Starting phenix.real_space_refine on Fri Mar 6 09:32:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vw0_21409/03_2026/6vw0_21409.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vw0_21409/03_2026/6vw0_21409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vw0_21409/03_2026/6vw0_21409.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vw0_21409/03_2026/6vw0_21409.map" model { file = "/net/cci-nas-00/data/ceres_data/6vw0_21409/03_2026/6vw0_21409.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vw0_21409/03_2026/6vw0_21409.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.100 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 130 5.49 5 Mg 1 5.21 5 S 99 5.16 5 C 18357 2.51 5 N 5353 2.21 5 O 6002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29944 Number of models: 1 Model: "" Number of chains: 11 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: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1765 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 220} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 8584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8584 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1048} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 9914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1270, 9914 Classifications: {'peptide': 1270} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 57, 'TRANS': 1208} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 76} Chain: "F" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2527 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 313} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 33 Chain: "J" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 880 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 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: "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: 1329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1329 Classifications: {'DNA': 65} Link IDs: {'rna3p': 64} 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 19133 SG CYS D 891 112.726 89.320 99.740 1.00 96.90 S ATOM 19700 SG CYS D 968 109.936 90.565 97.781 1.00103.03 S ATOM 19742 SG CYS D 975 109.788 88.988 101.775 1.00 96.82 S ATOM 19760 SG CYS D 978 111.640 92.346 101.270 1.00 96.36 S ATOM 12571 SG CYS D 60 58.061 67.412 66.859 1.00120.11 S ATOM 12589 SG CYS D 62 56.210 67.389 63.688 1.00122.48 S ATOM 12724 SG CYS D 78 59.995 69.855 64.371 1.00120.64 S Time building chain proxies: 5.93, per 1000 atoms: 0.20 Number of scatterers: 29944 At special positions: 0 Unit cell: (140.4, 169, 187.2, 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 130 15.00 Mg 1 11.99 O 6002 8.00 N 5353 7.00 C 18357 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: 2.61 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 968 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 891 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 62 " Number of angles added : 6 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6480 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 43 sheets defined 41.8% alpha, 13.5% beta 52 base pairs and 94 stacking pairs defined. Time for finding SS restraints: 3.74 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 203 through 223 removed outlier: 4.064A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 44 removed outlier: 3.655A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 203 through 224 removed outlier: 4.216A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.424A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 removed outlier: 3.790A pdb=" N SER C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) removed outlier: 3.812A 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: 3.805A 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: 3.609A pdb=" N ASP C 276 " --> pdb=" O GLU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 301 removed outlier: 3.785A pdb=" N ALA C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU C 297 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 321 Processing helix chain 'C' and resid 334 through 350 Processing helix chain 'C' and resid 380 through 407 removed outlier: 3.778A pdb=" N ARG C 395 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.993A 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: 3.668A pdb=" N GLY C 448 " --> pdb=" O ASN C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 474 removed outlier: 3.787A pdb=" N ARG C 473 " --> pdb=" O GLY C 469 " (cutoff:3.500A) removed outlier: 3.676A 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 532 through 539 removed outlier: 3.705A pdb=" N HIS C 539 " --> pdb=" O GLU C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 593 removed outlier: 3.598A pdb=" N MET C 593 " --> pdb=" O VAL C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 631 through 637 Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 779 through 783 removed outlier: 3.771A pdb=" N ALA C 782 " --> pdb=" O GLU C 779 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP C 783 " --> pdb=" O VAL C 780 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 779 through 783' Processing helix chain 'C' and resid 815 through 825 Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 981 through 990 removed outlier: 3.557A pdb=" N SER C 990 " --> pdb=" O GLN C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1041 removed outlier: 3.513A pdb=" N LYS C1040 " --> pdb=" O LEU C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1080 removed outlier: 3.510A pdb=" N GLY C1080 " --> pdb=" O MET C1076 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1090 removed outlier: 3.845A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.140A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.635A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 84 through 90 removed outlier: 3.707A pdb=" N VAL D 87 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 109 removed outlier: 3.819A pdb=" N GLY D 109 " --> pdb=" O TRP D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 129 Processing helix chain 'D' and resid 141 through 185 Processing helix chain 'D' and resid 192 through 228 removed outlier: 3.758A pdb=" N VAL D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 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: 4.083A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.600A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 