 0.8326 (OUTLIER) cc_final: 0.8044 (p) REVERT: D 7 PHE cc_start: 0.7802 (m-80) cc_final: 0.7363 (m-80) REVERT: D 9 GLU cc_start: 0.7873 (mp0) cc_final: 0.7103 (mm-30) REVERT: D 30 LYS cc_start: 0.8834 (mttt) cc_final: 0.8340 (mtmm) REVERT: D 37 ARG cc_start: 0.8388 (ttm170) cc_final: 0.8086 (ttm170) REVERT: D 59 GLU cc_start: 0.7797 (mt-10) cc_final: 0.6870 (mm-30) REVERT: D 66 LYS cc_start: 0.8501 (mmtp) cc_final: 0.8008 (mmtt) REVERT: D 69 ARG cc_start: 0.8258 (tpt-90) cc_final: 0.7831 (tpt-90) REVERT: D 108 LYS cc_start: 0.8884 (tptt) cc_final: 0.8423 (tppp) REVERT: D 205 MET cc_start: 0.1522 (mmt) cc_final: 0.0967 (mmt) REVERT: D 233 GLN cc_start: 0.7843 (mt0) cc_final: 0.7485 (mt0) REVERT: D 243 GLU cc_start: 0.9100 (pt0) cc_final: 0.8207 (tp30) REVERT: D 310 MET cc_start: 0.8251 (tpt) cc_final: 0.7664 (tpp) REVERT: D 329 GLN cc_start: 0.8443 (tt0) cc_final: 0.8013 (tm-30) REVERT: D 445 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8629 (ptpp) REVERT: D 478 ARG cc_start: 0.7842 (mmp80) cc_final: 0.7584 (mmp80) REVERT: D 617 GLU cc_start: 0.9076 (tt0) cc_final: 0.8725 (tt0) REVERT: D 787 GLN cc_start: 0.8479 (tp40) cc_final: 0.8115 (tm-30) REVERT: D 800 ILE cc_start: 0.8759 (tp) cc_final: 0.8516 (tp) REVERT: D 842 GLU cc_start: 0.8427 (pt0) cc_final: 0.8194 (pt0) REVERT: D 910 LEU cc_start: 0.8455 (mp) cc_final: 0.8220 (mt) REVERT: D 972 THR cc_start: 0.8430 (p) cc_final: 0.8211 (p) REVERT: D 1137 GLU cc_start: 0.8554 (tp30) cc_final: 0.8204 (tp30) REVERT: D 1227 GLN cc_start: 0.8110 (tt0) cc_final: 0.7763 (tt0) REVERT: D 1244 LYS cc_start: 0.8386 (mmmm) cc_final: 0.7825 (mmmt) REVERT: D 1268 ARG cc_start: 0.8209 (ttp-110) cc_final: 0.7742 (ttp-170) REVERT: E 79 VAL cc_start: 0.7395 (m) cc_final: 0.7080 (m) REVERT: E 105 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7414 (pm20) REVERT: F 229 ARG cc_start: 0.8063 (mtt90) cc_final: 0.7432 (mmt-90) REVERT: F 319 ASP cc_start: 0.8292 (m-30) cc_final: 0.8039 (m-30) REVERT: F 333 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7758 (mt-10) REVERT: F 381 ARG cc_start: 0.8167 (tmm-80) cc_final: 0.7342 (tmm-80) REVERT: F 440 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7753 (mp0) REVERT: J 101 ARG cc_start: 0.9155 (mmt180) cc_final: 0.8704 (mmm160) REVERT: J 104 LEU cc_start: 0.9121 (mt) cc_final: 0.8188 (mt) REVERT: M 87 ARG cc_start: 0.9466 (mtp85) cc_final: 0.8869 (ptp-170) REVERT: M 94 GLU cc_start: 0.9286 (tt0) cc_final: 0.8727 (tm-30) REVERT: M 132 ARG cc_start: 0.9500 (ttm170) cc_final: 0.8978 (mtt180) outliers start: 129 outliers final: 64 residues processed: 734 average time/residue: 0.1831 time to fit residues: 206.9530 Evaluate side-chains 662 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 590 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 915 ILE Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 445 LYS Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 473 LYS Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 897 ILE Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1039 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1169 ASP Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 512 SER Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 83 ASP Chi-restraints excluded: chain M residue 32 LYS Chi-restraints excluded: chain M residue 34 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 154 optimal weight: 0.7980 chunk 260 optimal weight: 5.9990 chunk 213 optimal weight: 1.9990 chunk 232 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 329 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 294 optimal weight: 9.9990 chunk 347 optimal weight: 50.0000 chunk 88 optimal weight: 10.0000 chunk 261 optimal weight: 20.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN A 119 HIS B 17 ASN B 36 ASN B 119 HIS ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1104 HIS ** F 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.186740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.115463 restraints weight = 41751.472| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.16 r_work: 0.3218 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29797 Z= 0.169 Angle : 0.690 12.284 40747 Z= 0.359 Chirality : 0.045 0.271 4640 Planarity : 0.006 0.082 5037 Dihedral : 15.618 173.690 4868 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.57 % Favored : 94.40 % Rotamer: Outliers : 5.10 % Allowed : 20.01 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.14), residues: 3483 helix: 0.45 (0.14), residues: 1383 sheet: -1.25 (0.27), residues: 354 loop : -1.59 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 558 TYR 0.023 0.002 TYR B 32 PHE 0.015 0.002 PHE C 61 TRP 0.012 0.001 TRP J 82 HIS 0.006 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (29789) covalent geometry : angle 0.68985 / 0.36 (40735) hydrogen bonds : bond 0.04457 / 3.00 ( 1271) hydrogen bonds : angle 4.84932 / 3.40 ( 3563) metal coordination : bond 0.00996 / 0.51 ( 8) metal coordination : angle 1.70037 / 0.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 642 time to evaluate : 0.807 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 12 ASP cc_start: 0.8194 (t0) cc_final: 0.7071 (p0) REVERT: A 100 GLN cc_start: 0.8584 (tp-100) cc_final: 0.8365 (tp-100) REVERT: B 3 ILE cc_start: 0.8705 (tp) cc_final: 0.8356 (tt) REVERT: B 12 ASP cc_start: 0.8114 (t0) cc_final: 0.7568 (m-30) REVERT: B 17 ASN cc_start: 0.7951 (OUTLIER) cc_final: 0.7591 (p0) REVERT: B 27 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7928 (tm-30) REVERT: B 32 TYR cc_start: 0.9080 (m-10) cc_final: 0.8765 (m-10) REVERT: B 45 SER cc_start: 0.8566 (t) cc_final: 0.8356 (m) REVERT: B 79 ASN cc_start: 0.9435 (m-40) cc_final: 0.9125 (m-40) REVERT: B 213 LYS cc_start: 0.8427 (tmmt) cc_final: 0.7800 (mtmm) REVERT: C 62 GLU cc_start: 0.8536 (mt-10) cc_final: 0.7869 (mm-30) REVERT: C 92 GLU cc_start: 0.7635 (pt0) cc_final: 0.7327 (pt0) REVERT: C 111 ARG cc_start: 0.8043 (ttp-110) cc_final: 0.7613 (ttp-110) REVERT: C 127 MET cc_start: 0.8792 (ptm) cc_final: 0.8495 (ptp) REVERT: C 168 ILE cc_start: 0.8896 (mm) cc_final: 0.8643 (mm) REVERT: C 186 TYR cc_start: 0.7567 (m-80) cc_final: 0.7134 (m-80) REVERT: C 225 ARG cc_start: 0.7641 (ttm-80) cc_final: 0.6853 (ttm110) REVERT: C 227 ASP cc_start: 0.8602 (t0) cc_final: 0.8341 (t0) REVERT: C 232 GLN cc_start: 0.6600 (OUTLIER) cc_final: 0.5787 (tp40) REVERT: C 307 ASP cc_start: 0.7556 (t0) cc_final: 0.7348 (t0) REVERT: C 366 GLU cc_start: 0.8906 (pt0) cc_final: 0.8384 (pm20) REVERT: C 401 ARG cc_start: 0.8626 (tpp80) cc_final: 0.8071 (ttm-80) REVERT: C 440 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.7316 (tpt) REVERT: C 570 TYR cc_start: 0.7975 (OUTLIER) cc_final: 0.7606 (t80) REVERT: C 587 VAL cc_start: 0.9066 (OUTLIER) cc_final: 0.8828 (m) REVERT: C 659 THR cc_start: 0.7268 (p) cc_final: 0.6707 (p) REVERT: C 670 TYR cc_start: 0.8963 (m-80) cc_final: 0.8472 (m-80) REVERT: C 709 ASP cc_start: 0.8489 (t70) cc_final: 0.8143 (t0) REVERT: C 723 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.8937 (mm) REVERT: C 770 THR cc_start: 0.8116 (p) cc_final: 0.7819 (t) REVERT: C 818 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7290 (tm-30) REVERT: C 978 ASP cc_start: 0.8000 (p0) cc_final: 0.7735 (p0) REVERT: C 1037 VAL cc_start: 0.8343 (OUTLIER) cc_final: 0.8092 (p) REVERT: C 1039 ASP cc_start: 0.7770 (m-30) cc_final: 0.7528 (t0) REVERT: C 1110 GLU cc_start: 0.8482 (mt-10) cc_final: 0.7902 (mp0) REVERT: C 1136 GLU cc_start: 0.8562 (tt0) cc_final: 0.8333 (tt0) REVERT: D 7 PHE cc_start: 0.7717 (m-80) cc_final: 0.7344 (m-80) REVERT: D 9 GLU cc_start: 0.7867 (mp0) cc_final: 0.7632 (mp0) REVERT: D 30 LYS cc_start: 0.8905 (mttt) cc_final: 0.8423 (mtmm) REVERT: D 37 ARG cc_start: 0.8398 (ttm170) cc_final: 0.8091 (ttm170) REVERT: D 56 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7430 (ttm110) REVERT: D 69 ARG cc_start: 0.8325 (tpt-90) cc_final: 0.7895 (tpt-90) REVERT: D 108 LYS cc_start: 0.8908 (tptt) cc_final: 0.8449 (tppp) REVERT: D 233 GLN cc_start: 0.7834 (mt0) cc_final: 0.7441 (mt0) REVERT: D 243 GLU cc_start: 0.8992 (pt0) cc_final: 0.8282 (tp30) REVERT: D 295 ARG cc_start: 0.7803 (mtm-85) cc_final: 0.7225 (mmm-85) REVERT: D 310 MET cc_start: 0.8001 (tpt) cc_final: 0.7548 (tpp) REVERT: D 329 GLN cc_start: 0.8436 (tt0) cc_final: 0.7844 (tm-30) REVERT: D 464 ASN cc_start: 0.8696 (t0) cc_final: 0.8361 (t0) REVERT: D 617 GLU cc_start: 0.9138 (tt0) cc_final: 0.8846 (tt0) REVERT: D 787 GLN cc_start: 0.8515 (tp40) cc_final: 0.8145 (tm-30) REVERT: D 826 ASN cc_start: 0.7600 (t0) cc_final: 0.6873 (t0) REVERT: D 828 LYS cc_start: 0.8923 (mppt) cc_final: 0.8691 (mmtm) REVERT: D 910 LEU cc_start: 0.8442 (mp) cc_final: 0.8201 (mt) REVERT: D 957 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8772 (tt) REVERT: D 972 THR cc_start: 0.8429 (p) cc_final: 0.8216 (p) REVERT: D 1129 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7973 (mm-30) REVERT: D 1137 GLU cc_start: 0.8585 (tp30) cc_final: 0.8274 (tp30) REVERT: D 1227 GLN cc_start: 0.8074 (tt0) cc_final: 0.7706 (tt0) REVERT: D 1228 GLU cc_start: 0.7785 (tp30) cc_final: 0.7506 (tp30) REVERT: D 1268 ARG cc_start: 0.8243 (ttp-110) cc_final: 0.7862 (ttp-170) REVERT: E 105 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7439 (pm20) REVERT: F 229 ARG cc_start: 0.7918 (mtt90) cc_final: 0.7394 (mmt-90) REVERT: F 252 ARG cc_start: 0.8936 (mtp180) cc_final: 0.8709 (mtp85) REVERT: F 258 TYR cc_start: 0.8026 (t80) cc_final: 0.7807 (t80) REVERT: F 282 MET cc_start: 0.9334 (mmm) cc_final: 0.8617 (mmm) REVERT: F 286 ARG cc_start: 0.9148 (mtt90) cc_final: 0.8823 (ptt-90) REVERT: F 333 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7823 (mt-10) REVERT: F 346 TYR cc_start: 0.8284 (t80) cc_final: 0.7866 (t80) REVERT: F 378 LYS cc_start: 0.8579 (ttpt) cc_final: 0.7783 (tptt) REVERT: F 381 ARG cc_start: 0.8242 (tmm-80) cc_final: 0.6532 (tmm-80) REVERT: F 425 GLN cc_start: 0.7818 (pt0) cc_final: 0.7568 (pt0) REVERT: F 440 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7700 (mp0) REVERT: F 511 MET cc_start: 0.9050 (tpt) cc_final: 0.8413 (tpt) REVERT: J 90 SER cc_start: 0.9043 (t) cc_final: 0.8793 (t) REVERT: M 36 VAL cc_start: 0.9222 (OUTLIER) cc_final: 0.8328 (m) REVERT: M 75 ARG cc_start: 0.7969 (mmt-90) cc_final: 0.7523 (mmt90) REVERT: M 87 ARG cc_start: 0.9495 (mtp85) cc_final: 0.8940 (ptp-170) REVERT: M 94 GLU cc_start: 0.9267 (tt0) cc_final: 0.8729 (tm-30) REVERT: M 126 ARG cc_start: 0.9325 (ttp80) cc_final: 0.9120 (ttp80) outliers start: 149 outliers final: 84 residues processed: 739 average time/residue: 0.1773 time to fit residues: 203.1758 Evaluate side-chains 672 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 577 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 915 ILE Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 473 LYS Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 718 ASP Chi-restraints excluded: chain D residue 897 ILE Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 1039 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain D residue 1169 ASP Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 466 THR Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 83 ASP Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 32 LYS Chi-restraints excluded: chain M residue 34 TYR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 338 optimal weight: 40.0000 chunk 95 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 218 optimal weight: 6.9990 chunk 206 optimal weight: 0.9990 chunk 153 optimal weight: 0.0670 chunk 72 optimal weight: 9.9990 chunk 336 optimal weight: 40.0000 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 HIS B 119 HIS ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN D 854 HIS E 69 ASN ** F 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 461 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 = 0.4235 r_free = 0.4235 target = 0.185651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.112333 restraints weight = 41672.658| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.20 r_work: 0.3183 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 29797 Z= 0.191 Angle : 0.699 11.502 40747 Z= 0.363 Chirality : 0.046 0.352 4640 Planarity : 0.005 0.073 5037 Dihedral : 15.620 172.872 4868 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 5.47 % Allowed : 20.49 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.14), residues: 3483 helix: 0.54 (0.14), residues: 1379 sheet: -1.44 (0.26), residues: 381 loop : -1.47 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 830 TYR 0.029 0.002 TYR B 168 PHE 0.017 0.002 PHE D 651 TRP 0.011 0.001 TRP D 723 HIS 0.006 0.001 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (29789) covalent geometry : angle 0.69810 / 0.36 (40735) hydrogen bonds : bond 0.04341 / 2.94 ( 1271) hydrogen bonds : angle 4.80124 / 3.37 ( 3563) metal coordination : bond 0.01013 / 0.51 ( 8) metal coordination : angle 2.16401 / 1.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 599 time to evaluate : 0.849 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 71 GLU cc_start: 0.7138 (mp0) cc_final: 0.6903 (mp0) REVERT: A 189 PHE cc_start: 0.8547 (p90) cc_final: 0.7891 (p90) REVERT: B 12 ASP cc_start: 0.8094 (t0) cc_final: 0.7546 (m-30) REVERT: B 27 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7990 (tm-30) REVERT: B 45 SER cc_start: 0.8663 (t) cc_final: 0.8436 (m) REVERT: B 71 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8800 (mp0) REVERT: B 99 LYS cc_start: 0.9505 (tppt) cc_final: 0.9033 (tptt) REVERT: B 110 ILE cc_start: 0.8955 (mm) cc_final: 0.8473 (tp) REVERT: B 168 TYR cc_start: 0.8797 (m-10) cc_final: 0.8540 (m-80) REVERT: B 200 ASN cc_start: 0.8274 (p0) cc_final: 0.8045 (p0) REVERT: B 213 LYS cc_start: 0.8440 (tmmt) cc_final: 0.7811 (mtmm) REVERT: C 62 GLU cc_start: 0.8588 (mt-10) cc_final: 0.7948 (mm-30) REVERT: C 92 GLU cc_start: 0.7669 (pt0) cc_final: 0.7397 (pt0) REVERT: C 111 ARG cc_start: 0.8065 (ttp-110) cc_final: 0.7685 (ttp-110) REVERT: C 127 MET cc_start: 0.8833 (ptm) cc_final: 0.8470 (ptp) REVERT: C 168 ILE cc_start: 0.8905 (mm) cc_final: 0.8618 (mm) REVERT: C 186 TYR cc_start: 0.7561 (m-80) cc_final: 0.7322 (m-80) REVERT: C 225 ARG cc_start: 0.7778 (ttm-80) cc_final: 0.6986 (ttm110) REVERT: C 227 ASP cc_start: 0.8599 (t0) cc_final: 0.8334 (t0) REVERT: C 355 MET cc_start: 0.4925 (tpt) cc_final: 0.2998 (tpt) REVERT: C 366 GLU cc_start: 0.9022 (pt0) cc_final: 0.8486 (pm20) REVERT: C 373 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.7718 (m-80) REVERT: C 440 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.7312 (tpt) REVERT: C 570 TYR cc_start: 0.8064 (OUTLIER) cc_final: 0.7744 (t80) REVERT: C 670 TYR cc_start: 0.9023 (m-80) cc_final: 0.8552 (m-80) REVERT: C 709 ASP cc_start: 0.8529 (t70) cc_final: 0.8173 (t0) REVERT: C 770 THR cc_start: 0.8028 (p) cc_final: 0.7754 (t) REVERT: C 779 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8142 (tm-30) REVERT: C 818 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7385 (tm-30) REVERT: C 978 ASP cc_start: 0.8163 (p0) cc_final: 0.7868 (p0) REVERT: C 1037 VAL cc_start: 0.8390 (OUTLIER) cc_final: 0.8185 (p) REVERT: C 1039 ASP cc_start: 0.7819 (m-30) cc_final: 0.7547 (t0) REVERT: C 1044 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.8797 (ttt90) REVERT: C 1136 GLU cc_start: 0.8578 (tt0) cc_final: 0.8358 (tt0) REVERT: D 7 PHE cc_start: 0.7844 (m-80) cc_final: 0.7592 (m-80) REVERT: D 9 GLU cc_start: 0.7928 (mp0) cc_final: 0.7607 (mm-30) REVERT: D 37 ARG cc_start: 0.8427 (ttm170) cc_final: 0.8121 (ttm170) REVERT: D 56 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7554 (ttm110) REVERT: D 66 LYS cc_start: 0.8602 (mmtt) cc_final: 0.8225 (mmtp) REVERT: D 71 LYS cc_start: 0.8430 (ttpp) cc_final: 0.8227 (ttpp) REVERT: D 108 LYS cc_start: 0.8915 (tptt) cc_final: 0.8435 (tppp) REVERT: D 143 MET cc_start: 0.4320 (ptm) cc_final: 0.3980 (tmm) REVERT: D 205 MET cc_start: 0.1860 (mmt) cc_final: 0.1658 (mmt) REVERT: D 233 GLN cc_start: 0.7810 (mt0) cc_final: 0.7503 (mt0) REVERT: D 243 GLU cc_start: 0.9007 (pt0) cc_final: 0.8253 (tp30) REVERT: D 295 ARG cc_start: 0.7739 (mtm-85) cc_final: 0.7195 (mmm-85) REVERT: D 310 MET cc_start: 0.8031 (tpp) cc_final: 0.7574 (tpp) REVERT: D 329 GLN cc_start: 0.8473 (tt0) cc_final: 0.8044 (tm-30) REVERT: D 464 ASN cc_start: 0.8738 (t0) cc_final: 0.8358 (t0) REVERT: D 478 ARG cc_start: 0.7934 (mmp80) cc_final: 0.7727 (mmp80) REVERT: D 580 ASP cc_start: 0.7891 (t0) cc_final: 0.7647 (t0) REVERT: D 617 GLU cc_start: 0.9113 (tt0) cc_final: 0.8804 (tt0) REVERT: D 733 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8090 (ppp) REVERT: D 787 GLN cc_start: 0.8568 (tp40) cc_final: 0.8168 (tm-30) REVERT: D 790 ARG cc_start: 0.8641 (tpp80) cc_final: 0.8118 (tpp80) REVERT: D 826 ASN cc_start: 0.7811 (t0) cc_final: 0.7247 (t0) REVERT: D 900 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6760 (mm-30) REVERT: D 910 LEU cc_start: 0.8456 (mp) cc_final: 0.8201 (mt) REVERT: D 1129 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7989 (mm-30) REVERT: D 1227 GLN cc_start: 0.8073 (tt0) cc_final: 0.7804 (mt0) REVERT: D 1228 GLU cc_start: 0.7833 (tp30) cc_final: 0.7473 (tp30) REVERT: D 1244 LYS cc_start: 0.8476 (mmmt) cc_final: 0.8052 (mmmm) REVERT: D 1268 ARG cc_start: 0.8320 (ttp-110) cc_final: 0.7927 (ttp-170) REVERT: E 105 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7463 (pm20) REVERT: F 229 ARG cc_start: 0.7890 (mtt90) cc_final: 0.7495 (mmt-90) REVERT: F 258 TYR cc_start: 0.8034 (t80) cc_final: 0.7825 (t80) REVERT: F 282 MET cc_start: 