Starting phenix.real_space_refine on Thu Nov 20 03:07:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6eec_9041/11_2025/6eec_9041_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6eec_9041/11_2025/6eec_9041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6eec_9041/11_2025/6eec_9041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6eec_9041/11_2025/6eec_9041.map" model { file = "/net/cci-nas-00/data/ceres_data/6eec_9041/11_2025/6eec_9041_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6eec_9041/11_2025/6eec_9041_neut_trim.cif" } resolution = 3.55 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= 0.006 sd= 0.103 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 128 5.49 5 Mg 1 5.21 5 S 99 5.16 5 C 18335 2.51 5 N 5337 2.21 5 O 5994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29896 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: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1759 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 220} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 8593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8593 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1048} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 9873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1266, 9873 Classifications: {'peptide': 1266} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 57, 'TRANS': 1204} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 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: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2518 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 310} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "J" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 881 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "O" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1336 Classifications: {'DNA': 65} Link IDs: {'rna3p': 64} Chain: "P" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1289 Classifications: {'DNA': 63} Link IDs: {'rna3p': 62} Chain breaks: 1 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: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'C0L': 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 19132 SG CYS D 891 108.225 61.944 83.263 1.00 76.82 S ATOM 19699 SG CYS D 968 104.599 62.438 85.049 1.00 78.10 S ATOM 19741 SG CYS D 975 105.542 63.855 82.129 1.00 73.35 S ATOM 19759 SG CYS D 978 105.701 60.556 81.261 1.00 75.60 S ATOM 12574 SG CYS D 60 79.742 106.887 124.743 1.00 98.08 S ATOM 12592 SG CYS D 62 78.833 107.222 128.102 1.00 98.16 S ATOM 12727 SG CYS D 78 80.787 104.199 127.363 1.00 91.64 S Time building chain proxies: 6.54, per 1000 atoms: 0.22 Number of scatterers: 29896 At special positions: 0 Unit cell: (131.3, 180.7, 191.1, 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 99 16.00 P 128 15.00 Mg 1 11.99 O 5994 8.00 N 5337 7.00 C 18335 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: 2.69 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 968 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 891 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 62 " Number of angles added : 6 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6464 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 41 sheets defined 42.6% alpha, 11.9% beta 56 base pairs and 94 stacking pairs defined. Time for finding SS restraints: 4.03 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 225 removed outlier: 3.908A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 46 removed outlier: 3.725A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.595A pdb=" N ALA B 209 " --> pdb=" O ARG B 205 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.305A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 removed outlier: 3.694A pdb=" N ALA C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 233 through 241 removed outlier: 3.672A 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: 3.586A pdb=" N ALA C 273 " --> pdb=" O GLY C 269 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP C 276 " --> pdb=" O GLU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 297 removed outlier: 4.241A pdb=" N LEU C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 321 Processing helix chain 'C' and resid 334 through 349 Processing helix chain 'C' and resid 380 through 407 removed outlier: 4.077A pdb=" N ARG C 395 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU C 402 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.907A 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: 3.729A pdb=" N LYS C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 474 removed outlier: 4.333A pdb=" N ARG C 473 " --> pdb=" O GLY C 469 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 469 through 474' Processing helix chain 'C' and resid 534 through 539 removed outlier: 3.847A pdb=" N ARG C 538 " --> pdb=" O ASP C 534 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS C 539 " --> pdb=" O GLU C 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 534 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 637 removed outlier: 4.398A pdb=" N ARG C 633 " --> pdb=" O GLY C 629 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA C 635 " --> pdb=" O GLU C 631 " (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 922 through 926 Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 954 through 958 removed outlier: 4.255A pdb=" N ARG C 958 " --> pdb=" O TRP C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 991 removed outlier: 3.890A 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 1079 removed outlier: 3.821A pdb=" N CYS C1073 " --> pdb=" O GLY C1069 " (cutoff:3.500A) Processing helix chain 'C' and resid 1082 through 1091 Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.274A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.865A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 removed outlier: 3.911A pdb=" N GLN D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER D 24 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 104 through 107 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 removed outlier: 4.238A pdb=" N LYS D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE D 128 " --> pdb=" O ASP D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 147 through 187 removed outlier: 4.126A pdb=" N GLU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 3.520A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 246 removed outlier: 4.393A pdb=" N ASP D 246 " --> pdb=" O ARG D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 250 No H-bonds generated for 'chain 'D' and resid 248 through 250' Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 269 through 284 Processing helix chain 'D' and resid 285 through 305 removed outlier: 3.668A pdb=" N LYS D 289 " --> pdb=" O LYS D 285 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) Processing helix 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: 4.152A 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: 3.607A pdb=" N ASN D 396 " --> pdb=" O GLY D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 405 Processing helix chain 'D' and resid 444 through 452 removed outlier: 4.251A 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 removed outlier: 3.683A pdb=" N ALA D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 492 removed outlier: 4.368A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) 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 578 through 590 removed outlier: 3.835A pdb=" N THR D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 656 through 660 removed outlier: 4.406A pdb=" N GLY D 659 " --> pdb=" O TRP D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 677 removed outlier: 3.665A pdb=" N VAL D 671 " --> pdb=" O THR D 667 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D 677 " --> pdb=" O PHE D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 726 removed outlier: 3.760A pdb=" N GLN D 711 " --> pdb=" O ILE D 707 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.640A pdb=" N ILE D 745 " --> pdb=" O ARG D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 805 removed outlier: 4.107A pdb=" N VAL D 803 " --> pdb=" O ILE D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 818 removed outlier: 3.859A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 3.862A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY D 871 " --> pdb=" O THR D 867 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR D 872 " --> pdb=" O ALA D 868 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 removed outlier: 3.790A pdb=" N ILE D 949 " --> pdb=" O GLY D 945 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1005 