Starting phenix.real_space_refine on Mon Sep 14 10:51:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6eec_9041/09_2026/6eec_9041_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6eec_9041/09_2026/6eec_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 { model { file = "/net/cci-nas-00/data/ceres_data/6eec_9041/09_2026/6eec_9041_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6eec_9041/09_2026/6eec_9041_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6eec_9041/09_2026/6eec_9041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6eec_9041/09_2026/6eec_9041.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 6.14, per 1000 atoms: 0.21 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: 2.81 Conformation dependent library (CDL) restraints added in 1.4 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: 4.54 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: 8.86 Time building geometry restraints manager: 3.75 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: 4748 0.149 - 0.297: 34 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: 1.080 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: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 38.190 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 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= 0.605 Angle : 1.068 33.145 42082 Z= 0.640 Chirality : 0.055 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/Z covalent geometry : bond 0.01066 / 0.60 (30661) covalent geometry : angle 1.04419 / 0.64 (42076) hydrogen bonds : bond 0.16071 / 11.11 ( 1298) hydrogen bonds : angle 7.08857 / 4.97 ( 3575) metal coordination : bond 0.07288 / 3.68 ( 7) metal coordination : angle 18.98244 / 9.06 ( 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 : 1.109 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: 0.8489 (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 630 MET cc_start: 0.8985 (mmm) cc_final: 0.8713 (tpp) REVERT: C 645 GLU cc_start: 0.8549 (tp30) cc_final: 0.8306 (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: 0.8022 (mm-30) outliers start: 16 outliers final: 8 residues processed: 485 average time/residue: 0.2239 time to fit residues: 166.6690 Evaluate side-chains 267 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 256 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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... 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 920 HIS C1035 HIS C1054 GLN D 239 ASN D 307 ASN D 396 ASN D 416 ASN D 494 HIS ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN D 657 GLN D 687 GLN D 693 GLN D 771 ASN D 797 ASN D1001 GLN D1139 GLN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 GLN J 21 ASN M 14 HIS M 102 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.100418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.070885 restraints weight = 70023.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.073254 restraints weight = 32722.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.074739 restraints weight = 20768.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.075621 restraints weight = 15992.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.076151 restraints weight = 13844.318| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 30668 Z= 0.175 Angle : 0.772 10.263 42082 Z= 0.401 Chirality : 0.049 0.330 4789 Planarity : 0.006 0.091 5084 Dihedral : 20.461 179.714 5293 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.68 % Favored : 93.26 % Rotamer: Outliers : 1.99 % Allowed : 8.25 % Favored : 89.76 % 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: -2.45 (0.13), residues: 3488 helix: -0.27 (0.13), residues: 1368 sheet: -2.84 (0.24), residues: 386 loop : -2.51 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 487 TYR 0.019 0.002 TYR D 915 PHE 0.025 0.002 PHE D1226 TRP 0.017 0.002 TRP C 70 HIS 0.007 0.001 HIS C 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (30661) covalent geometry : angle 0.76862 / 0.40 (42076) hydrogen bonds : bond 0.05440 / 3.75 ( 1298) hydrogen bonds : angle 5.40584 / 3.80 ( 3575) metal coordination : bond 0.00760 / 0.40 ( 7) metal coordination : angle 5.67890 / 2.94 ( 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 382 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 324 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8764 (pttt) cc_final: 0.8524 (ptmm) REVERT: B 123 MET cc_start: 0.8320 (tpp) cc_final: 0.8110 (tpp) REVERT: B 177 LYS cc_start: 0.8972 (ptpp) cc_final: 0.8729 (ptpp) REVERT: B 226 ASN cc_start: 0.8766 (t0) cc_final: 0.8488 (t0) REVERT: C 293 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.6918 (tm-30) REVERT: C 355 MET cc_start: 0.7719 (tmm) cc_final: 0.7400 (tmm) REVERT: C 394 SER cc_start: 0.9092 (m) cc_final: 0.8874 (p) REVERT: C 463 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8560 (pp) REVERT: C 584 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8338 (ptp90) REVERT: C 586 MET cc_start: 0.9286 (ptm) cc_final: 0.8755 (ptm) REVERT: C 779 GLU cc_start: 0.8272 (tt0) cc_final: 0.7648 (tp30) REVERT: C 1071 MET cc_start: 0.8765 (mtp) cc_final: 0.8547 (mtt) REVERT: D 211 ARG cc_start: 0.7791 (mmt-90) cc_final: 0.7559 (mtp-110) REVERT: D 379 ASP cc_start: 0.8182 (m-30) cc_final: 0.7802 (m-30) REVERT: E 50 LYS cc_start: 0.8406 (ptpt) cc_final: 0.7722 (pttp) REVERT: E 70 GLN cc_start: 0.7091 (tt0) cc_final: 0.6766 (tt0) REVERT: E 88 GLN cc_start: 0.8164 (tp40) cc_final: 0.7907 (tp40) REVERT: F 220 GLU cc_start: 0.7959 (tt0) cc_final: 0.7514 (tp30) REVERT: F 258 TYR cc_start: 0.8943 (t80) cc_final: 0.8646 (t80) REVERT: F 263 MET cc_start: 0.8484 (tmm) cc_final: 0.8241 (tmm) REVERT: J 76 LYS cc_start: 0.8095 (pmtt) cc_final: 0.7712 (pmtt) REVERT: J 84 MET cc_start: 0.8570 (mpp) cc_final: 0.7359 (mpp) REVERT: M 4 LYS cc_start: 0.7948 (mtmm) cc_final: 0.7534 (mmtt) REVERT: M 7 ASP cc_start: 0.7949 (m-30) cc_final: 0.7638 (m-30) REVERT: M 37 LEU cc_start: 0.9286 (tt) cc_final: 0.9063 (tp) REVERT: M 72 GLN cc_start: 0.8787 (tt0) cc_final: 0.8398 (tm-30) REVERT: M 95 LYS cc_start: 0.9102 (mtmt) cc_final: 0.8872 (mtmm) outliers start: 58 outliers final: 28 residues processed: 360 average time/residue: 0.1929 time to fit residues: 112.0990 Evaluate side-chains 280 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 249 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 120 ASP Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain C residue 463 LEU 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 1181 ILE Chi-restraints excluded: chain E residue 53 LEU 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: 6.9990 chunk 230 optimal weight: 1.9990 chunk 203 optimal weight: 8.9990 chunk 333 optimal weight: 40.0000 chunk 149 optimal weight: 0.5980 chunk 38 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 201 optimal weight: 0.5980 chunk 237 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 HIS ** C 891 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1251 ASN E 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.099957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.070165 restraints weight = 69882.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.072525 restraints weight = 32946.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.074007 restraints weight = 21029.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.074910 restraints weight = 16208.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.075425 restraints weight = 14029.111| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 30668 Z= 0.170 Angle : 0.691 15.348 42082 Z= 0.363 Chirality : 0.046 0.340 4789 Planarity : 0.005 0.057 5084 Dihedral : 20.203 178.548 5272 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.31 % Favored : 93.66 % Rotamer: Outliers : 2.91 % Allowed : 9.97 % Favored : 87.12 % 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: -1.82 (0.14), residues: 3488 helix: 0.27 (0.14), residues: 1375 sheet: -2.54 (0.24), residues: 389 loop : -2.16 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 487 TYR 0.045 0.001 TYR D 915 PHE 0.016 0.002 PHE D 7 TRP 0.037 0.002 TRP D 656 HIS 0.006 0.001 HIS C 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (30661) covalent geometry : angle 0.68886 / 0.36 (42076) hydrogen bonds : bond 0.04871 / 3.36 ( 1298) hydrogen bonds : angle 5.02133 / 3.52 ( 3575) metal coordination : bond 0.00481 / 0.31 ( 7) metal coordination : angle 4.25574 / 2.06 ( 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 358 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 273 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8814 (pttt) cc_final: 0.8542 (ptmm) REVERT: B 177 LYS cc_start: 0.8910 (ptpp) cc_final: 0.8694 (ptpp) REVERT: B 226 ASN cc_start: 0.8766 (t0) cc_final: 0.8520 (t0) REVERT: C 293 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7534 (tt0) REVERT: C 394 SER cc_start: 0.9127 (m) cc_final: 0.8826 (p) REVERT: C 404 MET cc_start: 0.8764 (ttt) cc_final: 0.8291 (ttp) REVERT: C 463 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8857 (pt) REVERT: C 584 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8310 (ptp90) REVERT: C 586 MET cc_start: 0.9267 (ptm) cc_final: 0.8591 (ppp) REVERT: C 779 GLU cc_start: 0.8252 (tt0) cc_final: 0.7656 (tp30) REVERT: D 379 ASP cc_start: 0.8145 (m-30) cc_final: 0.7787 (m-30) REVERT: E 66 ASP cc_start: 0.8152 (m-30) cc_final: 0.7750 (m-30) REVERT: E 88 GLN cc_start: 0.8225 (tp40) cc_final: 0.8008 (tp40) REVERT: F 220 GLU cc_start: 0.8002 (tt0) cc_final: 0.7536 (tp30) REVERT: F 258 TYR cc_start: 0.8990 (t80) cc_final: 0.8705 (t80) REVERT: F 511 MET cc_start: 0.8914 (tpp) cc_final: 0.8636 (tpp) REVERT: J 76 LYS cc_start: 0.8192 (pmtt) cc_final: 0.7636 (pttt) REVERT: M 4 LYS cc_start: 0.7901 (mtmm) cc_final: 0.7531 (mmtt) REVERT: M 7 ASP cc_start: 0.8025 (m-30) cc_final: 0.7718 (m-30) REVERT: M 72 GLN cc_start: 0.8791 (tt0) cc_final: 0.8469 (tm-30) REVERT: M 95 LYS cc_start: 0.9051 (mtmt) cc_final: 0.8828 (mtmm) outliers start: 85 outliers final: 44 residues processed: 338 average time/residue: 0.1867 time to fit residues: 104.1220 Evaluate side-chains 283 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 236 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 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 C residue 96 ILE 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 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 584 ARG 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 985 LEU 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 82 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 159 ARG 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 774 LEU Chi-restraints excluded: chain D residue 804 ASP Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain F residue 359 MET 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 135 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 99 optimal weight: 10.0000 chunk 169 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 287 optimal weight: 10.0000 chunk 167 optimal weight: 0.7980 chunk 244 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.100408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.070858 restraints weight = 69426.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.073169 restraints weight = 32506.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.074645 restraints weight = 20776.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.075552 restraints weight = 16032.