0.9282 (mmm) cc_final: 0.8715 (mmm) REVERT: F 286 ARG cc_start: 0.9022 (mtt90) cc_final: 0.8580 (mmt-90) REVERT: F 333 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7809 (mt-10) REVERT: F 378 LYS cc_start: 0.8599 (ttpt) cc_final: 0.7846 (tptt) REVERT: F 381 ARG cc_start: 0.8259 (tmm-80) cc_final: 0.6686 (tmm-80) REVERT: F 440 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7658 (mp0) REVERT: M 75 ARG cc_start: 0.7884 (mmt-90) cc_final: 0.7498 (mmt90) REVERT: M 87 ARG cc_start: 0.9389 (mtp85) cc_final: 0.8920 (ptp-170) REVERT: M 94 GLU cc_start: 0.9255 (tt0) cc_final: 0.8711 (tm-30) REVERT: M 126 ARG cc_start: 0.9381 (ttp80) cc_final: 0.9139 (ttp80) outliers start: 160 outliers final: 97 residues processed: 703 average time/residue: 0.1852 time to fit residues: 203.5109 Evaluate side-chains 673 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 568 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 915 ILE Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1044 ARG Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 473 LYS Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 718 ASP Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 878 VAL Chi-restraints excluded: chain D residue 897 ILE Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1033 GLU Chi-restraints excluded: chain D residue 1039 VAL Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain D residue 1169 ASP Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 466 THR Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 83 ASP Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 32 LYS Chi-restraints excluded: chain M residue 34 TYR Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 144 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 94 optimal weight: 0.0970 chunk 72 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 170 optimal weight: 10.0000 chunk 221 optimal weight: 0.9990 chunk 175 optimal weight: 50.0000 chunk 315 optimal weight: 0.9980 chunk 273 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 323 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 HIS B 17 ASN B 119 HIS B 124 HIS C 150 GLN ** C 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 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 = 0.4253 r_free = 0.4253 target = 0.187329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114505 restraints weight = 41667.395| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.20 r_work: 0.3214 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29797 Z= 0.139 Angle : 0.677 14.724 40747 Z= 0.349 Chirality : 0.044 0.272 4640 Planarity : 0.005 0.081 5037 Dihedral : 15.596 172.509 4868 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.79 % Favored : 95.18 % Rotamer: Outliers : 4.28 % Allowed : 22.17 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.84 (0.14), residues: 3483 helix: 0.72 (0.14), residues: 1371 sheet: -1.40 (0.26), residues: 377 loop : -1.42 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG J 110 TYR 0.019 0.001 TYR M 34 PHE 0.022 0.001 PHE C 153 TRP 0.013 0.001 TRP D 723 HIS 0.006 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (29789) covalent geometry : angle 0.67622 / 0.35 (40735) hydrogen bonds : bond 0.04093 / 2.74 ( 1271) hydrogen bonds : angle 4.68807 / 3.29 ( 3563) metal coordination : bond 0.00724 / 0.36 ( 8) metal coordination : angle 2.02677 / 0.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 595 time to evaluate : 0.920 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 71 GLU cc_start: 0.7190 (mp0) cc_final: 0.6988 (mp0) REVERT: A 189 PHE cc_start: 0.8384 (p90) cc_final: 0.7840 (p90) REVERT: B 12 ASP cc_start: 0.8086 (t0) cc_final: 0.7560 (m-30) REVERT: B 27 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7972 (tm-30) REVERT: B 71 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8755 (mp0) REVERT: B 79 ASN cc_start: 0.9450 (m-40) cc_final: 0.9020 (m-40) REVERT: B 95 MET cc_start: 0.7911 (mmp) cc_final: 0.7137 (tpp) REVERT: B 99 LYS cc_start: 0.9511 (tppt) cc_final: 0.9109 (tptt) REVERT: B 141 GLU cc_start: 0.8374 (pt0) cc_final: 0.8093 (pm20) REVERT: B 144 ARG cc_start: 0.8217 (mtm180) cc_final: 0.7639 (mtm-85) REVERT: B 213 LYS cc_start: 0.8398 (tmmt) cc_final: 0.7771 (mttt) REVERT: C 62 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7839 (mm-30) REVERT: C 92 GLU cc_start: 0.7615 (pt0) cc_final: 0.7335 (pt0) REVERT: C 111 ARG cc_start: 0.8032 (ttp-110) cc_final: 0.7634 (ttp-110) REVERT: C 127 MET cc_start: 0.8810 (ptm) cc_final: 0.8440 (ptp) REVERT: C 136 THR cc_start: 0.8328 (m) cc_final: 0.7866 (p) REVERT: C 168 ILE cc_start: 0.8887 (mm) cc_final: 0.8612 (mm) REVERT: C 186 TYR cc_start: 0.7493 (m-80) cc_final: 0.7273 (m-80) REVERT: C 355 MET cc_start: 0.4922 (OUTLIER) cc_final: 0.2795 (tpt) REVERT: C 366 GLU cc_start: 0.9038 (pt0) cc_final: 0.8476 (pm20) REVERT: C 401 ARG cc_start: 0.8698 (tpp-160) cc_final: 0.8349 (tpp-160) REVERT: C 404 MET cc_start: 0.8938 (tmm) cc_final: 0.8646 (tmm) REVERT: C 435 GLN cc_start: 0.7769 (mm-40) cc_final: 0.7555 (mm-40) REVERT: C 440 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.7380 (tpt) REVERT: C 499 SER cc_start: 0.9136 (p) cc_final: 0.8933 (m) REVERT: C 570 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.7701 (t80) REVERT: C 587 VAL cc_start: 0.9121 (OUTLIER) cc_final: 0.8887 (m) REVERT: C 670 TYR cc_start: 0.9013 (m-80) cc_final: 0.8536 (m-80) REVERT: C 709 ASP cc_start: 0.8512 (t70) cc_final: 0.8170 (t0) REVERT: C 723 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8825 (mm) REVERT: C 770 THR cc_start: 0.7935 (p) cc_final: 0.7671 (t) REVERT: C 818 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7342 (tm-30) REVERT: C 978 ASP cc_start: 0.8043 (p0) cc_final: 0.7739 (p0) REVERT: C 1021 TYR cc_start: 0.9212 (m-80) cc_final: 0.8958 (m-10) REVERT: C 1037 VAL cc_start: 0.8357 (OUTLIER) cc_final: 0.8127 (p) REVERT: C 1039 ASP cc_start: 0.7784 (m-30) cc_final: 0.7486 (t0) REVERT: C 1136 GLU cc_start: 0.8526 (tt0) cc_final: 0.8325 (tt0) REVERT: D 7 PHE cc_start: 0.7894 (m-80) cc_final: 0.7596 (m-80) REVERT: D 9 GLU cc_start: 0.7915 (mp0) cc_final: 0.7706 (mp0) REVERT: D 37 ARG cc_start: 0.8384 (ttm170) cc_final: 0.8094 (ttm170) REVERT: D 56 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7311 (ttm110) REVERT: D 59 GLU cc_start: 0.7401 (mt-10) cc_final: 0.6478 (mt-10) REVERT: D 71 LYS cc_start: 0.8367 (ttpp) cc_final: 0.8139 (ttpp) REVERT: D 108 LYS cc_start: 0.8950 (tptt) cc_final: 0.8437 (tppp) REVERT: D 205 MET cc_start: 0.1913 (mmt) cc_final: 0.1681 (mmt) REVERT: D 242 ARG cc_start: 0.9090 (mtm110) cc_final: 0.8777 (mtm110) REVERT: D 243 GLU cc_start: 0.8974 (pt0) cc_final: 0.8271 (tp30) REVERT: D 295 ARG cc_start: 0.7762 (mtm-85) cc_final: 0.7243 (mmm-85) REVERT: D 310 MET cc_start: 0.7980 (tpp) cc_final: 0.7669 (mmm) REVERT: D 329 GLN cc_start: 0.8448 (tt0) cc_final: 0.8026 (tm-30) REVERT: D 464 ASN cc_start: 0.8764 (t0) cc_final: 0.8546 (t0) REVERT: D 580 ASP cc_start: 0.7817 (t0) cc_final: 0.7526 (t0) REVERT: D 617 GLU cc_start: 0.9041 (tt0) cc_final: 0.8810 (tt0) REVERT: D 733 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.8079 (ppp) REVERT: D 787 GLN cc_start: 0.8556 (tp40) cc_final: 0.8186 (tm-30) REVERT: D 826 ASN cc_start: 0.7642 (t0) cc_final: 0.7178 (t0) REVERT: D 842 GLU cc_start: 0.8333 (pt0) cc_final: 0.8048 (pt0) REVERT: D 910 LEU cc_start: 0.8447 (mp) cc_final: 0.8203 (mt) REVERT: D 1129 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7961 (mm-30) REVERT: D 1228 GLU cc_start: 0.7737 (tp30) cc_final: 0.7509 (mt-10) REVERT: D 1268 ARG cc_start: 0.8299 (ttp-110) cc_final: 0.7881 (ttp-170) REVERT: E 87 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8353 (tt) REVERT: E 105 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7366 (pm20) REVERT: F 229 ARG cc_start: 0.7890 (mtt90) cc_final: 0.7065 (mmt180) REVERT: F 248 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8703 (tm-30) REVERT: F 251 LYS cc_start: 0.9049 (mtmt) cc_final: 0.8818 (mmtm) REVERT: F 258 TYR cc_start: 0.8088 (t80) cc_final: 0.7875 (t80) REVERT: F 282 MET cc_start: 0.9261 (mmm) cc_final: 0.8757 (mmm) REVERT: F 286 ARG cc_start: 0.8983 (mtt90) cc_final: 0.8549 (mmt-90) REVERT: F 292 LYS cc_start: 0.9153 (ptmm) cc_final: 0.8775 (pttp) REVERT: F 308 LYS cc_start: 0.8736 (tttt) cc_final: 0.8466 (tttt) REVERT: F 322 GLN cc_start: 0.8598 (mm110) cc_final: 0.8320 (mm110) REVERT: F 333 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7894 (mt-10) REVERT: F 342 LYS cc_start: 0.8149 (tppt) cc_final: 0.7422 (tppp) REVERT: F 440 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7653 (mp0) REVERT: F 470 ARG cc_start: 0.9002 (ttt180) cc_final: 0.8485 (tpt-90) REVERT: M 75 ARG cc_start: 0.7858 (mmt-90) cc_final: 0.7475 (mmt90) REVERT: M 87 ARG