Processing helix chain 'D' and resid 1006 through 1010 Processing helix chain 'D' and resid 1027 through 1037 Processing helix chain 'D' and resid 1117 through 1145 Proline residue: D1127 - end of helix removed outlier: 3.872A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 4.274A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN D1160 " --> pdb=" O VAL D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1195 removed outlier: 4.231A 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 1224 Processing helix chain 'D' and resid 1228 through 1240 Processing helix chain 'D' and resid 1248 through 1254 removed outlier: 3.618A pdb=" N ILE D1253 " --> pdb=" O LYS D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.816A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 4.032A 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 71 Processing helix chain 'E' and resid 90 through 102 removed outlier: 3.608A pdb=" N ILE E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 219 removed outlier: 3.804A pdb=" N ALA F 215 " --> pdb=" O ALA F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 236 Processing helix chain 'F' and resid 242 through 266 Processing helix chain 'F' and resid 274 through 308 removed outlier: 5.377A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 335 removed outlier: 3.847A pdb=" N LEU F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 362 removed outlier: 3.909A pdb=" N TYR F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 391 Processing helix chain 'F' and resid 395 through 404 Processing helix chain 'F' and resid 406 through 417 removed outlier: 4.109A pdb=" N LEU F 411 " --> pdb=" O PRO F 407 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU F 412 " --> pdb=" O GLU F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 439 removed outlier: 3.702A pdb=" N ILE F 439 " --> pdb=" O GLY F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 465 Processing helix chain 'F' and resid 468 through 480 Processing helix chain 'F' and resid 488 through 497 Processing helix chain 'F' and resid 499 through 515 Processing helix chain 'F' and resid 516 through 521 Processing helix chain 'F' and resid 523 through 527 removed outlier: 3.600A pdb=" N LEU F 527 " --> pdb=" O ARG F 524 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 87 Processing helix chain 'J' and resid 90 through 110 Processing helix chain 'M' and resid 52 through 57 Processing helix chain 'M' and resid 63 through 75 Processing helix chain 'M' and resid 84 through 99 removed outlier: 3.754A pdb=" N GLY M 99 " --> pdb=" O LYS M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 118 removed outlier: 3.525A pdb=" N GLU M 117 " --> pdb=" O ARG M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 144 Processing helix chain 'M' and resid 146 through 160 removed outlier: 3.851A 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: 6.010A 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: 7.625A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A 141 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.759A pdb=" N GLY A 103 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 22 through 26 removed outlier: 6.153A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 49 Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.342A pdb=" N TYR B 96 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL B 93 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 99 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 134 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER B 53 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA8, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.746A pdb=" N ALA B 126 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB1, first strand: chain 'B' and resid 171 through 175 Processing sheet with id=AB2, first strand: chain 'C' and resid 96 through 97 Processing sheet with id=AB3, first strand: chain 'C' and resid 110 through 112 removed outlier: 5.573A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU C 133 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB5, first strand: chain 'C' and resid 378 through 379 removed outlier: 6.940A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 184 through 191 removed outlier: 3.882A pdb=" N ASP C 188 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 215 through 216 Processing sheet with id=AB8, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AB9, first strand: chain 'C' and resid 505 through 506 removed outlier: 3.616A pdb=" N LYS C 518 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC2, first strand: chain 'C' and resid 558 through 562 Processing sheet with id=AC3, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.187A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 667 through 671 removed outlier: 6.754A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC6, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 3.578A pdb=" N ALA C 886 " --> pdb=" O MET C1031 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 885 " --> pdb=" O GLY C 893 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU C 719 " --> pdb=" O MET C1028 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 748 through 760 removed outlier: 6.090A pdb=" N SER C 749 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LYS C 876 " --> pdb=" O SER C 749 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N HIS C 751 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA C 874 " --> pdb=" O HIS C 751 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU C 753 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR C 872 " --> pdb=" O GLU C 753 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N HIS C 755 " --> pdb=" O ARG C 870 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG C 870 " --> pdb=" O HIS C 755 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE C 757 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LEU C 868 " --> pdb=" O ILE C 757 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA C 759 " --> pdb=" O ASN C 866 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC9, first strand: chain 'C' and resid 801 through 803 Processing sheet with id=AD1, first strand: chain 'C' and resid 1136 through 1138 Processing sheet with id=AD2, first strand: chain 'D' and resid 93 through 102 removed outlier: 3.753A pdb=" N LEU D 97 " --> pdb=" O ASP D 315 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 10.726A pdb=" N ALA D 99 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 10.306A pdb=" N VAL D 313 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 234 through 235 removed outlier: 3.993A pdb=" N TYR D 134 " --> pdb=" O ILE D 235 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE D 136 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ALA D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 329 through 330 removed outlier: 4.002A pdb=" N GLN D 329 " --> pdb=" O SER J 9 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLU F 440 " --> pdb=" O GLY J 8 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 522 through 524 removed outlier: 7.187A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 440 through 441 Processing sheet with id=AD7, first strand: chain 'D' and resid 611 through 612 removed outlier: 3.550A pdb=" N VAL D 635 " --> pdb=" O ALA D 664 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA D 664 " --> pdb=" O VAL D 635 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 898 through 899 removed outlier: 3.804A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 929 through 930 Processing sheet with id=AE1, first strand: chain 'D' and resid 1053 through 1054 Processing sheet with id=AE2, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 6.321A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1271 through 1274 Processing sheet with id=AE4, first strand: chain 'J' and resid 39 through 45 Processing sheet with id=AE5, first strand: chain 'M' and resid 45 through 49 removed outlier: 3.761A pdb=" N ALA M 21 " --> pdb=" O VAL M 36 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LYS M 38 " --> pdb=" O VAL M 19 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N VAL M 19 " --> pdb=" O LYS M 38 " (cutoff:3.500A) 1155 hydrogen bonds defined for protein. 