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.075923 restraints weight = 13882.260| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30668 Z= 0.146 Angle : 0.654 15.088 42082 Z= 0.342 Chirality : 0.045 0.363 4789 Planarity : 0.004 0.061 5084 Dihedral : 20.004 178.458 5272 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.71 % Favored : 94.27 % Rotamer: Outliers : 2.95 % Allowed : 11.10 % Favored : 85.96 % 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: -1.48 (0.14), residues: 3488 helix: 0.54 (0.14), residues: 1388 sheet: -2.39 (0.23), residues: 413 loop : -1.95 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 487 TYR 0.034 0.001 TYR D 915 PHE 0.015 0.001 PHE J 44 TRP 0.027 0.002 TRP D 656 HIS 0.005 0.001 HIS E 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (30661) covalent geometry : angle 0.65301 / 0.34 (42076) hydrogen bonds : bond 0.04473 / 3.09 ( 1298) hydrogen bonds : angle 4.76412 / 3.33 ( 3575) metal coordination : bond 0.00381 / 0.26 ( 7) metal coordination : angle 3.35474 / 1.60 ( 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 345 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 259 time to evaluate : 1.214 Fit side-chains revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8845 (pttt) cc_final: 0.8563 (ptmm) REVERT: B 226 ASN cc_start: 0.8762 (t0) cc_final: 0.8539 (t0) REVERT: C 293 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: C 394 SER cc_start: 0.9118 (m) cc_final: 0.8788 (p) REVERT: C 404 MET cc_start: 0.8777 (ttt) cc_final: 0.8323 (ttp) REVERT: C 463 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8885 (pt) REVERT: C 584 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8270 (ptp90) REVERT: C 586 MET cc_start: 0.9281 (ptm) cc_final: 0.8596 (ppp) REVERT: C 779 GLU cc_start: 0.8278 (tt0) cc_final: 0.7659 (tp30) REVERT: D 379 ASP cc_start: 0.8128 (m-30) cc_final: 0.7736 (m-30) REVERT: D 491 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8663 (mp) REVERT: D 649 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7952 (tm-30) REVERT: D 1112 MET cc_start: 0.8433 (tpp) cc_final: 0.7996 (tpp) REVERT: E 88 GLN cc_start: 0.8109 (tp40) cc_final: 0.7883 (tp40) REVERT: F 220 GLU cc_start: 0.8001 (tt0) cc_final: 0.7524 (tp30) REVERT: F 258 TYR cc_start: 0.8990 (t80) cc_final: 0.8636 (t80) REVERT: F 511 MET cc_start: 0.8889 (tpp) cc_final: 0.8543 (tpp) REVERT: J 76 LYS cc_start: 0.8132 (pmtt) cc_final: 0.7621 (pttt) REVERT: J 84 MET cc_start: 0.8857 (mmt) cc_final: 0.8581 (mmt) REVERT: M 4 LYS cc_start: 0.7878 (mtmm) cc_final: 0.7514 (mmtt) REVERT: M 7 ASP cc_start: 0.7990 (m-30) cc_final: 0.7690 (m-30) REVERT: M 72 GLN cc_start: 0.8777 (tt0) cc_final: 0.8373 (tm-30) REVERT: M 95 LYS cc_start: 0.9062 (mtmt) cc_final: 0.8568 (mtmm) outliers start: 86 outliers final: 56 residues processed: 323 average time/residue: 0.1875 time to fit residues: 100.0652 Evaluate side-chains 287 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 227 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 131 LYS 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 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 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 584 ARG 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 841 HIS Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 20 ILE 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 145 HIS Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 159 ARG 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 491 ILE Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 804 ASP Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 899 VAL Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 359 MET Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 464 LEU 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 135 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 65 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 274 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 331 optimal weight: 50.0000 chunk 254 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 125 optimal weight: 0.0970 chunk 269 optimal weight: 0.7980 chunk 119 optimal weight: 10.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 685 ASN C 941 HIS ** D 505 HIS ** 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 = 0.3602 r_free = 0.3602 target = 0.099690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.069797 restraints weight = 70036.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.072138 restraints weight = 32960.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.073631 restraints weight = 21089.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.074530 restraints weight = 16295.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.075062 restraints weight = 14121.972| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30668 Z= 0.168 Angle : 0.644 14.680 42082 Z= 0.337 Chirality : 0.045 0.367 4789 Planarity : 0.004 0.062 5084 Dihedral : 19.865 179.291 5268 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.88 % Favored : 94.09 % Rotamer: Outliers : 3.39 % Allowed : 11.75 % Favored : 84.86 % 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: -1.21 (0.14), residues: 3488 helix: 0.78 (0.14), residues: 1384 sheet: -2.19 (0.24), residues: 406 loop : -1.82 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 517 TYR 0.051 0.001 TYR D 915 PHE 0.011 0.001 PHE C 430 TRP 0.037 0.002 TRP D 656 HIS 0.007 0.001 HIS C 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (30661) covalent geometry : angle 0.64281 / 0.34 (42076) hydrogen bonds : bond 0.04432 / 3.04 ( 1298) hydrogen bonds : angle 4.62577 / 3.23 ( 3575) metal coordination : bond 0.00584 / 0.41 ( 7) metal coordination : angle 2.88621 / 1.33 ( 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 345 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 246 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8876 (pttt) cc_final: 0.8589 (ptmm) REVERT: B 196 VAL cc_start: 0.8850 (OUTLIER) cc_final: 0.8592 (m) REVERT: B 198 THR cc_start: 0.9344 (p) cc_final: 0.9065 (t) REVERT: C 