cc_start: 0.9398 (mtp85) cc_final: 0.8882 (ptp-170) REVERT: M 94 GLU cc_start: 0.9255 (tt0) cc_final: 0.8698 (tm-30) REVERT: M 126 ARG cc_start: 0.9430 (ttp80) cc_final: 0.9199 (ttp80) outliers start: 125 outliers final: 86 residues processed: 670 average time/residue: 0.1772 time to fit residues: 185.7578 Evaluate side-chains 651 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 555 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 915 ILE Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 718 ASP Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 897 ILE Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 953 LEU Chi-restraints excluded: chain D residue 1039 VAL Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain D residue 1169 ASP Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 271 GLU Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 465 ASP Chi-restraints excluded: chain F residue 466 THR Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 32 LYS Chi-restraints excluded: chain M residue 34 TYR Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 109 ARG Chi-restraints excluded: chain M residue 111 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 297 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 233 optimal weight: 5.9990 chunk 191 optimal weight: 0.9990 chunk 97 optimal weight: 0.0040 chunk 41 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 HIS B 17 ASN B 119 HIS ** C 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 866 ASN ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1227 GLN ** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.187028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.114405 restraints weight = 41593.063| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.19 r_work: 0.3214 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29797 Z= 0.142 Angle : 0.664 10.703 40747 Z= 0.344 Chirality : 0.044 0.274 4640 Planarity : 0.005 0.078 5037 Dihedral : 15.575 171.932 4868 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.74 % Favored : 95.23 % Rotamer: Outliers : 4.65 % Allowed : 22.85 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.71 (0.14), residues: 3483 helix: 0.87 (0.14), residues: 1368 sheet: -1.38 (0.26), residues: 388 loop : -1.36 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 79 TYR 0.019 0.001 TYR M 34 PHE 0.014 0.001 PHE F 438 TRP 0.012 0.001 TRP D 723 HIS 0.006 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (29789) covalent geometry : angle 0.66344 / 0.34 (40735) hydrogen bonds : bond 0.03970 / 2.67 ( 1271) hydrogen bonds : angle 4.59932 / 3.23 ( 3563) metal coordination : bond 0.00707 / 0.36 ( 8) metal coordination : angle 2.20181 / 1.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 578 time to evaluate : 0.830 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: A 12 ASP cc_start: 0.8249 (t0) cc_final: 0.7503 (m-30) REVERT: A 71 GLU cc_start: 0.7267 (mp0) cc_final: 0.7030 (mp0) REVERT: A 151 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8235 (mp10) REVERT: A 189 PHE cc_start: 0.8338 (p90) cc_final: 0.7877 (p90) REVERT: B 12 ASP cc_start: 0.8132 (t0) cc_final: 0.7627 (m-30) REVERT: B 79 ASN cc_start: 0.9440 (m-40) cc_final: 0.9027 (m-40) REVERT: B 95 MET cc_start: 0.7826 (mmp) cc_final: 0.7184 (tpp) REVERT: B 99 LYS cc_start: 0.9499 (tppt) cc_final: 0.9150 (tptt) REVERT: B 124 HIS cc_start: 0.8486 (t-90) cc_final: 0.7973 (t-90) REVERT: B 141 GLU cc_start: 0.8377 (pt0) cc_final: 0.8091 (pm20) REVERT: B 190 ASP cc_start: 0.8921 (m-30) cc_final: 0.8653 (m-30) REVERT: B 213 LYS cc_start: 0.8410 (tmmt) cc_final: 0.7790 (mttt) REVERT: C 62 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8012 (mm-30) REVERT: C 92 GLU cc_start: 0.7623 (pt0) cc_final: 0.7366 (pt0) REVERT: C 127 MET cc_start: 0.8804 (ptm) cc_final: 0.8443 (ptp) REVERT: C 168 ILE cc_start: 0.8881 (mm) cc_final: 0.8611 (mm) REVERT: C 186 TYR cc_start: 0.7490 (m-80) cc_final: 0.7281 (m-80) REVERT: C 225 ARG cc_start: 0.7907 (ttm-80) cc_final: 0.7107 (ttm110) REVERT: C 227 ASP cc_start: 0.8588 (t0) cc_final: 0.8311 (t0) REVERT: C 355 MET cc_start: 0.5008 (OUTLIER) cc_final: 0.2910 (tpt) REVERT: C 366 GLU cc_start: 0.9052 (pt0) cc_final: 0.8501 (pm20) REVERT: C 373 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.7747 (m-80) REVERT: C 401 ARG cc_start: 0.8637 (tpp-160) cc_final: 0.8356 (tpp-160) REVERT: C 435 GLN cc_start: 0.7742 (mm-40) cc_final: 0.7530 (mm-40) REVERT: C 440 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.7406 (tpt) REVERT: C 570 TYR cc_start: 0.7990 (OUTLIER) cc_final: 0.7692 (t80) REVERT: C 587 VAL cc_start: 0.9123 (OUTLIER) cc_final: 0.8882 (m) REVERT: C 670 TYR cc_start: 0.9017 (m-80) cc_final: 0.8510 (m-80) REVERT: C 709 ASP cc_start: 0.8497 (t70) cc_final: 0.8156 (t0) REVERT: C 723 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8796 (mm) REVERT: C 770 THR cc_start: 0.8052 (p) cc_final: 0.7753 (t) REVERT: C 818 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7303 (tm-30) REVERT: C 978 ASP cc_start: 0.7970 (p0) cc_final: 0.7726 (p0) REVERT: C 1021 TYR cc_start: 0.9216 (m-80) cc_final: 0.8969 (m-10) REVERT: C 1037 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8125 (p) REVERT: C 1039 ASP cc_start: 0.7771 (m-30) cc_final: 0.7484 (t0) REVERT: C 1044 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8737 (ttt90) REVERT: D 7 PHE cc_start: 0.7891 (m-80) cc_final: 0.7642 (m-80) REVERT: D 9 GLU cc_start: 0.7896 (mp0) cc_final: 0.7449 (mp0) REVERT: D 30 LYS cc_start: 0.8893 (mttt) cc_final: 0.8533 (mtmm) REVERT: D 37 ARG cc_start: 0.8376 (ttm170) cc_final: 0.8086 (ttm170) REVERT: D 56 ARG cc_start: 0.7962 (ptp-110) cc_final: 0.7285 (ttm110) REVERT: D 59 GLU cc_start: 0.7461 (mt-10) cc_final: 0.6565 (mt-10) REVERT: D 66 LYS cc_start: 0.8502 (mmtt) cc_final: 0.8236 (mmtm) REVERT: D 71 LYS cc_start: 0.8383 (ttpp) cc_final: 0.8147 (ttpp) REVERT: D 108 LYS cc_start: 0.8971 (tptt) cc_final: 0.8460 (tppp) REVERT: D 143 MET cc_start: 0.4460 (OUTLIER) cc_final: 0.4214 (tmm) REVERT: D 205 MET cc_start: 0.1777 (mmt) cc_final: 0.1515 (mmt) REVERT: D 242 ARG cc_start: 0.9074 (mtm110) cc_final: 0.8751 (mtm110) REVERT: D 243 GLU cc_start: 0.8973 (pt0) cc_final: 0.8302 (tp30) REVERT: D 295 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.7278 (mmm-85) REVERT: D 310 MET cc_start: 0.7971 (tpp) cc_final: 0.7675 (mmm) REVERT: D 329 GLN cc_start: 0.8440 (tt0) cc_final: 0.8020 (tm-30) REVERT: D 445 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8614 (ptpp) REVERT: D 464 ASN cc_start: 0.8755 (t0) cc_final: 0.8501 (t0) REVERT: D 580 ASP cc_start: 0.7797 (t0) cc_final: 0.7500 (t0) REVERT: D 617 GLU cc_start: 0.9094 (tt0) cc_final: 0.8876 (tt0) REVERT: D 733 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8105 (ppp) REVERT: D 787 GLN cc_start: 0.8560 (tp40) cc_final: 0.8178 (tm-30) REVERT: D 790 ARG cc_start: 0.8610 (tpp80) cc_final: 0.8278 (tpp80) REVERT: D 826 ASN cc_start: 0.7702 (t0) cc_final: 0.7231 (t0) REVERT: D 842 GLU cc_start: 0.8328 (pt0) cc_final: 0.8038 (pt0) REVERT: D 910 LEU cc_start: 0.8443 (mp) cc_final: 0.8213 (mt) REVERT: D 1129 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8007 (mm-30) REVERT: D 1268 ARG cc_start: 0.8278 (ttp-110) cc_final: 0.7861 (ttp-170) REVERT: D 1279 ARG cc_start: 0.9010 (tpp80) cc_final: 0.8696 (tpp80) REVERT: E 105 GLU cc_start: 0.7707 (pm20) cc_final: 0.7436 (pm20) REVERT: F 224 SER cc_start: 0.5720 (m) cc_final: 0.5496 (p) REVERT: F 229 ARG cc_start: 0.7676 (mtt90) cc_final: 0.7248 (mmt180) REVERT: F 248 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8714 (tm-30) REVERT: F 251 LYS cc_start: 0.9066 (mtmt) cc_final: 0.8819 (mmtm) REVERT: F 258 TYR cc_start: 0.8103 (t80) cc_final: 0.7645 (t80) REVERT: F 263 MET cc_start: 0.9553 (mtt) cc_final: 0.9132 (mmm) REVERT: F 282 MET cc_start: 0.9313 (mmm) cc_final: 0.8897 (mmm) REVERT: F 286 ARG cc_start: 0.8987 (mtt90) cc_final: 0.8609 (mmt-90) REVERT: F 318 LEU cc_start: 0.8246 (mt) cc_final: 0.8025 (mt) REVERT: F 333 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7752 (mt-10) REVERT: F 372 MET cc_start: 0.8363 (mmm) cc_final: 0.7973 (tpp) REVERT: F 440 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7703 (mp0) REVERT: F 470 ARG cc_start: 0.9022 (ttt180) cc_final: 0.8525 (tpt-90) REVERT: M 75 ARG cc_start: 0.7904 (mmt-90) cc_final: 0.7514 (mmt90) REVERT: M 87 ARG cc_start: 0.9412 (mtp85) cc_final: 0.8891 (mmm160) REVERT: M 94 GLU cc_start: 0.9257 (tt0) cc_final: 0.8705 (tm-30) REVERT: M 126 ARG cc_start: 0.9424 (ttp80) cc_final: 0.9197 (ttp80) outliers start: 136 outliers final: 86 residues processed: 665 average time/residue: 0.1703 time to fit residues: 178.7759 Evaluate side-chains 639 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 542 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 915 ILE Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1044 ARG Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 445 LYS Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 718 ASP Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 897 ILE Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 1033 GLU Chi-restraints excluded: chain D residue 1039 VAL Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain D residue 1169 ASP Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 465 ASP Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 32 LYS Chi-restraints excluded: chain M residue 34 TYR Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 37 optimal weight: 4.9990 chunk 173 optimal weight: 50.0000 chunk 223 optimal weight: 2.9990 chunk 45 optimal weight: 0.0000 chunk 341 optimal weight: 5.9990 chunk 351 optimal weight: 50.0000 chunk 342 optimal weight: 30.0000 chunk 236 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 248 optimal weight: 8.9990 overall best weight: 2.