3285 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 145 hydrogen bonds 290 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 94 stacking parallelities Total time for adding SS restraints: 7.38 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 4909 1.27 - 1.41: 7366 1.41 - 1.54: 17933 1.54 - 1.67: 278 1.67 - 1.81: 175 Bond restraints: 30661 Sorted by residual: bond pdb=" C23 C0L C1201 " pdb=" O24 C0L C1201 " ideal model delta sigma weight residual 1.204 1.390 -0.186 2.00e-02 2.50e+03 8.61e+01 bond pdb=" CA TRP D 656 " pdb=" C TRP D 656 " ideal model delta sigma weight residual 1.524 1.412 0.112 1.26e-02 6.30e+03 7.84e+01 bond pdb=" CA ARG D 389 " pdb=" C ARG D 389 " ideal model delta sigma weight residual 1.523 1.430 0.093 1.06e-02 8.90e+03 7.64e+01 bond pdb=" CA ALA D 661 " pdb=" C ALA D 661 " ideal model delta sigma weight residual 1.521 1.414 0.107 1.24e-02 6.50e+03 7.51e+01 bond pdb=" CA SER F 305 " pdb=" C SER F 305 " ideal model delta sigma weight residual 1.523 1.412 0.111 1.30e-02 5.92e+03 7.34e+01 ... (remaining 30656 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.41: 41838 4.41 - 8.81: 199 8.81 - 13.22: 28 13.22 - 17.62: 10 17.62 - 22.03: 1 Bond angle restraints: 42076 Sorted by residual: angle pdb=" C LEU F 306 " pdb=" N ALA F 307 " pdb=" CA ALA F 307 " ideal model delta sigma weight residual 120.63 103.71 16.92 1.61e+00 3.86e-01 1.10e+02 angle pdb=" N ASP C 307 " pdb=" CA ASP C 307 " pdb=" C ASP C 307 " ideal model delta sigma weight residual 110.06 122.75 -12.69 1.43e+00 4.89e-01 7.87e+01 angle pdb=" N THR C 288 " pdb=" CA THR C 288 " pdb=" C THR C 288 " ideal model delta sigma weight residual 108.02 93.21 14.81 1.75e+00 3.27e-01 7.16e+01 angle pdb=" N LEU C 281 " pdb=" CA LEU C 281 " pdb=" C LEU C 281 " ideal model delta sigma weight residual 111.36 102.21 9.15 1.09e+00 8.42e-01 7.05e+01 angle pdb=" N VAL F 448 " pdb=" CA VAL F 448 " pdb=" C VAL F 448 " ideal model delta sigma weight residual 112.96 105.13 7.83 1.00e+00 1.00e+00 6.13e+01 ... (remaining 42071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 17712 35.53 - 71.07: 660 71.07 - 106.60: 17 106.60 - 142.14: 3 142.14 - 177.67: 8 Dihedral angle restraints: 18400 sinusoidal: 8352 harmonic: 10048 Sorted by residual: dihedral pdb=" CA PRO C 975 " pdb=" C PRO C 975 " pdb=" N VAL C 976 " pdb=" CA VAL C 976 " ideal model delta harmonic sigma weight residual 180.00 -150.89 -29.11 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA LYS C 229 " pdb=" C LYS C 229 " pdb=" N ARG C 230 " pdb=" CA ARG C 230 " ideal model delta harmonic sigma weight residual 180.00 150.96 29.04 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" C GLN D 657 " pdb=" N GLN D 657 " pdb=" CA GLN D 657 " pdb=" CB GLN D 657 " ideal model delta harmonic sigma weight residual -122.60 -136.69 14.09 0 2.50e+00 1.60e-01 3.17e+01 ... (remaining 18397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 4755 0.149 - 0.297: 27 0.297 - 0.446: 4 0.446 - 0.594: 1 0.594 - 0.743: 2 Chirality restraints: 4789 Sorted by residual: chirality pdb=" CA GLN D 657 " pdb=" N GLN D 657 " pdb=" C GLN D 657 " pdb=" CB GLN D 657 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" CA ASP D 660 " pdb=" N ASP D 660 " pdb=" C ASP D 660 " pdb=" CB ASP D 660 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" CA ASN D 384 " pdb=" N ASN D 384 " pdb=" C ASN D 384 " pdb=" CB ASN D 384 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.55e+00 ... (remaining 4786 not shown) Planarity restraints: 5084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 274 " -0.019 2.00e-02 2.50e+03 4.02e-02 1.61e+01 pdb=" C LEU C 274 " 0.069 2.00e-02 2.50e+03 pdb=" O LEU C 274 " -0.027 2.00e-02 2.50e+03 pdb=" N LEU C 275 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN D 657 " 0.065 5.00e-02 4.00e+02 9.57e-02 1.47e+01 pdb=" N PRO D 658 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO D 658 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO D 658 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 396 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" CG ASN D 396 " 0.063 2.00e-02 2.50e+03 pdb=" OD1 ASN D 396 " -0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN D 396 " -0.021 2.00e-02 2.50e+03 ... (remaining 5081 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 220 2.44 - 3.06: 22752 3.06 - 3.67: 46217 3.67 - 4.29: 67735 4.29 - 4.90: 108637 Nonbonded interactions: 245561 Sorted by model distance: nonbonded pdb=" O ALA C 273 " pdb=" N ASP C 276 " model vdw 1.828 3.120 nonbonded pdb=" OD2 ASP D 383 " pdb=" NE ARG D 386 " model vdw 1.857 3.120 nonbonded pdb=" N GLU C 466 " pdb=" OE1 GLU C 466 " model vdw 1.865 3.120 nonbonded pdb=" O THR C 294 " pdb=" OD1 ASN C 298 " model vdw 1.906 3.040 nonbonded pdb=" O ASP C 271 " pdb=" CD1 LEU C 275 " model vdw 1.913 3.460 ... (remaining 245556 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 or (resid 186 \ and (name N or name CA or name C or name O or name CB )) or resid 187 through 2 \ 23 or (resid 224 and (name N or name CA or name C or name O or name CB )) or res \ id 225 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 35.140 Find NCS groups from input model: 0.170 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.186 30668 Z= 0.550 Angle : 1.049 33.145 42082 Z= 0.584 Chirality : 0.054 0.743 4789 Planarity : 0.006 0.096 5084 Dihedral : 16.058 177.673 11936 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 36.22 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.64 % Favored : 88.07 % Rotamer: Outliers : 0.55 % Allowed : 3.70 % Favored : 95.75 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % 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: -3.74 (0.12), residues: 3488 helix: -1.43 (0.12), residues: 1361 sheet: -3.58 (0.22), residues: 394 loop : -3.13 (0.13), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 506 TYR 0.046 0.003 TYR E 56 PHE 0.040 0.003 PHE C 187 TRP 0.032 0.004 TRP F 283 HIS 0.015 0.002 HIS D 494 Details of bonding type rmsd covalent geometry : bond 0.01056 (30661) covalent geometry : angle 1.02396 (42076) hydrogen bonds : bond 0.16071 ( 1298) hydrogen bonds : angle 7.08857 ( 3575) metal coordination : bond 0.07288 ( 7) metal coordination : angle 18.98244 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 470 time to evaluate : 1.140 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: A 177 LYS cc_start: 0.8879 (pttt) cc_final: 0.8650 (ptmm) REVERT: B 177 LYS cc_start: 0.9071 (ptpp) cc_final: 0.8760 (ptpp) REVERT: B 195 ASP cc_start: 0.7732 (t0) cc_final: 0.7247 (t70) REVERT: B 226 ASN cc_start: 0.8686 (t160) cc_final: 0.8482 (t0) REVERT: C 258 MET cc_start: 0.8465 (mmm) cc_final: 0.8075 (mmt) REVERT: C 271 ASP cc_start: 0.8921 (OUTLIER) cc_final: 0.8490 (t70) REVERT: C 293 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: C 355 MET cc_start: 0.8068 (tmm) cc_final: 0.7616 (tmm) REVERT: C 393 MET cc_start: 0.8938 (mmt) cc_final: 0.8649 (mmt) REVERT: C 394 SER cc_start: 0.9123 (m) cc_final: 0.8918 (p) REVERT: C 441 ASP cc_start: 0.8376 (t70) cc_final: 0.8087 (t0) REVERT: C 467 ARG cc_start: 0.8449 (mmt180) cc_final: 0.8247 (mmt-90) REVERT: C 630 MET cc_start: 0.8985 (mmm) cc_final: 0.8713 (tpp) REVERT: C 645 GLU cc_start: 0.8549 (tp30) cc_final: 0.8305 (tp30) REVERT: C 661 MET cc_start: 0.8613 (tpt) cc_final: 0.8221 (tpt) REVERT: C 779 GLU cc_start: 0.8382 (tt0) cc_final: 0.7737 (tp30) REVERT: D 118 LEU cc_start: 0.9095 (mt) cc_final: 0.8856 (mt) REVERT: D 211 ARG cc_start: 0.7918 (mmt-90) cc_final: 0.7510 (mtp-110) REVERT: D 1106 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7637 (mm-30) REVERT: E 70 GLN cc_start: 0.6995 (tt0) cc_final: 0.6704 (tt0) REVERT: E 88 GLN cc_start: 0.8390 (tp40) cc_final: 0.7998 (tp40) REVERT: F 220 GLU cc_start: 0.8007 (tt0) cc_final: 0.7604 (tp30) REVERT: F 258 TYR cc_start: 0.8952 (t80) cc_final: 0.8663 (t80) REVERT: F 306 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8961 (mt) REVERT: F 411 LEU cc_start: 0.9043 (mt) cc_final: 0.8759 (pp) REVERT: F 511 MET cc_start: 0.9193 (tpt) cc_final: 0.8619 (tpp) REVERT: J 58 ASN cc_start: 0.9176 (t0) cc_final: 0.8472 (t0) REVERT: J 84 MET cc_start: 0.8505 (mpp) cc_final: 0.7548 (mpp) REVERT: M 4 LYS cc_start: 0.7794 (mtmm) cc_final: 0.7511 (mttt) REVERT: M 7 ASP cc_start: 0.7849 (m-30) cc_final: 0.7516 (m-30) REVERT: M 41 GLN cc_start: 0.8155 (tt0) cc_final: 0.7838 (tm-30) REVERT: M 124 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8029 (mm-30) outliers start: 16 outliers final: 8 residues processed: 485 average time/residue: 0.2306 time to fit residues: 169.9794 Evaluate side-chains 266 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 255 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain F residue 306 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS A 124 HIS B 226 ASN C 81 ASN C 141 ASN C 232 GLN C 298 ASN ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 ASN C 435 GLN C 841 HIS C 875 GLN ** C 891 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 HIS C1035 HIS ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN D 239 ASN D 307 ASN D 396 ASN D 416 ASN D 439 HIS D 494 HIS ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN D 687 GLN D 693 GLN D 748 HIS D 771 ASN D 797 ASN D1001 GLN D1139 GLN D1251 ASN E 106 HIS F 388 GLN J 21 ASN M 14 HIS M 31 GLN M 102 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.101039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.071401 restraints weight = 70014.