154 MET cc_start: 0.8711 (tpp) cc_final: 0.8207 (mpp) REVERT: C 293 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7543 (tt0) REVERT: C 394 SER cc_start: 0.9124 (m) cc_final: 0.8795 (p) REVERT: C 404 MET cc_start: 0.8687 (ttt) cc_final: 0.8456 (ttp) REVERT: C 584 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8262 (ptp90) REVERT: C 586 MET cc_start: 0.9294 (ptm) cc_final: 0.8576 (ppp) REVERT: C 779 GLU cc_start: 0.8290 (tt0) cc_final: 0.7681 (tp30) REVERT: D 379 ASP cc_start: 0.8142 (m-30) cc_final: 0.7739 (m-30) REVERT: D 817 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8564 (tt) REVERT: D 862 ASP cc_start: 0.8539 (t70) cc_final: 0.8118 (t0) REVERT: D 1112 MET cc_start: 0.8496 (tpp) cc_final: 0.8124 (tpp) REVERT: D 1139 GLN cc_start: 0.8758 (mm110) cc_final: 0.8532 (mm-40) REVERT: E 66 ASP cc_start: 0.8095 (m-30) cc_final: 0.7732 (m-30) REVERT: F 220 GLU cc_start: 0.8075 (tt0) cc_final: 0.7569 (tp30) REVERT: F 282 MET cc_start: 0.8743 (mmm) cc_final: 0.8516 (mmm) REVERT: F 325 ASN cc_start: 0.9001 (m-40) cc_final: 0.8714 (m110) REVERT: F 511 MET cc_start: 0.8872 (tpp) cc_final: 0.8500 (tpp) REVERT: J 76 LYS cc_start: 0.8087 (pmtt) cc_final: 0.7647 (pttt) REVERT: M 4 LYS cc_start: 0.7934 (mtmm) cc_final: 0.7527 (mmtt) REVERT: M 7 ASP cc_start: 0.7981 (m-30) cc_final: 0.7691 (m-30) REVERT: M 41 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7608 (tt0) REVERT: M 72 GLN cc_start: 0.8782 (tt0) cc_final: 0.8368 (tm-30) REVERT: M 95 LYS cc_start: 0.9095 (mtmt) cc_final: 0.8586 (mtmm) outliers start: 99 outliers final: 55 residues processed: 320 average time/residue: 0.1698 time to fit residues: 89.7656 Evaluate side-chains 284 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 225 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 131 LYS Chi-restraints excluded: chain A residue 178 VAL 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 150 VAL Chi-restraints excluded: chain B residue 196 VAL 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 226 ILE 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 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 610 ASN Chi-restraints excluded: chain C residue 683 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 841 HIS Chi-restraints excluded: chain C residue 985 LEU 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 338 SER Chi-restraints excluded: chain D residue 449 LEU 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 804 ASP Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 899 VAL Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 359 MET 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 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: 7.9990 chunk 192 optimal weight: 0.0770 chunk 238 optimal weight: 5.9990 chunk 226 optimal weight: 0.5980 chunk 156 optimal weight: 9.9990 chunk 215 optimal weight: 0.0030 chunk 350 optimal weight: 20.0000 chunk 325 optimal weight: 8.9990 chunk 314 optimal weight: 5.9990 overall best weight: 1.3352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1034 HIS ** D 505 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 = 0.3614 r_free = 0.3614 target = 0.100418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.070923 restraints weight = 69696.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.073288 restraints weight = 32668.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.074781 restraints weight = 20746.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.075660 restraints weight = 15979.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.076022 restraints weight = 13823.949| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30668 Z= 0.147 Angle : 0.627 14.719 42082 Z= 0.329 Chirality : 0.044 0.343 4789 Planarity : 0.004 0.065 5084 Dihedral : 19.764 179.001 5268 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.62 % Favored : 94.35 % Rotamer: Outliers : 2.57 % Allowed : 13.05 % Favored : 84.38 % 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: -1.02 (0.14), residues: 3488 helix: 0.92 (0.14), residues: 1383 sheet: -2.01 (0.24), residues: 401 loop : -1.72 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 159 TYR 0.020 0.001 TYR D 915 PHE 0.015 0.001 PHE J 40 TRP 0.035 0.002 TRP D 656 HIS 0.005 0.001 HIS D 854 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (30661) covalent geometry : angle 0.62589 / 0.33 (42076) hydrogen bonds : bond 0.04224 / 2.91 ( 1298) hydrogen bonds : angle 4.49733 / 3.14 ( 3575) metal coordination : bond 0.00444 / 0.31 ( 7) metal coordination : angle 2.52773 / 1.19 ( 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 322 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 247 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8876 (pttt) cc_final: 0.8548 (ptmm) REVERT: B 196 VAL cc_start: 0.8838 (OUTLIER) cc_final: 0.8612 (m) REVERT: C 154 MET cc_start: 0.8766 (tpp) cc_final: 0.8187 (mpp) REVERT: C 266 ASN cc_start: 0.8105 (p0) cc_final: 0.7674 (m110) REVERT: C 394 SER cc_start: 0.9111 (m) cc_final: 0.8783 (p) REVERT: C 404 MET cc_start: 0.8718 (ttt) cc_final: 0.8453 (ttp) REVERT: C 441 ASP cc_start: 0.8170 (t0) cc_final: 0.7954 (t0) REVERT: C 463 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8949 (pt) REVERT: C 584 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8235 (ptp90) REVERT: C 586 MET cc_start: 0.9274 (ptm) cc_final: 0.8552 (ppp) REVERT: C 779 GLU cc_start: 0.8286 (tt0) cc_final: 0.7694 (tp30) REVERT: C 1071 MET cc_start: 0.8742 (mtp) cc_final: 0.8359 (mtt) REVERT: D 379 ASP cc_start: 0.8131 (m-30) cc_final: 0.7728 (m-30) REVERT: D 649 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7848 (tm-30) REVERT: D 817 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8477 (tt) REVERT: D 862 ASP cc_start: 0.8522 (t70) cc_final: 0.8096 (t0) REVERT: D 1112 MET cc_start: 0.8482 (tpp) cc_final: 0.8269 (tpp) REVERT: D 1139 GLN cc_start: 0.8724 (mm110) cc_final: 0.7919 (mm-40) REVERT: E 66 ASP cc_start: 0.8126 (m-30) cc_final: 0.7679 (m-30) REVERT: F 220 GLU cc_start: 0.8091 (tt0) cc_final: 0.7579 (tp30) REVERT: F 282 MET cc_start: 0.8746 (mmm) cc_final: 0.8537 (mmm) REVERT: F 325 ASN cc_start: 0.8992 (m-40) cc_final: 0.8701 (m110) REVERT: F 511 MET cc_start: 0.8874 (tpp) cc_final: 0.8465 (tpp) REVERT: J 76 LYS cc_start: 0.8021 (pmtt) cc_final: 0.7589 (pttt) REVERT: J 84 MET cc_start: 0.8779 (mmt) cc_final: 0.8486 (mmt) REVERT: M 4 LYS cc_start: 0.7946 (mtmm) cc_final: 0.7516 (mmtt) REVERT: M 7 ASP cc_start: 0.7809 (m-30) cc_final: 0.7603 (m-30) REVERT: M 72 GLN cc_start: 0.8793 (tt0) cc_final: 0.8418 (tm-30) REVERT: M 95 LYS cc_start: 0.9106 (mtmt) cc_final: 0.8607 (mtmm) outliers start: 75 outliers final: 57 residues processed: 300 average time/residue: 0.1709 time to fit residues: 86.1023 Evaluate side-chains 292 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 231 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 131 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 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 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 226 ILE Chi-restraints excluded: chain C residue 288 THR 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 610 ASN 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 985 LEU 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 337 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 804 ASP Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 899 VAL Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 359 MET 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 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: 1.9990 chunk 183 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 260 optimal weight: 0.9990 chunk 176 optimal weight: 10.0000 chunk 321 optimal weight: 10.0000 chunk 240 optimal weight: 0.7980 chunk 201 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 GLN ** C1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 HIS D 540 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.100077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.070023 restraints weight = 69379.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.072383 restraints weight = 32745.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.073876 restraints weight = 20950.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.074783 restraints weight = 16215.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.075227 restraints weight = 14037.014| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30668 Z= 0.154 Angle : 0.619 13.654 42082 Z= 0.325 Chirality : 0.044 0.326 4789 Planarity : 0.004 0.062 5084 Dihedral : 19.676 179.057 5265 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.76 % Favored : 94.21 % Rotamer: Outliers : 2.81 % Allowed : 13.56 % Favored : 83.63 % 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: -0.84 (0.14), residues: 3488 helix: 1.05 (0.14), residues: 1379 sheet: -1.90 (0.25), residues: 404 loop : -1.60 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG M 87 TYR 0.015 0.001 TYR E 56 PHE 0.012 0.001 PHE C 252 TRP 0.035 0.002 TRP D 656 HIS 0.005 0.001 HIS D 854 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (30661) covalent geometry : angle 0.61827 / 0.32 (42076) hydrogen bonds : bond 0.04177 / 2.85 ( 1298) hydrogen bonds : angle 4.42243 / 3.09 ( 3575) metal coordination : bond 0.00504 / 0.35 ( 7) metal coordination : angle 2.29134 / 1.04 ( 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 327 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 245 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8877 (pttt) cc_final: 0.8554 (ptmm) REVERT: B 196 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8591 (m) REVERT: C 154 MET cc_start: 0.8752 (tpp) cc_final: 0.8135 (mpp) REVERT: C 181 ARG cc_start: 0.8503 (ptm160) cc_final: 0.8231 (ptm160) REVERT: C 394 SER cc_start: 0.9100 (m) cc_final: 0.8791 (p) REVERT: C 404 MET cc_start: 0.8755 (ttt) cc_final: 0.8467 (ttp) REVERT: C 441 ASP cc_start: 0.8153 (t0) cc_final: 0.7940 (t0) REVERT: C 463 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9012 (pt) REVERT: C 584 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8224 (ptp90) REVERT: C 586 MET cc_start: 0.9280 (ptm) cc_final: 0.8535 (ppp) REVERT: C 661 MET cc_start: 0.8641 (tpt) cc_final: 0.8371 (tpt) REVERT: C 779 GLU cc_start: 0.8294 (tt0) cc_final: 0.7707 (tp30) REVERT: C 1071 MET cc_start: 0.8801 (mtp) cc_final: 0.8425 (mtt) REVERT: C 1110 GLU cc_start: 0.8132 (mp0) cc_final: 0.7827 (mp0) REVERT: D 379 ASP cc_start: 0.8144 (m-30) cc_final: 0.7720 (m-30) REVERT: D 817 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8468 (tt) REVERT: D 862 ASP cc_start: 0.8510 (t70) cc_final: 0.8089 (t0) REVERT: D 1112 MET cc_start: 0.8603 (tpp) cc_final: 0.8376 (tpp) REVERT: D 1139 GLN cc_start: 0.8722 (mm110) cc_final: 0.7178 (mm-40) REVERT: E 66 ASP cc_start: 0.8232 (m-30) cc_final: 0.7856 (m-30) REVERT: E 88 GLN cc_start: 0.7876 (tp40) cc_final: 0.7458 (tp40) REVERT: F 220 GLU cc_start: 0.8116 (tt0) cc_final: 0.7589 (tp30) REVERT: F 282 MET cc_start: 0.8754 (mmm) cc_final: 0.8504 (mmm) REVERT: F 325 ASN cc_start: 0.8994 (m-40) cc_final: 0.8705 (m110) REVERT: F 437 ASP cc_start: 0.8524 (m-30) cc_final: 0.8253 (m-30) REVERT: F 511 MET cc_start: 0.8868 (tpp) cc_final: 0.8428 (tpp) REVERT: J 76 LYS cc_start: 0.7975 (pmtt) cc_final: 0.7543 (pttt) REVERT: M 4 LYS cc_start: 0.7846 (mtmm) cc_final: 0.7401 (mmtt) REVERT: M 41 GLN cc_start: 0.7813 (tm-30) cc_final: 0.7562 (tt0) REVERT: M 72 GLN cc_start: 0.8712 (tt0) cc_final: 0.8336 (tm-30) REVERT: M 95 LYS cc_start: 0.9070 (mtmt) cc_final: 0.8551 (mtmm) REVERT: M 147 ASP cc_start: 0.8619 (p0) cc_final: 0.8043 (m-30) outliers start: 82 outliers final: 65 residues