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 HIS B 17 ASN B 119 HIS C 141 ASN ** C 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 866 ASN ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 ASN ** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 22 HIS ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.183956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.110167 restraints weight = 41663.785| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.17 r_work: 0.3154 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 29797 Z= 0.226 Angle : 0.726 14.802 40747 Z= 0.372 Chirality : 0.046 0.308 4640 Planarity : 0.005 0.075 5037 Dihedral : 15.607 170.616 4868 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.74 % Favored : 94.23 % Rotamer: Outliers : 5.10 % Allowed : 22.96 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.72 (0.14), residues: 3483 helix: 0.86 (0.14), residues: 1376 sheet: -1.44 (0.26), residues: 383 loop : -1.37 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 186 TYR 0.019 0.002 TYR C1029 PHE 0.018 0.002 PHE F 438 TRP 0.010 0.001 TRP D 723 HIS 0.008 0.001 HIS D 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.23 (29789) covalent geometry : angle 0.72527 / 0.37 (40735) hydrogen bonds : bond 0.04258 / 2.89 ( 1271) hydrogen bonds : angle 4.67477 / 3.28 ( 3563) metal coordination : bond 0.01223 / 0.61 ( 8) metal coordination : angle 2.49953 / 1.21 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 559 time to evaluate : 0.835 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: A 71 GLU cc_start: 0.7535 (mp0) cc_final: 0.7207 (mp0) REVERT: A 189 PHE cc_start: 0.8500 (p90) cc_final: 0.7996 (p90) REVERT: B 12 ASP cc_start: 0.8137 (t0) cc_final: 0.7640 (m-30) REVERT: B 79 ASN cc_start: 0.9450 (m-40) cc_final: 0.9027 (m-40) REVERT: B 91 GLU cc_start: 0.8780 (pm20) cc_final: 0.8396 (pp20) REVERT: B 110 ILE cc_start: 0.9059 (mm) cc_final: 0.8082 (tp) REVERT: B 137 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8406 (mm-30) REVERT: B 185 GLN cc_start: 0.8729 (pm20) cc_final: 0.8516 (pm20) REVERT: B 190 ASP cc_start: 0.8961 (m-30) cc_final: 0.8711 (m-30) REVERT: B 213 LYS cc_start: 0.8450 (tmmt) cc_final: 0.7801 (mttt) REVERT: B 232 ILE cc_start: 0.8511 (mp) cc_final: 0.8270 (mt) REVERT: C 62 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8082 (mm-30) REVERT: C 92 GLU cc_start: 0.7488 (pt0) cc_final: 0.7246 (pt0) REVERT: C 127 MET cc_start: 0.8763 (ptm) cc_final: 0.8397 (ptp) REVERT: C 154 MET cc_start: 0.8522 (mmt) cc_final: 0.7717 (mmm) REVERT: C 160 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8952 (ttm) REVERT: C 168 ILE cc_start: 0.8914 (mm) cc_final: 0.8606 (mm) REVERT: C 186 TYR cc_start: 0.7624 (m-80) cc_final: 0.7374 (m-80) REVERT: C 225 ARG cc_start: 0.8044 (ttm-80) cc_final: 0.7228 (ttm110) REVERT: C 227 ASP cc_start: 0.8659 (t0) cc_final: 0.8345 (t0) REVERT: C 355 MET cc_start: 0.4958 (OUTLIER) cc_final: 0.2863 (tpt) REVERT: C 366 GLU cc_start: 0.9055 (pt0) cc_final: 0.8512 (pm20) REVERT: C 373 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8147 (m-80) REVERT: C 401 ARG cc_start: 0.8652 (tpp-160) cc_final: 0.8410 (tpp-160) REVERT: C 440 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.7345 (tpt) REVERT: C 570 TYR cc_start: 0.8012 (OUTLIER) cc_final: 0.7705 (t80) REVERT: C 579 MET cc_start: 0.7801 (tpt) cc_final: 0.7560 (tpt) REVERT: C 657 TYR cc_start: 0.7970 (p90) cc_final: 0.7559 (p90) REVERT: C 670 TYR cc_start: 0.9063 (m-80) cc_final: 0.8673 (m-80) REVERT: C 709 ASP cc_start: 0.8496 (t70) cc_final: 0.8126 (t0) REVERT: C 770 THR cc_start: 0.8200 (p) cc_final: 0.7908 (t) REVERT: C 818 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7344 (tm-30) REVERT: C 978 ASP cc_start: 0.8209 (p0) cc_final: 0.7911 (p0) REVERT: C 1039 ASP cc_start: 0.7918 (m-30) cc_final: 0.7546 (t0) REVERT: C 1044 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8776 (ttt90) REVERT: D 9 GLU cc_start: 0.7752 (mp0) cc_final: 0.7442 (mm-30) REVERT: D 37 ARG cc_start: 0.8424 (ttm170) cc_final: 0.8124 (ttm170) REVERT: D 56 ARG cc_start: 0.7998 (ptp-110) cc_final: 0.7273 (ttm110) REVERT: D 59 GLU cc_start: 0.7819 (mt-10) cc_final: 0.6764 (mt-10) REVERT: D 71 LYS cc_start: 0.8431 (ttpp) cc_final: 0.8213 (ttpp) REVERT: D 84 ARG cc_start: 0.8729 (ttm-80) cc_final: 0.8492 (ttm-80) REVERT: D 108 LYS cc_start: 0.9051 (tptt) cc_final: 0.8530 (tppp) REVERT: D 143 MET cc_start: 0.4575 (OUTLIER) cc_final: 0.4323 (tmm) REVERT: D 205 MET cc_start: 0.1633 (mmt) cc_final: 0.1362 (mmt) REVERT: D 242 ARG cc_start: 0.9050 (mtm110) cc_final: 0.8695 (mtm110) REVERT: D 295 ARG cc_start: 0.7795 (mtm-85) cc_final: 0.7269 (mmm-85) REVERT: D 310 MET cc_start: 0.8091 (tpp) cc_final: 0.7816 (mmm) REVERT: D 329 GLN cc_start: 0.8465 (tt0) cc_final: 0.8034 (tm-30) REVERT: D 413 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.7587 (m-10) REVERT: D 464 ASN cc_start: 0.8899 (t0) cc_final: 0.8660 (t0) REVERT: D 762 ARG cc_start: 0.7367 (ttp80) cc_final: 0.7134 (ttp80) REVERT: D 787 GLN cc_start: 0.8619 (tp40) cc_final: 0.8220 (tm-30) REVERT: D 790 ARG cc_start: 0.8560 (tpp80) cc_final: 0.8281 (tpp80) REVERT: D 826 ASN cc_start: 0.7946 (t0) cc_final: 0.7436 (t0) REVERT: D 910 LEU cc_start: 0.8450 (mp) cc_final: 0.8180 (mt) REVERT: D 1129 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8005 (tp30) REVERT: D 1228 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7788 (tp30) REVERT: D 1244 LYS cc_start: 0.8532 (mmmt) cc_final: 0.7725 (mmmt) REVERT: D 1268 ARG cc_start: 0.8380 (ttp-110) cc_final: 0.7946 (ttp-170) REVERT: D 1273 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7947 (mm-40) REVERT: D 1279 ARG cc_start: 0.8984 (tpp80) cc_final: 0.8675 (tpp80) REVERT: E 89 GLU cc_start: 0.6366 (tt0) cc_final: 0.6052 (tt0) REVERT: E 102 ASP cc_start: 0.8183 (m-30) cc_final: 0.7677 (m-30) REVERT: E 105 GLU cc_start: 0.7853 (pm20) cc_final: 0.7535 (pm20) REVERT: F 224 SER cc_start: 0.5856 (m) cc_final: 0.5566 (p) REVERT: F 229 ARG cc_start: 0.7700 (mtt90) cc_final: 0.6970 (mmt180) REVERT: F 233 LYS cc_start: 0.9040 (mttt) cc_final: 0.8765 (ptpt) REVERT: F 248 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8742 (tm-30) REVERT: F 251 LYS cc_start: 0.9092 (mtmt) cc_final: 0.8841 (mmtm) REVERT: F 282 MET cc_start: 0.9337 (mmm) cc_final: 0.8907 (mmm) REVERT: F 286 ARG cc_start: 0.9004 (mtt90) cc_final: 0.8622 (mmt-90) REVERT: F 290 ARG cc_start: 0.9281 (mtt90) cc_final: 0.8703 (mtt-85) REVERT: F 333 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7873 (mt-10) REVERT: F 372 MET cc_start: 0.8350 (mmm) cc_final: 0.7941 (tpp) REVERT: F 440 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7725 (mp0) REVERT: F 470 ARG cc_start: 0.9037 (ttt180) cc_final: 0.8532 (tpt-90) REVERT: M 32 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7897 (mppt) REVERT: M 75 ARG cc_start: 0.7925 (mmt-90) cc_final: 0.7523 (mmt90) REVERT: M 87 ARG cc_start: 0.9430 (mtp85) cc_final: 0.8958 (mmm160) REVERT: M 94 GLU cc_start: 0.9268 (tt0) cc_final: 0.8719 (tm-30) REVERT: M 114 ARG cc_start: 0.8273 (mmt180) cc_final: 0.7893 (mmt180) REVERT: M 126 ARG cc_start: 0.9434 (ttp80) cc_final: 0.9206 (ttp80) outliers start: 149 outliers final: 104 residues processed: 651 average time/residue: 0.1792 time to fit residues: 183.5532 Evaluate side-chains 643 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 530 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 915 ILE Chi-restraints excluded: chain C residue 972 VAL Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1044 ARG Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 718 ASP Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 897 ILE Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 1033 GLU Chi-restraints excluded: chain D residue 1039 VAL Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain D residue 1169 ASP Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 465 ASP Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 32 LYS Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 109 ARG Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 144 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 226 optimal weight: 0.4980 chunk 112 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 349 optimal weight: 50.0000 chunk 230 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 239 optimal weight: 3.9990 chunk 257 optimal weight: 1.9990 chunk 306 optimal weight: 0.8980 chunk 336 optimal weight: 0.0370 chunk 123 optimal weight: 9.