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.073781 restraints weight = 32738.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.075283 restraints weight = 20810.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.076212 restraints weight = 16007.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.076599 restraints weight = 13788.879| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 30668 Z= 0.166 Angle : 0.711 9.724 42082 Z= 0.370 Chirality : 0.045 0.236 4789 Planarity : 0.005 0.086 5084 Dihedral : 20.225 178.522 5293 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.39 % Favored : 93.55 % Rotamer: Outliers : 1.99 % Allowed : 8.08 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.14), residues: 3488 helix: -0.06 (0.13), residues: 1381 sheet: -2.83 (0.24), residues: 386 loop : -2.41 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1052 TYR 0.020 0.002 TYR C 278 PHE 0.021 0.002 PHE D1226 TRP 0.017 0.002 TRP C 70 HIS 0.005 0.001 HIS C 920 Details of bonding type rmsd covalent geometry : bond 0.00374 (30661) covalent geometry : angle 0.70742 (42076) hydrogen bonds : bond 0.04863 ( 1298) hydrogen bonds : angle 5.20271 ( 3575) metal coordination : bond 0.00578 ( 7) metal coordination : angle 5.73491 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 331 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8787 (pttt) cc_final: 0.8483 (ptmm) REVERT: B 123 MET cc_start: 0.8347 (tpp) cc_final: 0.8121 (tpp) REVERT: B 177 LYS cc_start: 0.8948 (ptpp) cc_final: 0.8713 (ptpp) REVERT: B 226 ASN cc_start: 0.8738 (t0) cc_final: 0.8487 (t0) REVERT: C 103 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8527 (ptt) REVERT: C 230 ARG cc_start: 0.7523 (ptp-170) cc_final: 0.7125 (ptm160) REVERT: C 293 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: C 355 MET cc_start: 0.7829 (tmm) cc_final: 0.7539 (tmm) REVERT: C 394 SER cc_start: 0.9088 (m) cc_final: 0.8841 (p) REVERT: C 404 MET cc_start: 0.8791 (ttt) cc_final: 0.8290 (ttm) REVERT: C 467 ARG cc_start: 0.8452 (mmt180) cc_final: 0.8243 (mmt-90) REVERT: C 584 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8336 (ptp90) REVERT: C 586 MET cc_start: 0.9259 (ptm) cc_final: 0.8652 (ptm) REVERT: C 779 GLU cc_start: 0.8261 (tt0) cc_final: 0.7634 (tp30) REVERT: C 1051 MET cc_start: 0.8298 (mmm) cc_final: 0.7895 (tpt) REVERT: D 160 LYS cc_start: 0.7457 (pptt) cc_final: 0.7202 (mtpt) REVERT: D 379 ASP cc_start: 0.8151 (m-30) cc_final: 0.7783 (m-30) REVERT: D 576 MET cc_start: 0.8780 (ttp) cc_final: 0.8558 (ttp) REVERT: E 56 TYR cc_start: 0.8598 (t80) cc_final: 0.8386 (t80) REVERT: E 62 ARG cc_start: 0.8478 (mtt-85) cc_final: 0.8126 (mtt-85) REVERT: E 66 ASP cc_start: 0.8386 (m-30) cc_final: 0.7990 (m-30) REVERT: E 70 GLN cc_start: 0.7142 (tt0) cc_final: 0.6791 (tt0) REVERT: F 220 GLU cc_start: 0.7998 (tt0) cc_final: 0.7533 (tp30) REVERT: F 258 TYR cc_start: 0.8988 (t80) cc_final: 0.8685 (t80) REVERT: F 263 MET cc_start: 0.8478 (tmm) cc_final: 0.8216 (tmm) REVERT: J 7 ARG cc_start: 0.8090 (ptp-170) cc_final: 0.7872 (ptp90) REVERT: J 28 GLN cc_start: 0.7489 (mt0) cc_final: 0.7218 (mt0) REVERT: J 29 ILE cc_start: 0.9198 (mt) cc_final: 0.8989 (mp) REVERT: J 76 LYS cc_start: 0.8209 (pmtt) cc_final: 0.7666 (ttpt) REVERT: J 84 MET cc_start: 0.8567 (mpp) cc_final: 0.8328 (mmt) REVERT: M 4 LYS cc_start: 0.7979 (mtmm) cc_final: 0.7551 (mmtt) REVERT: M 7 ASP cc_start: 0.7991 (m-30) cc_final: 0.7698 (m-30) REVERT: M 72 GLN cc_start: 0.8852 (tt0) cc_final: 0.8532 (tm-30) outliers start: 58 outliers final: 31 residues processed: 371 average time/residue: 0.1994 time to fit residues: 118.0036 Evaluate side-chains 284 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 250 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 795 GLU Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 516 HIS Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 21 ASN Chi-restraints excluded: chain M residue 43 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 259 optimal weight: 0.8980 chunk 230 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 333 optimal weight: 10.0000 chunk 149 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 HIS C 685 ASN ** C 891 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 941 HIS ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN D 657 GLN ** D 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN M 31 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.098867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.069083 restraints weight = 70027.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.071390 restraints weight = 33159.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.072865 restraints weight = 21269.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.073763 restraints weight = 16422.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.074237 restraints weight = 14200.453| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 30668 Z= 0.208 Angle : 0.671 13.713 42082 Z= 0.350 Chirality : 0.044 0.195 4789 Planarity : 0.005 0.057 5084 Dihedral : 19.944 179.773 5272 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.45 % Favored : 93.52 % Rotamer: Outliers : 3.32 % Allowed : 10.21 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % 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: -1.66 (0.14), residues: 3488 helix: 0.50 (0.14), residues: 1382 sheet: -2.63 (0.23), residues: 420 loop : -2.09 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 259 TYR 0.026 0.002 TYR D 915 PHE 0.015 0.002 PHE D1226 TRP 0.036 0.002 TRP D 656 HIS 0.008 0.001 HIS D 653 Details of bonding type rmsd covalent geometry : bond 0.00478 (30661) covalent geometry : angle 0.66969 (42076) hydrogen bonds : bond 0.04652 ( 1298) hydrogen bonds : angle 4.87483 ( 3575) metal coordination : bond 0.00782 ( 7) metal coordination : angle 4.04876 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 262 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8862 (pttt) cc_final: 0.8593 (ptmm) REVERT: B 177 LYS cc_start: 0.8931 (ptpp) cc_final: 0.8646 (ptpp) REVERT: C 191 ILE cc_start: 0.9247 (mt) cc_final: 0.8949 (tp) REVERT: C 258 MET cc_start: 0.8710 (mmm) cc_final: 0.8204 (mmt) REVERT: C 293 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.6939 (tm-30) REVERT: C 394 SER cc_start: 0.9141 (m) cc_final: 0.8829 (p) REVERT: C 404 MET cc_start: 0.8738 (ttt) cc_final: 0.8385 (ttp) REVERT: C 463 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8715 (pt) REVERT: C 467 ARG cc_start: 0.8472 (mmt180) cc_final: 0.8271 (mmt-90) REVERT: C 584 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8271 (ptp90) REVERT: C 586 MET cc_start: 0.9266 (ptm) cc_final: 0.8608 (ppp) REVERT: C 779 GLU cc_start: 0.8278 (tt0) cc_final: 0.7677 (tp30) REVERT: D 379 ASP cc_start: 0.8175 (m-30) cc_final: 0.7781 (m-30) REVERT: D 1112 MET cc_start: 0.8294 (mmp) cc_final: 0.8088 (mmp) REVERT: F 220 GLU cc_start: 0.8086 (tt0) cc_final: 0.7605 (tp30) REVERT: F 258 TYR cc_start: 0.9010 (t80) cc_final: 0.8643 (t80) REVERT: F 325 ASN cc_start: 0.8996 (m-40) cc_final: 0.8757 (m110) REVERT: F 424 ASP cc_start: 0.8508 (m-30) cc_final: 0.8197 (m-30) REVERT: J 29 ILE cc_start: 0.9233 (mt) cc_final: 0.9026 (mp) REVERT: J 76 LYS cc_start: 0.8127 (pmtt) cc_final: 0.7615 (pttt) REVERT: M 4 LYS cc_start: 0.7932 (mtmm) cc_final: 0.7483 (mmtt) REVERT: M 7 ASP cc_start: 0.8111 (m-30) cc_final: 0.7880 (m-30) REVERT: M 72 GLN cc_start: 0.8849 (tt0) cc_final: 0.8545 (tm-30) outliers start: 97 outliers final: 52 residues processed: 330 average time/residue: 0.1897 time to fit residues: 102.2627 Evaluate side-chains 279 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 224 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 610 ASN Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 623 ASP Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 516 HIS Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 98 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 99 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 287 optimal weight: 9.9990 chunk 167 optimal weight: 4.9990 chunk 244 optimal weight: 0.3980 chunk 67 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 GLN ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.098064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.068371 restraints weight = 69506.