processed: 302 average time/residue: 0.1743 time to fit residues: 87.4770 Evaluate side-chains 295 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 226 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 131 LYS Chi-restraints excluded: chain A residue 178 VAL 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 127 MET Chi-restraints excluded: chain C residue 165 THR 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 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 610 ASN Chi-restraints excluded: chain C residue 683 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 985 LEU 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 162 VAL Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 654 SER 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 804 ASP Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 899 VAL Chi-restraints excluded: chain D residue 1161 MET Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain F residue 326 LEU 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 M residue 43 ASP Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 71 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 328 optimal weight: 0.6980 chunk 147 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 264 optimal weight: 20.0000 chunk 90 optimal weight: 0.8980 chunk 334 optimal weight: 20.0000 chunk 140 optimal weight: 0.6980 chunk 69 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 323 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN E 70 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.101311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.071437 restraints weight = 69464.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.073829 restraints weight = 32608.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.075337 restraints weight = 20791.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.076231 restraints weight = 16083.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.076776 restraints weight = 13920.736| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 0.035 30668 Z= 0.124 Angle : 0.604 13.390 42082 Z= 0.317 Chirality : 0.044 0.318 4789 Planarity : 0.004 0.109 5084 Dihedral : 19.592 178.645 5265 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.33 % Favored : 94.64 % Rotamer: Outliers : 2.36 % Allowed : 14.76 % 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: -0.67 (0.15), residues: 3488 helix: 1.20 (0.14), residues: 1372 sheet: -1.82 (0.24), residues: 411 loop : -1.48 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 159 TYR 0.020 0.001 TYR D 915 PHE 0.013 0.001 PHE C 252 TRP 0.029 0.001 TRP D 656 HIS 0.006 0.001 HIS D 854 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (30661) covalent geometry : angle 0.60329 / 0.32 (42076) hydrogen bonds : bond 0.03908 / 2.66 ( 1298) hydrogen bonds : angle 4.29543 / 3.01 ( 3575) metal coordination : bond 0.00286 / 0.20 ( 7) metal coordination : angle 1.94792 / 0.91 ( 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 336 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 267 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8875 (pttt) cc_final: 0.8498 (ptmm) REVERT: B 165 ASP cc_start: 0.8273 (m-30) cc_final: 0.7689 (m-30) REVERT: B 196 VAL cc_start: 0.8769 (OUTLIER) cc_final: 0.8489 (m) REVERT: B 198 THR cc_start: 0.9371 (p) cc_final: 0.9078 (t) REVERT: C 103 MET cc_start: 0.8911 (ptt) cc_final: 0.8311 (ptt) REVERT: C 154 MET cc_start: 0.8772 (tpp) cc_final: 0.8195 (mpp) REVERT: C 394 SER cc_start: 0.9083 (m) cc_final: 0.8768 (p) REVERT: C 404 MET cc_start: 0.8720 (ttt) cc_final: 0.8243 (ttp) REVERT: C 441 ASP cc_start: 0.8042 (t0) cc_final: 0.7792 (t0) REVERT: C 463 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9010 (pt) REVERT: C 584 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8191 (ptp90) REVERT: C 586 MET cc_start: 0.9252 (ptm) cc_final: 0.8393 (ppp) REVERT: C 758 ASP cc_start: 0.8052 (p0) cc_final: 0.7495 (p0) REVERT: C 779 GLU cc_start: 0.8285 (tt0) cc_final: 0.7705 (tp30) REVERT: C 927 ASN cc_start: 0.8251 (p0) cc_final: 0.7880 (p0) REVERT: C 1071 MET cc_start: 0.8732 (mtp) cc_final: 0.8349 (mtt) REVERT: C 1110 GLU cc_start: 0.7981 (mp0) cc_final: 0.7726 (mp0) REVERT: D 379 ASP cc_start: 0.8137 (m-30) cc_final: 0.7696 (m-30) REVERT: D 862 ASP cc_start: 0.8481 (t70) cc_final: 0.8229 (t0) REVERT: D 1112 MET cc_start: 0.8873 (tpp) cc_final: 0.8669 (tpp) REVERT: E 66 ASP cc_start: 0.8229 (m-30) cc_final: 0.7848 (m-30) REVERT: E 88 GLN cc_start: 0.7770 (tp40) cc_final: 0.7373 (tp40) REVERT: F 220 GLU cc_start: 0.8039 (tt0) cc_final: 0.7543 (tp30) REVERT: F 263 MET cc_start: 0.8774 (tmm) cc_final: 0.8478 (tmm) REVERT: F 282 MET cc_start: 0.8747 (mmm) cc_final: 0.8495 (mmm) REVERT: F 313 ARG cc_start: 0.6693 (mmt180) cc_final: 0.6464 (mmt180) REVERT: F 325 ASN cc_start: 0.8973 (m-40) cc_final: 0.8657 (m110) REVERT: F 437 ASP cc_start: 0.8526 (m-30) cc_final: 0.8242 (m-30) REVERT: F 511 MET cc_start: 0.8862 (tpp) cc_final: 0.8385 (tpp) REVERT: J 76 LYS cc_start: 0.7960 (pmtt) cc_final: 0.7461 (pttt) REVERT: M 72 GLN cc_start: 0.8709 (tt0) cc_final: 0.8271 (tm-30) REVERT: M 95 LYS cc_start: 0.9106 (mtmt) cc_final: 0.8569 (mtmm) REVERT: M 147 ASP cc_start: 0.8649 (p0) cc_final: 0.8101 (m-30) outliers start: 69 outliers final: 53 residues processed: 315 average time/residue: 0.1742 time to fit residues: 90.7528 Evaluate side-chains 289 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 233 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 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 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 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 610 ASN 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 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 148 LEU 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 338 SER Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 804 ASP Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 899 VAL Chi-restraints excluded: chain D residue 1143 ARG Chi-restraints excluded: chain D residue 1161 MET Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 516 HIS Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 71 PHE 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: 8.9990 chunk 73 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 219 optimal weight: 5.9990 chunk 318 optimal weight: 10.0000 chunk 338 optimal weight: 40.0000 chunk 49 optimal weight: 10.0000 chunk 174 optimal weight: 20.0000 chunk 190 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 552 GLN ** D1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.097978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.067746 restraints weight = 69882.