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 HIS B 17 ASN B 119 HIS ** C 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 866 ASN ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 HIS ** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.186769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.113997 restraints weight = 41656.514| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 3.19 r_work: 0.3206 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 29797 Z= 0.138 Angle : 0.707 15.532 40747 Z= 0.361 Chirality : 0.045 0.277 4640 Planarity : 0.005 0.072 5037 Dihedral : 15.577 170.545 4868 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.48 % Favored : 95.49 % Rotamer: Outliers : 3.73 % Allowed : 24.73 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.61 (0.14), residues: 3483 helix: 0.96 (0.14), residues: 1369 sheet: -1.39 (0.26), residues: 386 loop : -1.30 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 111 TYR 0.045 0.001 TYR F 258 PHE 0.014 0.001 PHE C 139 TRP 0.016 0.001 TRP D 723 HIS 0.010 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (29789) covalent geometry : angle 0.70554 / 0.36 (40735) hydrogen bonds : bond 0.03900 / 2.64 ( 1271) hydrogen bonds : angle 4.55951 / 3.20 ( 3563) metal coordination : bond 0.00720 / 0.36 ( 8) metal coordination : angle 2.31932 / 1.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 559 time to evaluate : 0.888 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: A 133 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8385 (tppt) REVERT: A 189 PHE cc_start: 0.8472 (p90) cc_final: 0.7984 (p90) REVERT: B 12 ASP cc_start: 0.8111 (t0) cc_final: 0.7632 (m-30) REVERT: B 27 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7549 (pp20) REVERT: B 79 ASN cc_start: 0.9431 (m-40) cc_final: 0.8981 (m-40) REVERT: B 95 MET cc_start: 0.8134 (tpp) cc_final: 0.7662 (tpp) REVERT: B 99 LYS cc_start: 0.9245 (tptt) cc_final: 0.8899 (tptt) REVERT: B 110 ILE cc_start: 0.8992 (mm) cc_final: 0.8252 (tp) REVERT: B 124 HIS cc_start: 0.8337 (t-90) cc_final: 0.7916 (t-90) REVERT: B 125 ILE cc_start: 0.9598 (pt) cc_final: 0.9289 (mt) REVERT: B 185 GLN cc_start: 0.8661 (pm20) cc_final: 0.8052 (pm20) REVERT: B 190 ASP cc_start: 0.8912 (m-30) cc_final: 0.8668 (m-30) REVERT: B 213 LYS cc_start: 0.8472 (tmmt) cc_final: 0.7802 (mttt) REVERT: B 232 ILE cc_start: 0.8481 (mp) cc_final: 0.8168 (mt) REVERT: C 121 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7718 (tm-30) REVERT: C 127 MET cc_start: 0.8743 (ptm) cc_final: 0.8013 (ptp) REVERT: C 136 THR cc_start: 0.8283 (m) cc_final: 0.7797 (p) REVERT: C 154 MET cc_start: 0.8426 (mmt) cc_final: 0.7551 (mmm) REVERT: C 168 ILE cc_start: 0.8874 (mm) cc_final: 0.8570 (mm) REVERT: C 225 ARG cc_start: 0.8086 (ttm-80) cc_final: 0.7325 (ttm110) REVERT: C 227 ASP cc_start: 0.8578 (t0) cc_final: 0.8259 (t0) REVERT: C 355 MET cc_start: 0.5058 (OUTLIER) cc_final: 0.2976 (tpt) REVERT: C 366 GLU cc_start: 0.9066 (pt0) cc_final: 0.8511 (pm20) REVERT: C 373 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.7920 (m-80) REVERT: C 401 ARG cc_start: 0.8606 (tpp-160) cc_final: 0.8290 (tpp-160) REVERT: C 435 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7602 (mm-40) REVERT: C 440 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.7675 (tpt) REVERT: C 570 TYR cc_start: 0.8000 (OUTLIER) cc_final: 0.7713 (t80) REVERT: C 579 MET cc_start: 0.7743 (tpt) cc_final: 0.7507 (tpt) REVERT: C 657 TYR cc_start: 0.7872 (p90) cc_final: 0.7492 (p90) REVERT: C 670 TYR cc_start: 0.9002 (m-80) cc_final: 0.8598 (m-80) REVERT: C 709 ASP cc_start: 0.8452 (t70) cc_final: 0.8115 (t0) REVERT: C 770 THR cc_start: 0.8133 (p) cc_final: 0.7844 (t) REVERT: C 818 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7309 (tm-30) REVERT: C 978 ASP cc_start: 0.7894 (p0) cc_final: 0.7662 (p0) REVERT: C 1021 TYR cc_start: 0.9223 (m-80) cc_final: 0.8983 (m-10) REVERT: C 1039 ASP cc_start: 0.7836 (m-30) cc_final: 0.7474 (t0) REVERT: D 37 ARG cc_start: 0.8385 (ttm170) cc_final: 0.8076 (ttm170) REVERT: D 56 ARG cc_start: 0.7991 (ptp-110) cc_final: 0.7284 (ttm110) REVERT: D 59 GLU cc_start: 0.7530 (mt-10) cc_final: 0.6650 (mt-10) REVERT: D 71 LYS cc_start: 0.8413 (ttpp) cc_final: 0.8180 (ttpp) REVERT: D 84 ARG cc_start: 0.8751 (ttm-80) cc_final: 0.8490 (ttm-80) REVERT: D 108 LYS cc_start: 0.8995 (tptt) cc_final: 0.8490 (tppp) REVERT: D 143 MET cc_start: 0.4587 (OUTLIER) cc_final: 0.4315 (tmm) REVERT: D 205 MET cc_start: 0.1620 (mmt) cc_final: 0.1368 (mmt) REVERT: D 242 ARG cc_start: 0.9022 (mtm110) cc_final: 0.8656 (mtm110) REVERT: D 295 ARG cc_start: 0.7788 (mtm-85) cc_final: 0.7177 (mmm-85) REVERT: D 310 MET cc_start: 0.7963 (tpp) cc_final: 0.7624 (mmm) REVERT: D 329 GLN cc_start: 0.8471 (tt0) cc_final: 0.7902 (tm-30) REVERT: D 464 ASN cc_start: 0.8891 (t0) cc_final: 0.8612 (t0) REVERT: D 617 GLU cc_start: 0.9174 (tt0) cc_final: 0.8916 (tt0) REVERT: D 747 ASP cc_start: 0.9117 (t0) cc_final: 0.8758 (t70) REVERT: D 787 GLN cc_start: 0.8602 (tp40) cc_final: 0.8234 (tm-30) REVERT: D 790 ARG cc_start: 0.8525 (tpp80) cc_final: 0.8202 (tpp80) REVERT: D 826 ASN cc_start: 0.7793 (t0) cc_final: 0.7285 (t0) REVERT: D 910 LEU cc_start: 0.8428 (mp) cc_final: 0.8149 (mt) REVERT: D 1129 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7871 (tp30) REVERT: D 1131 GLN cc_start: 0.8525 (mt0) cc_final: 0.8168 (mt0) REVERT: D 1228 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7698 (tp30) REVERT: D 1268 ARG cc_start: 0.8307 (ttp-110) cc_final: 0.7863 (ttp-170) REVERT: D 1279 ARG cc_start: 0.8957 (tpp80) cc_final: 0.8659 (tpp80) REVERT: E 89 GLU cc_start: 0.6202 (tt0) cc_final: 0.5888 (tt0) REVERT: E 105 GLU cc_start: 0.7777 (pm20) cc_final: 0.7461 (pm20) REVERT: F 229 ARG cc_start: 0.7670 (mtt90) cc_final: 0.7054 (mmt180) REVERT: F 246 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8949 (mm-30) REVERT: F 248 GLU cc_start: 0.9071 (tm-30) cc_final: 0.8752 (tm-30) REVERT: F 251 LYS cc_start: 0.9082 (mtmt) cc_final: 0.8829 (mmtm) REVERT: F 263 MET cc_start: 0.9512 (mtt) cc_final: 0.8777 (mmm) REVERT: F 282 MET cc_start: 0.9287 (mmm) cc_final: 0.9070 (mmm) REVERT: F 290 ARG cc_start: 0.9291 (mtt90) cc_final: 0.8674 (mtt-85) REVERT: F 333 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7846 (mt-10) REVERT: F 372 MET cc_start: 0.8372 (mmm) cc_final: 0.7979 (tpp) REVERT: F 440 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7643 (mp0) REVERT: F 470 ARG cc_start: 0.9059 (ttt180) cc_final: 0.7692 (tpt-90) REVERT: M 32 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7760 (mppt) REVERT: M 75 ARG cc_start: 0.7949 (mmt-90) cc_final: 0.7569 (mmt90) REVERT: M 87 ARG cc_start: 0.9428 (mtp85) cc_final: 0.8941 (mmm160) REVERT: M 94 GLU cc_start: 0.9264 (tt0) cc_final: 0.8709 (tm-30) REVERT: M 118 ARG cc_start: 0.8635 (ttp80) cc_final: 0.8402 (ttp80) outliers start: 109 outliers final: 84 residues processed: 622 average time/residue: 0.1723 time to fit residues: 168.7333 Evaluate side-chains 628 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 536 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 824 ILE Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 915 ILE Chi-restraints excluded: chain C residue 972 VAL Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 718 ASP Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 897 ILE Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 1039 VAL Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain D residue 1169 ASP Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 465 ASP Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 81 HIS Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain M residue 32 LYS Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 109 ARG Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 144 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 255 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 335 optimal weight: 20.0000 chunk 288 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 241 optimal weight: 8.9990 chunk 32 