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.070637 restraints weight = 33074.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.072087 restraints weight = 21261.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.072957 restraints weight = 16462.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.073415 restraints weight = 14281.729| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 30668 Z= 0.228 Angle : 0.664 15.141 42082 Z= 0.345 Chirality : 0.044 0.218 4789 Planarity : 0.005 0.062 5084 Dihedral : 19.877 179.545 5268 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.48 % Favored : 93.49 % Rotamer: Outliers : 3.90 % Allowed : 11.03 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % 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: 3488 helix: 0.70 (0.14), residues: 1394 sheet: -2.33 (0.24), residues: 403 loop : -1.94 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1143 TYR 0.042 0.002 TYR D 915 PHE 0.013 0.002 PHE J 44 TRP 0.027 0.002 TRP D 656 HIS 0.005 0.001 HIS D 854 Details of bonding type rmsd covalent geometry : bond 0.00528 (30661) covalent geometry : angle 0.66275 (42076) hydrogen bonds : bond 0.04468 ( 1298) hydrogen bonds : angle 4.71342 ( 3575) metal coordination : bond 0.00866 ( 7) metal coordination : angle 3.27486 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 237 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8898 (pttt) cc_final: 0.8618 (ptmm) REVERT: B 177 LYS cc_start: 0.8923 (ptpp) cc_final: 0.8658 (ptpp) REVERT: B 196 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8634 (m) REVERT: C 103 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.7989 (ptt) REVERT: C 191 ILE cc_start: 0.9231 (mt) cc_final: 0.8889 (tp) REVERT: C 280 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8458 (tptp) REVERT: C 293 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7503 (tt0) REVERT: C 394 SER cc_start: 0.9154 (m) cc_final: 0.8834 (p) REVERT: C 404 MET cc_start: 0.8721 (ttt) cc_final: 0.8064 (ttt) REVERT: C 463 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8952 (pt) REVERT: C 467 ARG cc_start: 0.8514 (mmt180) cc_final: 0.8217 (mmt-90) REVERT: C 584 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8236 (ptp90) REVERT: C 586 MET cc_start: 0.9245 (ptm) cc_final: 0.8579 (ppp) REVERT: C 672 MET cc_start: 0.9397 (mmt) cc_final: 0.9175 (mmt) REVERT: C 779 GLU cc_start: 0.8285 (tt0) cc_final: 0.7692 (tp30) REVERT: C 1051 MET cc_start: 0.8304 (mmm) cc_final: 0.7890 (mmm) REVERT: D 310 MET cc_start: 0.8593 (tpp) cc_final: 0.8326 (tpp) REVERT: D 338 SER cc_start: 0.9329 (OUTLIER) cc_final: 0.8702 (t) REVERT: D 379 ASP cc_start: 0.8191 (m-30) cc_final: 0.7772 (m-30) REVERT: D 623 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7550 (t0) REVERT: D 817 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8673 (tt) REVERT: D 1112 MET cc_start: 0.8330 (mmp) cc_final: 0.8086 (mmp) REVERT: E 66 ASP cc_start: 0.8131 (m-30) cc_final: 0.7796 (m-30) REVERT: F 220 GLU cc_start: 0.8151 (tt0) cc_final: 0.7638 (tp30) REVERT: F 325 ASN cc_start: 0.9004 (m-40) cc_final: 0.8769 (m110) REVERT: F 328 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8926 (tt) REVERT: F 424 ASP cc_start: 0.8562 (m-30) cc_final: 0.8294 (m-30) REVERT: J 28 GLN cc_start: 0.7760 (mt0) cc_final: 0.7558 (mt0) REVERT: J 29 ILE cc_start: 0.9302 (mt) cc_final: 0.9093 (mp) REVERT: J 76 LYS cc_start: 0.8023 (pmtt) cc_final: 0.7573 (pttt) REVERT: M 4 LYS cc_start: 0.7715 (mtmm) cc_final: 0.7351 (mmtt) REVERT: M 7 ASP cc_start: 0.8013 (m-30) cc_final: 0.7790 (m-30) REVERT: M 72 GLN cc_start: 0.8828 (tt0) cc_final: 0.8495 (tm-30) outliers start: 114 outliers final: 58 residues processed: 322 average time/residue: 0.1848 time to fit residues: 98.5931 Evaluate side-chains 292 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 224 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 610 ASN Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 753 GLU Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 623 ASP Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 516 HIS Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 71 PHE Chi-restraints excluded: chain M residue 98 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 65 optimal weight: 10.0000 chunk 186 optimal weight: 2.9990 chunk 274 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 331 optimal weight: 20.0000 chunk 254 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 269 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 HIS ** D 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.097389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.067403 restraints weight = 70205.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.069664 restraints weight = 33489.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.071091 restraints weight = 21573.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.071951 restraints weight = 16790.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.072460 restraints weight = 14578.285| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 30668 Z= 0.257 Angle : 0.679 11.936 42082 Z= 0.353 Chirality : 0.044 0.198 4789 Planarity : 0.005 0.061 5084 Dihedral : 19.811 177.442 5268 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.59 % Favored : 93.38 % Rotamer: Outliers : 3.49 % Allowed : 12.40 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % 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: -1.19 (0.14), residues: 3488 helix: 0.82 (0.14), residues: 1395 sheet: -2.24 (0.24), residues: 400 loop : -1.83 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1143 TYR 0.042 0.002 TYR D 915 PHE 0.013 0.002 PHE D 335 TRP 0.033 0.002 TRP D 656 HIS 0.006 0.001 HIS C 751 Details of bonding type rmsd covalent geometry : bond 0.00594 (30661) covalent geometry : angle 0.67851 (42076) hydrogen bonds : bond 0.04538 ( 1298) hydrogen bonds : angle 4.64675 ( 3575) metal coordination : bond 0.00996 ( 7) metal coordination : angle 2.79817 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 233 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8920 (pttt) cc_final: 0.8604 (ptmm) REVERT: B 177 LYS cc_start: 0.8937 (ptpp) cc_final: 0.8665 (ptpp) REVERT: B 196 VAL cc_start: 0.8883 (OUTLIER) cc_final: 0.8621 (m) REVERT: C 154 MET cc_start: 0.8780 (tpp) cc_final: 0.8081 (mpp) REVERT: C 191 ILE cc_start: 0.9226 (mt) cc_final: 0.8870 (tp) REVERT: C 394 SER cc_start: 0.9216 (m) cc_final: 0.8847 (p) REVERT: C 463 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.8813 (pt) REVERT: C 467 ARG cc_start: 0.8513 (mmt180) cc_final: 0.8202 (mmt-90) REVERT: C 584 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8092 (ptp90) REVERT: C 586 MET cc_start: 0.9265 (ptm) cc_final: 0.8630 (ppp) REVERT: C 758 ASP cc_start: 0.8051 (p0) cc_final: 0.7497 (p0) REVERT: C 779 GLU cc_start: 0.8311 (tt0) cc_final: 0.7727 (tp30) REVERT: C 1051 MET cc_start: 0.8313 (mmm) cc_final: 0.7871 (mmm) REVERT: C 1079 TYR cc_start: 0.9163 (m-80) cc_final: 0.8926 (m-10) REVERT: C 1110 GLU cc_start: 0.8291 (mp0) cc_final: 0.7986 (mp0) REVERT: D 623 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7563 (t0) REVERT: D 1112 MET cc_start: 0.8281 (mmp) cc_final: 0.8020 (mmp) REVERT: E 66 ASP cc_start: 0.8273 (m-30) cc_final: 0.7931 (m-30) REVERT: F 220 GLU cc_start: 0.8194 (tt0) cc_final: 0.7671 (tp30) REVERT: F 325 ASN cc_start: 0.9022 (m-40) cc_final: 0.8786 (m110) REVERT: F 424 ASP cc_start: 0.8631 (m-30) cc_final: 0.8339 (m-30) REVERT: F 437 ASP cc_start: 0.8463 (m-30) cc_final: 0.8193 (m-30) REVERT: J 76 LYS cc_start: 0.7916 (pmtt) cc_final: 0.7482 (pttt) REVERT: M 4 LYS cc_start: 0.7686 (mtmm) cc_final: 0.7359 (mmtt) REVERT: M 7 ASP cc_start: 0.7953 (m-30) cc_final: 0.7742 (m-30) REVERT: M 41 GLN cc_start: 0.7864 (tm-30) cc_final: 0.7638 (tm-30) REVERT: M 72 GLN cc_start: 0.8786 (tt0) cc_final: 0.8308 (tm-30) outliers start: 102 outliers final: 73 residues processed: 310 average time/residue: 0.1890 time to fit residues: 96.8010 Evaluate side-chains 294 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 217 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 610 ASN Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 623 ASP Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain F residue 516 HIS Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 21 ASN Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 71 PHE Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 98 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 146 optimal weight: 3.9990 chunk 311 optimal weight: 1.9990 chunk 317 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 chunk 238 optimal weight: 6.9990 chunk 226 optimal weight: 3.9990 chunk 156 optimal weight: 0.0010 chunk 215 optimal weight: 1.9990 chunk 350 optimal weight: 1.9990 chunk 325 optimal weight: 10.0000 chunk 314 optimal weight: 5.