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.070032 restraints weight = 33475.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.071471 restraints weight = 21606.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.072345 restraints weight = 16840.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.072771 restraints weight = 14606.991| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 30668 Z= 0.268 Angle : 0.695 11.519 42082 Z= 0.362 Chirality : 0.046 0.340 4789 Planarity : 0.005 0.078 5084 Dihedral : 19.668 179.596 5265 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.54 % Favored : 93.43 % Rotamer: Outliers : 2.67 % Allowed : 14.83 % Favored : 82.50 % 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 (0.14), residues: 3488 helix: 1.11 (0.14), residues: 1388 sheet: -1.77 (0.24), residues: 419 loop : -1.63 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 113 TYR 0.018 0.002 TYR E 56 PHE 0.031 0.002 PHE B 189 TRP 0.024 0.002 TRP D 656 HIS 0.008 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.27 (30661) covalent geometry : angle 0.69471 / 0.36 (42076) hydrogen bonds : bond 0.04520 / 3.11 ( 1298) hydrogen bonds : angle 4.45874 / 3.10 ( 3575) metal coordination : bond 0.01102 / 0.78 ( 7) metal coordination : angle 2.38855 / 1.09 ( 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 303 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 225 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8907 (pttt) cc_final: 0.8574 (ptmm) REVERT: C 264 LYS cc_start: 0.8361 (mtmt) cc_final: 0.8159 (mttp) REVERT: C 394 SER cc_start: 0.9136 (m) cc_final: 0.8816 (p) REVERT: C 404 MET cc_start: 0.8766 (ttt) cc_final: 0.8311 (ttp) REVERT: C 441 ASP cc_start: 0.8119 (t0) cc_final: 0.7855 (t0) REVERT: C 463 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9078 (pt) REVERT: C 584 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8310 (ptp90) REVERT: C 586 MET cc_start: 0.9296 (ptm) cc_final: 0.8514 (ppp) REVERT: C 661 MET cc_start: 0.8627 (tpt) cc_final: 0.8246 (tpt) REVERT: C 758 ASP cc_start: 0.8071 (p0) cc_final: 0.7535 (p0) REVERT: C 779 GLU cc_start: 0.8356 (tt0) cc_final: 0.7760 (tp30) REVERT: C 1071 MET cc_start: 0.8908 (mtp) cc_final: 0.8589 (mtt) REVERT: C 1110 GLU cc_start: 0.8251 (mp0) cc_final: 0.7919 (mp0) REVERT: D 817 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8666 (tt) REVERT: D 862 ASP cc_start: 0.8553 (t70) cc_final: 0.8137 (t0) REVERT: D 1112 MET cc_start: 0.8634 (tpp) cc_final: 0.8425 (tpp) REVERT: D 1139 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8358 (mm-40) REVERT: E 66 ASP cc_start: 0.8416 (m-30) cc_final: 0.8028 (m-30) REVERT: F 220 GLU cc_start: 0.8196 (tt0) cc_final: 0.7650 (tp30) REVERT: F 263 MET cc_start: 0.8826 (tmm) cc_final: 0.8534 (tmm) REVERT: F 282 MET cc_start: 0.8774 (mmm) cc_final: 0.8548 (mmm) REVERT: F 437 ASP cc_start: 0.8484 (m-30) cc_final: 0.8233 (m-30) REVERT: F 511 MET cc_start: 0.8871 (tpp) cc_final: 0.8432 (tpp) REVERT: J 76 LYS cc_start: 0.8090 (pmtt) cc_final: 0.7587 (pttt) REVERT: M 72 GLN cc_start: 0.8782 (tt0) cc_final: 0.8302 (tm-30) REVERT: M 95 LYS cc_start: 0.9128 (mtmt) cc_final: 0.8638 (mtmm) REVERT: M 147 ASP cc_start: 0.8693 (p0) cc_final: 0.8095 (m-30) outliers start: 78 outliers final: 60 residues processed: 281 average time/residue: 0.1761 time to fit residues: 82.4445 Evaluate side-chains 283 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 220 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 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 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 295 LEU 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 610 ASN Chi-restraints excluded: chain C residue 683 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 1009 MET Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 148 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 337 THR Chi-restraints excluded: chain D residue 654 SER 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 804 ASP Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 1143 ARG Chi-restraints excluded: chain D residue 1161 MET Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain F residue 516 HIS 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 86 SER Chi-restraints excluded: chain M residue 110 ASP 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: 0.5980 chunk 143 optimal weight: 0.2980 chunk 162 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 310 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN E 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.100812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.070922 restraints weight = 69252.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.073285 restraints weight = 32581.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.074786 restraints weight = 20853.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.075672 restraints weight = 16113.