optimal weight: 30.0000 chunk 159 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 HIS B 17 ASN B 119 HIS ** C 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 866 ASN ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 461 GLN ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.185409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.112045 restraints weight = 41610.980| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.18 r_work: 0.3182 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29797 Z= 0.172 Angle : 0.723 19.075 40747 Z= 0.366 Chirality : 0.045 0.281 4640 Planarity : 0.005 0.069 5037 Dihedral : 15.584 169.716 4868 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.28 % Favored : 94.69 % Rotamer: Outliers : 3.73 % Allowed : 24.91 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.60 (0.14), residues: 3483 helix: 0.95 (0.14), residues: 1377 sheet: -1.38 (0.26), residues: 381 loop : -1.29 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 470 TYR 0.027 0.001 TYR F 258 PHE 0.015 0.001 PHE C 139 TRP 0.012 0.001 TRP D 723 HIS 0.009 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (29789) covalent geometry : angle 0.72155 / 0.37 (40735) hydrogen bonds : bond 0.03986 / 2.70 ( 1271) hydrogen bonds : angle 4.56039 / 3.20 ( 3563) metal coordination : bond 0.00881 / 0.44 ( 8) metal coordination : angle 2.44447 / 1.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 544 time to evaluate : 0.859 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: A 100 GLN cc_start: 0.8481 (tp-100) cc_final: 0.8052 (tp-100) REVERT: A 189 PHE cc_start: 0.8520 (p90) cc_final: 0.8100 (p90) REVERT: B 12 ASP cc_start: 0.8132 (t0) cc_final: 0.7662 (m-30) REVERT: B 27 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7566 (pp20) REVERT: B 79 ASN cc_start: 0.9427 (m-40) cc_final: 0.8966 (m-40) REVERT: B 99 LYS cc_start: 0.9243 (tptt) cc_final: 0.8854 (tptt) REVERT: B 110 ILE cc_start: 0.9019 (mm) cc_final: 0.8427 (tp) REVERT: B 185 GLN cc_start: 0.8740 (pm20) cc_final: 0.8174 (pm20) REVERT: B 190 ASP cc_start: 0.8922 (m-30) cc_final: 0.8658 (m-30) REVERT: B 213 LYS cc_start: 0.8482 (tmmt) cc_final: 0.7813 (mttt) REVERT: B 232 ILE cc_start: 0.8500 (mp) cc_final: 0.8290 (mt) REVERT: C 127 MET cc_start: 0.8758 (ptm) cc_final: 0.8386 (ptp) REVERT: C 136 THR cc_start: 0.8275 (m) cc_final: 0.7837 (p) REVERT: C 154 MET cc_start: 0.8431 (mmt) cc_final: 0.7604 (mmm) REVERT: C 168 ILE cc_start: 0.8901 (mm) cc_final: 0.8607 (mm) REVERT: C 225 ARG cc_start: 0.8093 (ttm-80) cc_final: 0.7300 (ttm110) REVERT: C 226 ILE cc_start: 0.8567 (mt) cc_final: 0.8262 (tp) REVERT: C 355 MET cc_start: 0.5141 (OUTLIER) cc_final: 0.3026 (tpt) REVERT: C 366 GLU cc_start: 0.9082 (pt0) cc_final: 0.8535 (pm20) REVERT: C 373 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8114 (m-80) REVERT: C 393 MET cc_start: 0.8519 (mmt) cc_final: 0.8200 (mmt) REVERT: C 401 ARG cc_start: 0.8620 (tpp-160) cc_final: 0.8332 (tpp-160) REVERT: C 440 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.7454 (tpt) REVERT: C 570 TYR cc_start: 0.8002 (OUTLIER) cc_final: 0.7726 (t80) REVERT: C 579 MET cc_start: 0.7754 (tpt) cc_final: 0.7494 (tpt) REVERT: C 657 TYR cc_start: 0.7897 (p90) cc_final: 0.7473 (p90) REVERT: C 661 MET cc_start: 0.8377 (tpp) cc_final: 0.7957 (tpp) REVERT: C 670 TYR cc_start: 0.9030 (m-80) cc_final: 0.8612 (m-80) REVERT: C 709 ASP cc_start: 0.8471 (t70) cc_final: 0.8112 (t0) REVERT: C 770 THR cc_start: 0.8179 (p) cc_final: 0.7891 (t) REVERT: C 818 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7322 (tm-30) REVERT: C 961 ASP cc_start: 0.8084 (t0) cc_final: 0.7689 (t0) REVERT: C 978 ASP cc_start: 0.8082 (p0) cc_final: 0.7837 (p0) REVERT: C 1039 ASP cc_start: 0.7830 (m-30) cc_final: 0.7475 (t0) REVERT: C 1044 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8727 (ttt90) REVERT: D 37 ARG cc_start: 0.8392 (ttm170) cc_final: 0.8091 (ttm170) REVERT: D 56 ARG cc_start: 0.8030 (ptp-110) cc_final: 0.7267 (ttm110) REVERT: D 59 GLU cc_start: 0.7675 (mt-10) cc_final: 0.6688 (mt-10) REVERT: D 71 LYS cc_start: 0.8441 (ttpp) cc_final: 0.8225 (ttpp) REVERT: D 84 ARG cc_start: 0.8762 (ttm-80) cc_final: 0.8495 (ttm-80) REVERT: D 108 LYS cc_start: 0.9031 (tptt) cc_final: 0.8523 (tppp) REVERT: D 143 MET cc_start: 0.4726 (OUTLIER) cc_final: 0.4461 (tmm) REVERT: D 205 MET cc_start: 0.1747 (mmt) cc_final: 0.1480 (mmt) REVERT: D 242 ARG cc_start: 0.9012 (mtm110) cc_final: 0.8652 (mtm110) REVERT: D 295 ARG cc_start: 0.7791 (mtm-85) cc_final: 0.7258 (mmm-85) REVERT: D 310 MET cc_start: 0.8047 (tpp) cc_final: 0.7731 (mmm) REVERT: D 329 GLN cc_start: 0.8498 (tt0) cc_final: 0.8028 (tm-30) REVERT: D 413 PHE cc_start: 0.7852 (OUTLIER) cc_final: 0.7459 (m-10) REVERT: D 464 ASN cc_start: 0.8959 (t0) cc_final: 0.8578 (t0) REVERT: D 617 GLU cc_start: 0.9227 (tt0) cc_final: 0.8995 (tt0) REVERT: D 747 ASP cc_start: 0.9138 (t0) cc_final: 0.8813 (t70) REVERT: D 790 ARG cc_start: 0.8534 (tpp80) cc_final: 0.8255 (tpp80) REVERT: D 826 ASN cc_start: 0.7909 (t0) cc_final: 0.7402 (t0) REVERT: D 910 LEU cc_start: 0.8447 (mp) cc_final: 0.8172 (mt) REVERT: D 1129 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8003 (tp30) REVERT: D 1233 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8380 (mp) REVERT: D 1268 ARG cc_start: 0.8322 (ttp-110) cc_final: 0.7864 (ttp-170) REVERT: D 1279 ARG cc_start: 0.8942 (tpp80) cc_final: 0.8643 (tpp80) REVERT: E 42 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8083 (mm-30) REVERT: E 89 GLU cc_start: 0.6145 (tt0) cc_final: 0.5853 (tt0) REVERT: E 102 ASP cc_start: 0.8179 (m-30) cc_final: 0.7656 (m-30) REVERT: F 224 SER cc_start: 0.5742 (m) cc_final: 0.5087 (p) REVERT: F 229 ARG cc_start: 0.7619 (mtt90) cc_final: 0.7167 (mmt180) REVERT: F 233 LYS cc_start: 0.8968 (mttt) cc_final: 0.8691 (mptt) REVERT: F 248 GLU cc_start: 0.9068 (tm-30) cc_final: 0.8769 (tm-30) REVERT: F 251 LYS cc_start: 0.9104 (mtmt) cc_final: 0.8840 (mmtm) REVERT: F 290 ARG cc_start: 0.9288 (mtt90) cc_final: 0.8673 (mtt-85) REVERT: F 333 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7804 (mt-10) REVERT: F 372 MET cc_start: 0.8390 (mmm) cc_final: 0.7991 (tpp) REVERT: F 440 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7686 (mp0) REVERT: F 505 GLN cc_start: 0.9350 (mm110) cc_final: 0.8968 (mm110) REVERT: J 84 MET cc_start: 0.8614 (tpp) cc_final: 0.8317 (tpt) REVERT: M 75 ARG cc_start: 0.7953 (mmt-90) cc_final: 0.7568 (mmt90) REVERT: M 87 ARG cc_start: 0.9426 (mtp85) cc_final: 0.8952 (mmm160) REVERT: M 94 GLU cc_start: 0.9262 (tt0) cc_final: 0.8698 (tm-30) REVERT: M 118 ARG cc_start: 0.8717 (ttp80) cc_final: 0.8474 (ttp80) outliers start: 109 outliers final: 92 residues processed: 611 average time/residue: 0.1777 time to fit residues: 171.0305 Evaluate side-chains 633 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 533 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 586 MET Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 636 ILE Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 915 ILE Chi-restraints excluded: chain C residue 972 VAL Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1044 ARG Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 718 ASP Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 897 ILE Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 1033 GLU Chi-restraints excluded: chain D residue 1039 VAL Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain D residue 1169 ASP Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1233 LEU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 465 ASP Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 81 HIS Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain M residue 32 LYS Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 109 ARG Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 144 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 171 optimal weight: 20.0000 chunk 86 optimal weight: 2.9990 chunk 329 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 164 optimal weight: 0.6980 chunk 188 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 HIS B 17 ASN B 119 HIS C 142 ASN ** C 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 HIS ** 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 = 0.4226 r_free = 0.4226 target = 0.184686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.111068 restraints weight = 41354.232| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.19 r_work: 0.3164 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 29797 Z= 0.196 Angle : 0.742 18.282 40747 Z= 0.376 Chirality : 0.046 0.481 4640 Planarity : 0.006 0.137 5037 Dihedral : 15.609 168.845 4868 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.40 % Favored : 94.57 % Rotamer: Outliers : 3.59 % Allowed : 25.04 