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.099257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.069154 restraints weight = 69356.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.071492 restraints weight = 32810.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.072949 restraints weight = 21013.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.073862 restraints weight = 16336.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.074297 restraints weight = 14141.631| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30668 Z= 0.153 Angle : 0.610 11.219 42082 Z= 0.319 Chirality : 0.042 0.166 4789 Planarity : 0.004 0.062 5084 Dihedral : 19.653 179.240 5265 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.68 % Favored : 94.29 % Rotamer: Outliers : 3.05 % Allowed : 13.36 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % 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: -0.80 (0.15), residues: 3488 helix: 1.10 (0.14), residues: 1382 sheet: -1.79 (0.26), residues: 384 loop : -1.63 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1143 TYR 0.012 0.001 TYR E 56 PHE 0.012 0.001 PHE C 430 TRP 0.036 0.002 TRP D 656 HIS 0.005 0.001 HIS D 854 Details of bonding type rmsd covalent geometry : bond 0.00341 (30661) covalent geometry : angle 0.60912 (42076) hydrogen bonds : bond 0.03975 ( 1298) hydrogen bonds : angle 4.42575 ( 3575) metal coordination : bond 0.00399 ( 7) metal coordination : angle 2.17843 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 249 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8894 (pttt) cc_final: 0.8577 (ptmm) REVERT: B 177 LYS cc_start: 0.8871 (ptpp) cc_final: 0.8625 (ptpp) REVERT: B 196 VAL cc_start: 0.8762 (OUTLIER) cc_final: 0.8489 (m) REVERT: C 103 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8537 (ptt) REVERT: C 154 MET cc_start: 0.8752 (tpp) cc_final: 0.8147 (mpp) REVERT: C 191 ILE cc_start: 0.9180 (mt) cc_final: 0.8824 (tp) REVERT: C 394 SER cc_start: 0.9148 (m) cc_final: 0.8812 (p) REVERT: C 404 MET cc_start: 0.8654 (ttp) cc_final: 0.8159 (ttp) REVERT: C 463 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8751 (pt) REVERT: C 467 ARG cc_start: 0.8477 (mmt180) cc_final: 0.8202 (mmt-90) REVERT: C 584 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8223 (ptp90) REVERT: C 586 MET cc_start: 0.9246 (ptm) cc_final: 0.8629 (ppp) REVERT: C 758 ASP cc_start: 0.8158 (p0) cc_final: 0.7607 (p0) REVERT: C 779 GLU cc_start: 0.8308 (tt0) cc_final: 0.7735 (tp30) REVERT: C 1051 MET cc_start: 0.8292 (mmm) cc_final: 0.7828 (mmm) REVERT: C 1087 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7389 (mm-30) REVERT: C 1110 GLU cc_start: 0.8162 (mp0) cc_final: 0.7893 (mp0) REVERT: D 379 ASP cc_start: 0.8148 (m-30) cc_final: 0.7736 (m-30) REVERT: D 623 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7574 (t0) REVERT: D 862 ASP cc_start: 0.8564 (t70) cc_final: 0.8150 (t0) REVERT: D 1112 MET cc_start: 0.8363 (mmp) cc_final: 0.8112 (mmp) REVERT: D 1139 GLN cc_start: 0.8741 (mm110) cc_final: 0.7824 (mm-40) REVERT: F 220 GLU cc_start: 0.8124 (tt0) cc_final: 0.7622 (tp30) REVERT: F 257 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9129 (mp) REVERT: F 281 MET cc_start: 0.7895 (ppp) cc_final: 0.7693 (ppp) REVERT: F 325 ASN cc_start: 0.8960 (m-40) cc_final: 0.8724 (m110) REVERT: F 424 ASP cc_start: 0.8573 (m-30) cc_final: 0.8237 (m-30) REVERT: F 437 ASP cc_start: 0.8458 (m-30) cc_final: 0.8213 (m-30) REVERT: J 28 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.7280 (pm20) REVERT: J 76 LYS cc_start: 0.7895 (pmtt) cc_final: 0.7475 (pttt) REVERT: M 4 LYS cc_start: 0.7703 (mtmm) cc_final: 0.7377 (mmtt) REVERT: M 41 GLN cc_start: 0.7820 (tm-30) cc_final: 0.7605 (tm-30) REVERT: M 147 ASP cc_start: 0.8649 (p0) cc_final: 0.8050 (m-30) outliers start: 89 outliers final: 60 residues processed: 315 average time/residue: 0.1776 time to fit residues: 92.4715 Evaluate side-chains 291 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 224 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 610 ASN Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 623 ASP Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 516 HIS Chi-restraints excluded: chain J residue 21 ASN Chi-restraints excluded: chain J residue 28 GLN Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 71 PHE Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 98 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 10 optimal weight: 9.9990 chunk 209 optimal weight: 0.9990 chunk 183 optimal weight: 7.9990 chunk 27 optimal weight: 0.4980 chunk 260 optimal weight: 10.0000 chunk 176 optimal weight: 10.0000 chunk 321 optimal weight: 3.9990 chunk 240 optimal weight: 0.3980 chunk 201 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.100252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.070173 restraints weight = 69085.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.072518 restraints weight = 32645.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.074007 restraints weight = 20941.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.074839 restraints weight = 16197.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.075397 restraints weight = 14128.529| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 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 : 0.003 0.046 30668 Z= 0.133 Angle : 0.593 10.595 42082 Z= 0.311 Chirality : 0.041 0.161 4789 Planarity : 0.004 0.061 5084 Dihedral : 19.492 179.251 5265 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.39 % Favored : 94.58 % Rotamer: Outliers : 3.12 % Allowed : 14.01 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % 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 (0.15), residues: 3488 helix: 1.28 (0.14), residues: 1382 sheet: -1.67 (0.26), residues: 391 loop : -1.54 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1143 TYR 0.018 0.001 TYR D 915 PHE 0.009 0.001 PHE C 430 TRP 0.031 0.001 TRP D 656 HIS 0.006 0.001 HIS D 854 Details of bonding type rmsd covalent geometry : bond 0.00297 (30661) covalent geometry : angle 0.59302 (42076) hydrogen bonds : bond 0.03777 ( 1298) hydrogen bonds : angle 4.29808 ( 3575) metal coordination : bond 0.00308 ( 7) metal coordination : angle 1.87906 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 243 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8880 (pttt) cc_final: 0.8557 (ptmm) REVERT: B 165 ASP cc_start: 0.8177 (m-30) cc_final: 0.7598 (m-30) REVERT: B 177 LYS cc_start: 0.8813 (ptpp) cc_final: 0.8566 (ptpp) REVERT: B 196 VAL cc_start: 0.8702 (OUTLIER) cc_final: 0.8485 (m) REVERT: C 154 MET cc_start: 0.8673 (tpp) cc_final: 0.8236 (mpp) REVERT: C 191 ILE cc_start: 0.9148 (mt) cc_final: 0.8744 (tp) REVERT: C 258 MET cc_start: 0.8592 (mmm) cc_final: 0.8392 (mmm) REVERT: C 394 SER cc_start: 0.9124 (m) cc_final: 0.8805 (p) REVERT: C 404 MET cc_start: 0.8603 (ttp) cc_final: 0.8101 (ttp) REVERT: C 410 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7928 (tm-30) REVERT: C 463 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8748 (pt) REVERT: C 467 ARG cc_start: 0.8489 (mmt180) cc_final: 0.8197 (mmt-90) REVERT: C 584 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8082 (ptp90) REVERT: C 586 MET cc_start: 0.9266 (ptm) cc_final: 0.8519 (ppp) REVERT: C 758 ASP cc_start: 0.8091 (p0) cc_final: 0.7507 (p0) REVERT: C 779 GLU cc_start: 0.8321 (tt0) cc_final: 0.7740 (tp30) REVERT: C 1051 MET cc_start: 0.8283 (mmm) cc_final: 0.7801 (mmm) REVERT: C 1087 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7320 (mm-30) REVERT: C 1088 LEU cc_start: 0.8933 (mt) cc_final: 0.8685 (mt) REVERT: C 1110 GLU cc_start: 0.8022 (mp0) cc_final: 0.7732 (mp0) REVERT: D 379 ASP cc_start: 0.8135 (m-30) cc_final: 0.7717 (m-30) REVERT: D 623 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7668 (t0) REVERT: D 862 ASP cc_start: 0.8539 (t70) cc_final: 0.8127 (t0) REVERT: D 958 THR cc_start: 0.8516 (p) cc_final: 0.8081 (t) REVERT: D 1112 MET cc_start: 0.8319 (mmp) cc_final: 0.8075 (mmp) REVERT: D 1139 GLN cc_start: 0.8614 (mm110) cc_final: 0.8171 (mm-40) REVERT: E 42 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8131 (tt0) REVERT: F 220 GLU cc_start: 0.8125 (tt0) cc_final: 0.7610 (tp30) REVERT: F 263 MET cc_start: 0.8811 (tmm) cc_final: 0.8487 (tmm) REVERT: F 281 MET cc_start: 0.7976 (ppp) cc_final: 0.7715 (ppp) REVERT: F 313 ARG cc_start: 0.5661 (mmt180) cc_final: 0.5242 (mmt180) REVERT: F 325 ASN cc_start: 0.8955 (m-40) cc_final: 0.8718 (m110) REVERT: F 424 ASP cc_start: 0.8572 (m-30) cc_final: 0.8305 (m-30) REVERT: F 437 ASP cc_start: 0.8488 (m-30) cc_final: 0.8226 (m-30) REVERT: F 465 ASP cc_start: 0.8792 (m-30) cc_final: 0.8213 (p0) REVERT: J 28 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7686 (pm20) REVERT: J 76 LYS cc_start: 0.7958 (pmtt) cc_final: 0.7460 (pttt) REVERT: M 4 LYS cc_start: 0.8064 (mtmm) cc_final: 0.7860 (mmtt) REVERT: M 147 ASP cc_start: 0.8635 (p0) cc_final: 0.8035 (m-30) outliers start: 91 outliers final: 60 residues processed: 312 average time/residue: 0.1822 time to fit residues: 93.7410 Evaluate side-chains 287 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 222 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 623 ASP Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 1143 ARG Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain F residue 516 HIS Chi-restraints excluded: chain J residue 28 GLN Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 71 PHE Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 98 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 328 optimal weight: 0.0370 chunk 147 optimal weight: 0.9990 chunk 134 optimal weight: 0.2980 chunk 264 optimal weight: 20.0000 chunk 90 optimal weight: 6.9990 chunk 334 optimal weight: 6.9990 chunk 140 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 323 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN J 28 GLN M 13 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.101732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.071912 restraints weight = 69430.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.074266 restraints weight = 32561.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.075698 restraints weight = 20796.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.076638 restraints weight = 16224.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.077133 restraints weight = 14000.836| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30668 Z= 0.119 Angle : 0.578 10.292 42082 Z= 0.302 Chirality : 0.041 0.163 4789 Planarity : 0.004 0.059 5084 Dihedral : 19.349 178.863 5265 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.93 % Favored : 95.04 % Rotamer: Outliers : 2.53 % Allowed : 15.21 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % 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: -0.46 (0.15), residues: 3488 helix: 1.42 (0.14), residues: 1381 sheet: -1.59 (0.25), residues: 387 loop : -1.47 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1143 TYR 0.012 0.001 TYR E 56 PHE 0.013 0.001 PHE B 189 TRP 0.027 0.001 TRP D 656 HIS 0.006 0.001 HIS D 854 Details of bonding type rmsd covalent geometry : bond 0.00262 (30661) covalent geometry : angle 0.57755 (42076) hydrogen bonds : bond 0.03530 ( 1298) hydrogen bonds : angle 4.19115 ( 3575) metal coordination : bond 0.00208 ( 7) metal coordination : angle 1.53123 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 263 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8868 (pttt) cc_final: 0.8506 (ptmm) REVERT: B 177 LYS cc_start: 0.8784 (ptpp) cc_final: 0.8530 (ptpp) REVERT: B 196 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8440 (m) REVERT: C 103 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8608 (ptt) REVERT: C 154 MET cc_start: 0.8618 (tpp) cc_final: 0.8266 (mpp) REVERT: C 191 ILE cc_start: 0.9141 (mt) cc_final: 0.8671 (tp) REVERT: C 264 LYS cc_start: 0.8316 (mtmt) cc_final: 0.8112 (mttp) REVERT: C 394 SER cc_start: 0.9108 (m) cc_final: 0.8775 (p) REVERT: C 404 MET cc_start: 0.8570 (ttp) cc_final: 0.8251 (ttp) REVERT: C 463 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8762 (pt) REVERT: C 467 ARG cc_start: 0.8479 (mmt180) cc_final: 0.8190 (mmt-90) REVERT: C 584 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8245 (ptp90) REVERT: C 586 MET cc_start: 0.9184 (ptm) cc_final: 0.8300 (ppp) REVERT: C 758 ASP cc_start: 0.8057 (p0) cc_final: 0.7471 (p0) REVERT: C 779 GLU cc_start: 0.8346 (tt0) cc_final: 0.7792 (tp30) REVERT: C 1051 MET cc_start: 0.8248 (mmm) cc_final: 0.7717 (mmm) REVERT: C 1087 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7141 (mm-30) REVERT: C 1088 LEU cc_start: 0.8914 (mt) cc_final: 0.8667 (mt) REVERT: C 1094 ASP cc_start: 0.8697 (m-30) cc_final: 0.8488 (m-30) REVERT: C 1110 GLU cc_start: 0.7942 (mp0) cc_final: 0.7687 (mp0) REVERT: C 1119 GLU cc_start: 0.7763 (tp30) cc_final: 0.7490 (tp30) REVERT: D 379 ASP cc_start: 0.8084 (m-30) cc_final: 0.7637 (m-30) REVERT: D 428 SER cc_start: 0.9241 (t) cc_final: 0.8979 (m) REVERT: D 474 ARG cc_start: 0.8237 (ttp-110) cc_final: 0.7855 (mmm-85) REVERT: D 576 MET cc_start: 0.8544 (ttp) cc_final: 0.8325 (ttp) REVERT: D 623 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7639 (t0) REVERT: D 862 ASP cc_start: 0.8471 (t70) cc_final: 0.8222 (t0) REVERT: D 958 THR cc_start: 0.8495 (p) cc_final: 0.8099 (t) REVERT: D 1112 MET cc_start: 0.8336 (mmp) cc_final: 0.8094 (mmp) REVERT: D 1139 GLN cc_start: 0.8397 (mm110) cc_final: 0.8145 (mm-40) REVERT: F 220 GLU cc_start: 0.8133 (tt0) cc_final: 0.7601 (tp30) REVERT: F 281 MET cc_start: 0.7999 (ppp) cc_final: 0.7739 (ppp) REVERT: F 313 ARG cc_start: 0.5567 (mmt180) cc_final: 0.5079 (mmt180) REVERT: F 325 ASN cc_start: 0.8938 (m-40) cc_final: 0.8698 (m110) REVERT: F 424 ASP cc_start: 0.8536 (m-30) cc_final: 0.8264 (m-30) REVERT: F 465 ASP cc_start: 0.8580 (m-30) cc_final: 0.8193 (p0) REVERT: J 28 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7765 (pm20) REVERT: J 76 LYS cc_start: 0.7961 (pmtt) cc_final: 0.7426 (pttm) REVERT: M 147 ASP cc_start: 0.8560 (p0) cc_final: 0.7960 (m-30) outliers start: 74 outliers final: 46 residues processed: 314 average time/residue: 0.1961 time to fit residues: 99.9308 Evaluate side-chains 280 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 228 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 623 ASP Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 1143 ARG Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 516 HIS Chi-restraints excluded: chain J residue 28 GLN Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 71 PHE Chi-restraints excluded: chain M residue 85 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 162 optimal weight: 7.9990 chunk 128 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 219 optimal weight: 6.9990 chunk 318 optimal weight: 6.9990 chunk 338 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 174 optimal weight: 20.0000 chunk 190 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 HIS D 771 ASN D 942 GLN D1110 GLN E 70 GLN J 28 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.096307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.066092 restraints weight = 70319.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.068331 restraints weight = 34080.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.069737 restraints weight = 22109.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.070585 restraints weight = 17283.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.070999 restraints weight = 15039.459| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.103 30668 Z= 0.351 Angle : 0.741 9.737 42082 Z= 0.384 Chirality : 0.046 0.198 4789 Planarity : 0.005 0.080 5084 Dihedral : 19.538 176.220 5265 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.31 % Favored : 92.66 % Rotamer: Outliers : 2.77 % Allowed : 15.62 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % 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: -0.76 (0.14), residues: 3488 helix: 1.11 (0.14), residues: 1391 sheet: -1.78 (0.26), residues: 385 loop : -1.60 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1143 TYR 0.019 0.002 TYR E 56 PHE 0.025 0.002 PHE B 189 TRP 0.023 0.002 TRP D 656 HIS 0.007 0.001 HIS D 103 Details of bonding type rmsd covalent geometry : bond 0.00811 (30661) covalent geometry : angle 0.74067 (42076) hydrogen bonds : bond 0.04752 ( 1298) hydrogen bonds : angle 4.57504 ( 3575) metal coordination : bond 0.01475 ( 7) metal coordination : angle 2.51415 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 221 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8941 (pttt) cc_final: 0.8629 (ptmm) REVERT: B 177 LYS cc_start: 0.8946 (ptpp) cc_final: 0.8663 (ptpp) REVERT: C 103 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8457 (ptt) REVERT: C 191 ILE cc_start: 0.9201 (mt) cc_final: 0.8822 (tp) REVERT: C 264 LYS cc_start: 0.8394 (mtmt) cc_final: 0.8146 (mttp) REVERT: C 394 SER cc_start: 0.9258 (m) cc_final: 0.8978 (t) REVERT: C 404 MET cc_start: 0.8624 (ttp) cc_final: 0.8251 (ttp) REVERT: C 463 