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.076216 restraints weight = 13950.927| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30668 Z= 0.126 Angle : 0.617 9.733 42082 Z= 0.324 Chirality : 0.044 0.316 4789 Planarity : 0.005 0.103 5084 Dihedral : 19.574 179.094 5265 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.39 % Favored : 94.58 % Rotamer: Outliers : 1.95 % Allowed : 15.68 % Favored : 82.36 % 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: -0.58 (0.15), residues: 3488 helix: 1.27 (0.14), residues: 1380 sheet: -1.64 (0.26), residues: 384 loop : -1.50 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 159 TYR 0.015 0.001 TYR D 915 PHE 0.015 0.001 PHE C 252 TRP 0.026 0.002 TRP D 656 HIS 0.006 0.001 HIS E 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 (30661) covalent geometry : angle 0.61636 / 0.32 (42076) hydrogen bonds : bond 0.03973 / 2.70 ( 1298) hydrogen bonds : angle 4.28607 / 2.99 ( 3575) metal coordination : bond 0.00250 / 0.17 ( 7) metal coordination : angle 1.96273 / 0.94 ( 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 290 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 233 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8878 (pttt) cc_final: 0.8547 (ptmm) REVERT: B 196 VAL cc_start: 0.8773 (OUTLIER) cc_final: 0.8555 (m) REVERT: C 103 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8516 (ptt) REVERT: C 258 MET cc_start: 0.8048 (mmm) cc_final: 0.7705 (mtp) REVERT: C 264 LYS cc_start: 0.8320 (mtmt) cc_final: 0.8104 (mttp) REVERT: C 394 SER cc_start: 0.9085 (m) cc_final: 0.8769 (p) REVERT: C 404 MET cc_start: 0.8721 (ttt) cc_final: 0.8294 (ttt) REVERT: C 441 ASP cc_start: 0.7937 (t0) cc_final: 0.7649 (t0) REVERT: C 463 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9064 (pt) REVERT: C 584 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8210 (ptp90) REVERT: C 586 MET cc_start: 0.9259 (ptm) cc_final: 0.8513 (ppp) REVERT: C 758 ASP cc_start: 0.8003 (p0) cc_final: 0.7423 (p0) REVERT: C 779 GLU cc_start: 0.8323 (tt0) cc_final: 0.7725 (tp30) REVERT: C 1071 MET cc_start: 0.8851 (mtp) cc_final: 0.8494 (mtt) REVERT: C 1110 GLU cc_start: 0.8056 (mp0) cc_final: 0.7740 (mp0) REVERT: D 379 ASP cc_start: 0.8135 (m-30) cc_final: 0.7744 (m-30) REVERT: D 817 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8413 (tt) REVERT: D 862 ASP cc_start: 0.8507 (t70) cc_final: 0.8089 (t0) REVERT: D 958 THR cc_start: 0.8376 (p) cc_final: 0.8034 (t) REVERT: E 66 ASP cc_start: 0.8359 (m-30) cc_final: 0.7926 (m-30) REVERT: E 88 GLN cc_start: 0.7876 (tp40) cc_final: 0.7447 (tt0) REVERT: F 220 GLU cc_start: 0.8079 (tt0) cc_final: 0.7568 (tp30) REVERT: F 257 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9114 (mp) REVERT: F 263 MET cc_start: 0.8813 (tmm) cc_final: 0.8509 (tmm) REVERT: F 437 ASP cc_start: 0.8448 (m-30) cc_final: 0.8183 (m-30) REVERT: F 511 MET cc_start: 0.8851 (tpp) cc_final: 0.8370 (tpp) REVERT: J 76 LYS cc_start: 0.7960 (pmtt) cc_final: 0.7458 (pttt) REVERT: M 95 LYS cc_start: 0.9122 (mtmt) cc_final: 0.8600 (mtmm) REVERT: M 147 ASP cc_start: 0.8620 (p0) cc_final: 0.8093 (m-30) outliers start: 57 outliers final: 48 residues processed: 274 average time/residue: 0.1683 time to fit residues: 77.1511 Evaluate side-chains 284 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 230 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 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 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 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 610 ASN 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 1009 MET Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 148 LEU 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 337 THR Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 804 ASP Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 1161 MET Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 516 HIS Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 71 PHE Chi-restraints excluded: chain M residue 86 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 17 optimal weight: 2.9990 chunk 298 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 328 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 199 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN M 13 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.098969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.068655 restraints weight = 69798.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.070968 restraints weight = 33375.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.072439 restraints weight = 21559.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.073317 restraints weight = 16738.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.073815 restraints weight = 14529.836| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3570 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= 0.221 Angle : 0.657 9.587 42082 Z= 0.343 Chirality : 0.045 0.329 4789 Planarity : 0.005 0.104 5084 Dihedral : 19.575 179.819 5265 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.16 % Favored : 93.81 % Rotamer: Outliers : 2.26 % Allowed : 15.55 % Favored : 82.19 % 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: -0.62 (0.15), residues: 3488 helix: 1.27 (0.14), residues: 1379 sheet: -1.63 (0.25), residues: 394 loop : -1.55 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D1143 TYR 0.016 0.001 TYR E 56 PHE 0.035 0.002 PHE B 189 TRP 0.025 0.001 TRP D 656 HIS 0.008 0.001 HIS E 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.22 (30661) covalent geometry : angle 0.65634 / 0.34 (42076) hydrogen bonds : bond 0.04244 / 2.90 ( 1298) hydrogen bonds : angle 4.35983 / 3.03 ( 3575) metal coordination : bond 0.00869 / 0.61 ( 7) metal coordination : angle 2.12631 / 0.93 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5537.12 seconds wall clock time: 96 minutes 21.47 seconds (5781.47 seconds total)