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.64 (0.14), residues: 3483 helix: 0.90 (0.14), residues: 1377 sheet: -1.40 (0.26), residues: 381 loop : -1.29 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG M 126 TYR 0.030 0.002 TYR M 89 PHE 0.034 0.002 PHE D1061 TRP 0.011 0.001 TRP D 484 HIS 0.009 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (29789) covalent geometry : angle 0.74065 / 0.38 (40735) hydrogen bonds : bond 0.04037 / 2.74 ( 1271) hydrogen bonds : angle 4.61196 / 3.23 ( 3563) metal coordination : bond 0.01006 / 0.50 ( 8) metal coordination : angle 2.55588 / 1.16 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 536 time to evaluate : 0.823 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: A 189 PHE cc_start: 0.8562 (p90) cc_final: 0.8102 (p90) REVERT: B 1 MET cc_start: 0.7219 (ttm) cc_final: 0.6823 (ttm) REVERT: B 12 ASP cc_start: 0.8153 (t0) cc_final: 0.7672 (m-30) REVERT: B 27 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7535 (pp20) REVERT: B 79 ASN cc_start: 0.9430 (m-40) cc_final: 0.8981 (m-40) REVERT: B 95 MET cc_start: 0.7639 (tpp) cc_final: 0.7207 (tpp) REVERT: B 99 LYS cc_start: 0.9279 (tptt) cc_final: 0.8898 (tptt) REVERT: B 110 ILE cc_start: 0.9098 (mm) cc_final: 0.8311 (tp) REVERT: B 185 GLN cc_start: 0.8758 (pm20) cc_final: 0.8126 (pm20) REVERT: B 190 ASP cc_start: 0.8949 (m-30) cc_final: 0.8687 (m-30) REVERT: B 213 LYS cc_start: 0.8499 (tmmt) cc_final: 0.7829 (mttt) REVERT: B 232 ILE cc_start: 0.8521 (mp) cc_final: 0.8292 (mt) REVERT: C 127 MET cc_start: 0.8742 (ptm) cc_final: 0.8374 (ptp) REVERT: C 136 THR cc_start: 0.8313 (m) cc_final: 0.7882 (p) REVERT: C 154 MET cc_start: 0.8508 (mmt) cc_final: 0.7692 (mmm) REVERT: C 163 LYS cc_start: 0.8755 (mttm) cc_final: 0.8544 (mmtp) REVERT: C 225 ARG cc_start: 0.8170 (ttm-80) cc_final: 0.7342 (ttm110) REVERT: C 226 ILE cc_start: 0.8507 (mt) cc_final: 0.8232 (tp) REVERT: C 355 MET cc_start: 0.5144 (OUTLIER) cc_final: 0.3055 (tpt) REVERT: C 366 GLU cc_start: 0.9158 (pt0) cc_final: 0.8586 (pm20) REVERT: C 373 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.8244 (m-80) REVERT: C 393 MET cc_start: 0.8651 (mmt) cc_final: 0.8320 (mmt) REVERT: C 401 ARG cc_start: 0.8624 (tpp-160) cc_final: 0.8355 (tpp-160) REVERT: C 404 MET cc_start: 0.8678 (tmm) cc_final: 0.8445 (tmm) REVERT: C 440 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.7447 (tpt) REVERT: C 531 LEU cc_start: 0.8868 (mt) cc_final: 0.8658 (mt) REVERT: C 570 TYR cc_start: 0.7983 (OUTLIER) cc_final: 0.7691 (t80) REVERT: C 579 MET cc_start: 0.7805 (tpt) cc_final: 0.7552 (tpt) REVERT: C 651 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8205 (tt0) REVERT: C 657 TYR cc_start: 0.7939 (p90) cc_final: 0.7485 (p90) REVERT: C 661 MET cc_start: 0.8350 (tpp) cc_final: 0.8044 (tpp) REVERT: C 709 ASP cc_start: 0.8438 (t70) cc_final: 0.8084 (t0) REVERT: C 770 THR cc_start: 0.8247 (p) cc_final: 0.7964 (t) REVERT: C 818 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7277 (tm-30) REVERT: C 961 ASP cc_start: 0.8108 (t0) cc_final: 0.7709 (t0) REVERT: C 978 ASP cc_start: 0.8143 (p0) cc_final: 0.7905 (p0) REVERT: C 1039 ASP cc_start: 0.7733 (m-30) cc_final: 0.7423 (t0) REVERT: C 1044 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8775 (ttt90) REVERT: D 37 ARG cc_start: 0.8394 (ttm170) cc_final: 0.8109 (ttp-170) REVERT: D 56 ARG cc_start: 0.8061 (ptp-110) cc_final: 0.7537 (ttm110) REVERT: D 108 LYS cc_start: 0.9055 (tptt) cc_final: 0.8545 (tppp) REVERT: D 143 MET cc_start: 0.4758 (OUTLIER) cc_final: 0.4537 (tmm) REVERT: D 205 MET cc_start: 0.1749 (mmt) cc_final: 0.1488 (mmt) REVERT: D 242 ARG cc_start: 0.9005 (mtm110) cc_final: 0.8634 (mtm110) REVERT: D 295 ARG cc_start: 0.7818 (mtm-85) cc_final: 0.7152 (mmm-85) REVERT: D 310 MET cc_start: 0.8043 (tpp) cc_final: 0.7751 (mmm) REVERT: D 329 GLN cc_start: 0.8510 (tt0) cc_final: 0.8033 (tm-30) REVERT: D 413 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7493 (m-10) REVERT: D 464 ASN cc_start: 0.8992 (t0) cc_final: 0.8617 (t0) REVERT: D 617 GLU cc_start: 0.9230 (tt0) cc_final: 0.9005 (tt0) REVERT: D 650 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8825 (mm) REVERT: D 747 ASP cc_start: 0.9130 (t0) cc_final: 0.8808 (t70) REVERT: D 790 ARG cc_start: 0.8496 (tpp80) cc_final: 0.8236 (tpp80) REVERT: D 826 ASN cc_start: 0.7975 (t0) cc_final: 0.7507 (t0) REVERT: D 910 LEU cc_start: 0.8436 (mp) cc_final: 0.8154 (mt) REVERT: D 1129 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8009 (tp30) REVERT: D 1233 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8421 (mp) REVERT: D 1268 ARG cc_start: 0.8344 (ttp-110) cc_final: 0.7890 (ttp-170) REVERT: E 42 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8177 (mm-30) REVERT: E 89 GLU cc_start: 0.6198 (tt0) cc_final: 0.5906 (tt0) REVERT: E 102 ASP cc_start: 0.8167 (m-30) cc_final: 0.7966 (t70) REVERT: E 105 GLU cc_start: 0.8011 (pm20) cc_final: 0.7689 (pm20) REVERT: F 229 ARG cc_start: 0.7605 (mtt90) cc_final: 0.7268 (mmt180) REVERT: F 248 GLU cc_start: 0.9123 (tm-30) cc_final: 0.8809 (tm-30) REVERT: F 251 LYS cc_start: 0.9106 (mtmt) cc_final: 0.8840 (mmtm) REVERT: F 263 MET cc_start: 0.9527 (mtt) cc_final: 0.9138 (mtt) REVERT: F 283 TRP cc_start: 0.8987 (t-100) cc_final: 0.8519 (t-100) REVERT: F 290 ARG cc_start: 0.9299 (mtt90) cc_final: 0.8630 (mtt-85) REVERT: F 333 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7779 (mt-10) REVERT: F 372 MET cc_start: 0.8392 (mmm) cc_final: 0.7952 (tpp) REVERT: F 440 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7659 (mp0) REVERT: F 505 GLN cc_start: 0.9361 (mm110) cc_final: 0.8969 (mm110) REVERT: J 84 MET cc_start: 0.8658 (tpp) cc_final: 0.8335 (tpt) REVERT: M 75 ARG cc_start: 0.7962 (mmt-90) cc_final: 0.7577 (mmt90) REVERT: M 87 ARG cc_start: 0.9393 (mtp85) cc_final: 0.8958 (mmm160) REVERT: M 94 GLU cc_start: 0.9245 (tt0) cc_final: 0.8690 (tm-30) REVERT: M 118 ARG cc_start: 0.8762 (ttp80) cc_final: 0.8514 (ttp80) outliers start: 105 outliers final: 93 residues processed: 599 average time/residue: 0.1708 time to fit residues: 161.6084 Evaluate side-chains 619 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 517 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 586 MET Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 636 ILE Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 915 ILE Chi-restraints excluded: chain C residue 972 VAL Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1044 ARG Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 718 ASP Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 897 ILE Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 1033 GLU Chi-restraints excluded: chain D residue 1039 VAL Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain D residue 1169 ASP Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1233 LEU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 81 HIS Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain M residue 32 LYS Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 109 ARG Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 144 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 175 optimal weight: 10.0000 chunk 329 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 280 optimal weight: 0.0870 chunk 290 optimal weight: 20.0000 chunk 130 optimal weight: 0.7980 chunk 145 optimal weight: 0.0370 chunk 113 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 181 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 HIS B 17 ASN B 119 HIS C 141 ASN C 476 HIS C 539 HIS ** C 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.187291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114421 restraints weight = 41551.376| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.23 r_work: 0.3213 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 29797 Z= 0.136 Angle : 0.719 19.162 40747 Z= 0.363 Chirality : 0.045 0.435 4640 Planarity : 0.005 0.080 5037 Dihedral : 15.581 168.537 4868 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.74 % Favored : 95.23 % Rotamer: Outliers : 3.32 % Allowed : 25.38 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.54 (0.14), residues: 3483 helix: 1.00 (0.14), residues: 1369 sheet: -1.36 (0.26), residues: 381 loop : -1.23 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 114 TYR 0.045 0.001 TYR C 186 PHE 0.041 0.001 PHE D1061 TRP 0.021 0.001 TRP D 58 HIS 0.009 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (29789) covalent geometry : angle 0.71868 / 0.36 (40735) hydrogen bonds : bond 0.03767 / 2.55 ( 1271) hydrogen bonds : angle 4.51986 / 3.17 ( 3563) metal coordination : bond 0.00556 / 0.28 ( 8) metal coordination : angle 2.12379 / 1.00 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7891.06 seconds wall clock time: 135 minutes 6.62 seconds (8106.62 seconds total)