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.8890 (pt) REVERT: C 467 ARG cc_start: 0.8489 (mmt180) cc_final: 0.8199 (mmt-90) REVERT: C 584 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7612 (pmm-80) REVERT: C 586 MET cc_start: 0.9333 (ptm) cc_final: 0.8772 (ptm) REVERT: C 758 ASP cc_start: 0.7962 (p0) cc_final: 0.7385 (p0) REVERT: C 779 GLU cc_start: 0.8422 (tt0) cc_final: 0.8026 (tp30) REVERT: C 1051 MET cc_start: 0.8274 (mmm) cc_final: 0.7796 (mmm) REVERT: C 1110 GLU cc_start: 0.8208 (mp0) cc_final: 0.7904 (mp0) REVERT: D 623 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7609 (t0) REVERT: D 942 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7572 (mt0) REVERT: D 1145 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8235 (tm-30) REVERT: F 220 GLU cc_start: 0.8225 (tt0) cc_final: 0.7778 (tp30) REVERT: F 257 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9177 (mp) REVERT: F 263 MET cc_start: 0.8907 (tmm) cc_final: 0.8661 (tmm) REVERT: F 325 ASN cc_start: 0.9096 (m-40) cc_final: 0.8871 (m110) REVERT: F 328 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8852 (tt) REVERT: F 424 ASP cc_start: 0.8591 (m-30) cc_final: 0.8355 (m-30) REVERT: F 465 ASP cc_start: 0.8724 (m-30) cc_final: 0.8457 (m-30) REVERT: J 28 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7734 (pm20) REVERT: J 76 LYS cc_start: 0.7986 (pmtt) cc_final: 0.7421 (pttm) REVERT: M 72 GLN cc_start: 0.8752 (tt0) cc_final: 0.8335 (tm-30) REVERT: M 147 ASP cc_start: 0.8634 (p0) cc_final: 0.8038 (m-30) outliers start: 81 outliers final: 61 residues processed: 284 average time/residue: 0.1866 time to fit residues: 88.3437 Evaluate side-chains 278 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 209 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 623 ASP Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 942 GLN Chi-restraints excluded: chain D residue 1143 ARG Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain F residue 516 HIS Chi-restraints excluded: chain J residue 28 GLN Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 71 PHE Chi-restraints excluded: chain M residue 85 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 3 optimal weight: 1.9990 chunk 132 optimal weight: 0.0010 chunk 143 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 310 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 HIS ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.100431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.070361 restraints weight = 69143.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.072726 restraints weight = 32706.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.074228 restraints weight = 20995.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.075136 restraints weight = 16240.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.075655 restraints weight = 14055.677| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30668 Z= 0.125 Angle : 0.604 10.217 42082 Z= 0.316 Chirality : 0.042 0.184 4789 Planarity : 0.004 0.070 5084 Dihedral : 19.396 178.980 5265 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.02 % Favored : 94.95 % Rotamer: Outliers : 1.92 % Allowed : 16.37 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % 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: -0.46 (0.15), residues: 3488 helix: 1.37 (0.14), residues: 1380 sheet: -1.52 (0.26), residues: 391 loop : -1.44 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 27 TYR 0.014 0.001 TYR E 56 PHE 0.012 0.001 PHE D 673 TRP 0.025 0.002 TRP D 656 HIS 0.006 0.001 HIS D 854 Details of bonding type rmsd covalent geometry : bond 0.00275 (30661) covalent geometry : angle 0.60394 (42076) hydrogen bonds : bond 0.03717 ( 1298) hydrogen bonds : angle 4.25408 ( 3575) metal coordination : bond 0.00163 ( 7) metal coordination : angle 1.65854 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 231 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8879 (pttt) cc_final: 0.8559 (ptmm) REVERT: B 177 LYS cc_start: 0.8797 (ptpp) cc_final: 0.8582 (ptpp) REVERT: C 48 LEU cc_start: 0.9064 (tp) cc_final: 0.8842 (tt) REVERT: C 103 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8488 (ptt) REVERT: C 191 ILE cc_start: 0.9132 (mt) cc_final: 0.8746 (tp) REVERT: C 264 LYS cc_start: 0.8392 (mtmt) cc_final: 0.8183 (mttp) REVERT: C 394 SER cc_start: 0.9110 (m) cc_final: 0.8783 (p) REVERT: C 404 MET cc_start: 0.8547 (ttp) cc_final: 0.8165 (ttp) REVERT: C 463 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8793 (pt) REVERT: C 584 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8128 (ptp90) REVERT: C 586 MET cc_start: 0.9234 (ptm) cc_final: 0.8571 (ppp) REVERT: C 758 ASP cc_start: 0.8099 (p0) cc_final: 0.7484 (p0) REVERT: C 779 GLU cc_start: 0.8363 (tt0) cc_final: 0.7830 (tp30) REVERT: C 1051 MET cc_start: 0.8283 (mmm) cc_final: 0.7788 (mmm) REVERT: C 1088 LEU cc_start: 0.8940 (mt) cc_final: 0.8655 (mt) REVERT: C 1110 GLU cc_start: 0.7959 (mp0) cc_final: 0.7661 (mp0) REVERT: C 1119 GLU cc_start: 0.7706 (tp30) cc_final: 0.7399 (tp30) REVERT: D 379 ASP cc_start: 0.8097 (m-30) cc_final: 0.7675 (m-30) REVERT: D 623 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7595 (t0) REVERT: D 862 ASP cc_start: 0.8539 (t70) cc_final: 0.8124 (t0) REVERT: D 958 THR cc_start: 0.8505 (p) cc_final: 0.8112 (t) REVERT: D 1112 MET cc_start: 0.8134 (mmp) cc_final: 0.7896 (mmp) REVERT: D 1139 GLN cc_start: 0.8293 (mm110) cc_final: 0.8077 (mm-40) REVERT: D 1143 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.5982 (mtt90) REVERT: E 42 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7983 (tt0) REVERT: F 220 GLU cc_start: 0.8141 (tt0) cc_final: 0.7608 (tp30) REVERT: F 325 ASN cc_start: 0.8935 (m-40) cc_final: 0.8710 (m110) REVERT: F 328 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8710 (tt) REVERT: F 465 ASP cc_start: 0.8518 (m-30) cc_final: 0.8209 (p0) REVERT: J 28 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7617 (pm20) REVERT: J 76 LYS cc_start: 0.7978 (pmtt) cc_final: 0.7416 (pttm) REVERT: M 72 GLN cc_start: 0.8699 (tt0) cc_final: 0.8184 (tm-30) REVERT: M 147 ASP cc_start: 0.8540 (p0) cc_final: 0.7955 (m-30) outliers start: 56 outliers final: 43 residues processed: 275 average time/residue: 0.1856 time to fit residues: 84.7352 Evaluate side-chains 271 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 221 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 992 THR Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 623 ASP Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 1143 ARG Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 516 HIS Chi-restraints excluded: chain J residue 28 GLN Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 71 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 17 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 204 optimal weight: 0.6980 chunk 328 optimal weight: 6.9990 chunk 244 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 199 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN C 386 GLN ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 ASN ** D 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.099668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.069381 restraints weight = 69424.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.071720 restraints weight = 33179.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.073192 restraints weight = 21393.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.074060 restraints weight = 16607.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.074593 restraints weight = 14433.399| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30668 Z= 0.160 Angle : 0.602 9.757 42082 Z= 0.314 Chirality : 0.042 0.170 4789 Planarity : 0.004 0.075 5084 Dihedral : 19.339 178.135 5265 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.48 % Favored : 94.50 % Rotamer: Outliers : 2.29 % Allowed : 16.13 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % 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: -0.41 (0.15), residues: 3488 helix: 1.42 (0.14), residues: 1380 sheet: -1.50 (0.26), residues: 391 loop : -1.41 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D1143 TYR 0.023 0.001 TYR D 915 PHE 0.031 0.001 PHE B 189 TRP 0.023 0.001 TRP D 656 HIS 0.006 0.001 HIS D 854 Details of bonding type rmsd covalent geometry : bond 0.00368 (30661) covalent geometry : angle 0.60197 (42076) hydrogen bonds : bond 0.03807 ( 1298) hydrogen bonds : angle 4.25239 ( 3575) metal coordination : bond 0.00517 ( 7) metal coordination : angle 1.70073 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5736.48 seconds wall clock time: 99 minutes 26.32 seconds (5966.32 seconds total)