339 through 361 removed outlier: 4.026A 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 402 through 406 Processing helix chain 'D' and resid 411 through 417 Processing helix chain 'D' and resid 445 through 452 removed outlier: 4.324A 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 478 Processing helix chain 'D' and resid 481 through 492 removed outlier: 4.470A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 580 through 590 Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 667 through 675 removed outlier: 3.978A pdb=" N VAL D 671 " --> pdb=" O THR D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 726 removed outlier: 3.994A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.998A pdb=" N LYS D 755 " --> pdb=" O GLU D 751 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL D 756 " --> pdb=" O ARG D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 810 through 818 removed outlier: 3.984A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 4.148A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 882 through 884 No H-bonds generated for 'chain 'D' and resid 882 through 884' Processing helix chain 'D' and resid 945 through 956 removed outlier: 3.720A pdb=" N ILE D 949 " --> pdb=" O GLY D 945 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1005 removed outlier: 3.526A pdb=" N VAL D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1006 through 1010 removed outlier: 3.587A pdb=" N LEU D1010 " --> pdb=" O GLY D1007 " (cutoff:3.500A) Processing helix chain 'D' and resid 1027 through 1036 removed outlier: 3.597A pdb=" N VAL D1031 " --> pdb=" O GLY D1027 " (cutoff:3.500A) Processing helix chain 'D' and resid 1117 through 1145 Proline residue: D1127 - end of helix removed outlier: 4.160A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLN D1131 " --> pdb=" O PRO D1127 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE D1132 " --> pdb=" O ARG D1128 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG D1136 " --> pdb=" O ILE D1132 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA D1144 " --> pdb=" O GLU D1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 1151 through 1162 removed outlier: 3.623A pdb=" N VAL D1156 " --> pdb=" O LYS D1152 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE D1157 " --> pdb=" O HIS D1153 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D1162 " --> pdb=" O VAL D1158 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1195 removed outlier: 3.671A pdb=" N ALA D1188 " --> pdb=" O ALA D1184 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN D1190 " --> pdb=" O PHE D1186 " (cutoff:3.500A) removed outlier: 3.573A 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 1225 removed outlier: 3.799A pdb=" N ALA D1223 " --> pdb=" O SER D1219 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1228 through 1240 removed outlier: 3.666A pdb=" N LEU D1233 " --> pdb=" O THR D1229 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) Processing helix chain 'D' and resid 1248 through 1254 removed outlier: 3.702A pdb=" N VAL D1252 " --> pdb=" O LEU D1248 " (cutoff:3.500A) Processing helix chain 'D' and resid 1276 through 1281 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.771A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 49 through 70 Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'F' and resid 209 through 220 Processing helix chain 'F' and resid 226 through 236 Processing helix chain 'F' and resid 242 through 268 Processing helix chain 'F' and resid 274 through 299 removed outlier: 3.573A pdb=" N ASP F 289 " --> pdb=" O CYS F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 308 removed outlier: 3.648A pdb=" N VAL F 303 " --> pdb=" O ASN F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 334 removed outlier: 3.764A pdb=" N LEU F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 363 removed outlier: 3.773A pdb=" N TYR F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 390 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 406 through 417 Processing helix chain 'F' and resid 434 through 439 removed outlier: 4.052A pdb=" N ILE F 439 " --> pdb=" O GLY F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 467 removed outlier: 3.829A pdb=" N LEU F 467 " --> pdb=" O VAL F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 468 through 480 Processing helix chain 'F' and resid 488 through 496 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: 3.566A 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 76 Processing helix chain 'M' and resid 84 through 99 removed outlier: 3.853A pdb=" N GLY M 99 " --> pdb=" O LYS M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 118 Processing helix chain 'M' and resid 121 through 143 Processing helix chain 'M' and resid 146 through 160 removed outlier: 3.535A pdb=" N ALA M 159 " --> pdb=" O ASP M 155 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 6.027A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LYS A 191 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL A 178 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 193 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N TYR A 176 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASP A 195 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL A 174 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLU A 197 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.912A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 100 removed outlier: 3.532A pdb=" N SER A 166 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 105 removed outlier: 3.827A pdb=" N GLY A 103 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 126 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 13 through 15 removed outlier: 5.465A pdb=" N VAL B 13 " --> pdb=" O GLN B 20 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN B 20 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG B 18 " --> pdb=" O THR B 15 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LYS B 191 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL B 178 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE B 193 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR B 176 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP B 195 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL B 174 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLU B 197 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.252A pdb=" N TYR B 96 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER B 53 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU B 141 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL B 51 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY B 143 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ALA B 49 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE B 162 " --> pdb=" O ILE B 54 " (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 Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 147 removed outlier: 3.527A pdb=" N SER B 166 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.335A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.812A pdb=" N GLU C 146 " --> pdb=" O ASN C 141 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG M 47 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TYR M 34 " --> pdb=" O ILE M 22 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE M 22 " --> pdb=" O TYR M 34 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL M 36 " --> pdb=" O GLU M 20 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 110 through 112 removed outlier: 4.281A pdb=" N GLY C 155 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL C 135 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N PHE C 153 " --> pdb=" O VAL C 135 " (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 376 through 379 Processing sheet with id=AB6, first strand: chain 'C' and resid 184 through 191 removed outlier: 3.520A pdb=" N TYR C 186 " --> pdb=" O LYS C 203 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N HIS C 200 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 216 " --> pdb=" O HIS C 200 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL C 202 " --> pdb=" O PHE C 214 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE C 214 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU C 212 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AB8, first strand: chain 'C' and resid 505 through 506 removed outlier: 3.631A pdb=" N ARG C 505 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 523 through 530 removed outlier: 6.591A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS C 518 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 541 through 542 Processing sheet with id=AC2, first strand: chain 'C' and resid 558 through 559 removed outlier: 3.519A pdb=" N VAL C 571 " --> pdb=" O VAL C 559 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.534A 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: 5.896A pdb=" N MET C 661 " --> pdb=" O ILE C 650 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ILE C 650 " --> pdb=" O MET C 661 " (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: 6.935A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 765 through 766 removed outlier: 6.593A pdb=" N ASP C 761 " --> pdb=" O VAL C 865 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL C 865 " --> pdb=" O ASP C 761 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.183A 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 removed outlier: 6.851A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 944 through 945 Processing sheet with id=AD2, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 3.551A pdb=" N SER D 428 " --> pdb=" O MET D 541 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N CYS D 441 " --> pdb=" O MET D 515 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL D 517 " --> pdb=" O CYS D 441 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 7.531A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1067 through 1068 Processing sheet with id=AD5, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AD6, first strand: chain 'D' and resid 93 through 102 removed outlier: 7.047A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 11.663A pdb=" N ALA D 99 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 10.529A pdb=" N VAL D 313 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 233 through 235 removed outlier: 4.158A pdb=" N GLN D 233 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 327 through 329 removed outlier: 6.344A pdb=" N PHE D 335 " --> pdb=" O ILE F 421 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 611 through 612 removed outlier: 3.717A pdb=" N VAL D 635 " --> pdb=" O ALA D 664 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 898 through 899 removed outlier: 3.700A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 929 through 930 removed outlier: 6.699A pdb=" N ALA D 929 " --> pdb=" O ILE D 937 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1053 through 1054 removed outlier: 6.392A pdb=" N TYR D1062 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LYS D1079 " --> pdb=" O TYR D1062 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1164 through 1165 Processing sheet with id=AE5, first strand: chain 'D' and resid 1271 through 1273 removed outlier: 3.522A pdb=" N ALA D1271 " --> pdb=" O THR E 107 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 440 through 441 removed outlier: 5.639A pdb=" N GLU F 440 " --> pdb=" O GLY J 8 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'J' and resid 39 through 42 1184 hydrogen bonds defined for protein. 3405 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 134 hydrogen bonds 268 hydrogen bond angles 0 basepair planarities 52 basepair parallelities 94 stacking parallelities Total time for adding SS restraints: 7.21 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8180 1.33 - 1.45: 5644 1.45 - 1.57: 16459 1.57 - 1.69: 258 1.69 - 1.81: 175 Bond restraints: 30716 Sorted by residual: bond pdb=" C ILE C 723 " pdb=" N MET C 724 " ideal model delta sigma weight residual 1.339 1.208 0.131 5.57e-02 3.22e+02 5.54e+00 bond pdb=" CB TRP D 23 " pdb=" CG TRP D 23 " ideal model delta sigma weight residual 1.498 1.425 0.073 3.10e-02 1.04e+03 5.53e+00 bond pdb=" CB VAL D 880 " pdb=" CG2 VAL D 880 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.51e+00 bond pdb=" C3' DT O 42 " pdb=" O3' DT O 42 " ideal model delta sigma weight residual 1.422 1.488 -0.066 3.00e-02 1.11e+03 4.83e+00 bond pdb=" C3' DT P 105 " pdb=" O3' DT P 105 " ideal model delta sigma weight residual 1.422 1.485 -0.063 3.00e-02 1.11e+03 4.46e+00 ... (remaining 30711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 41493 3.00 - 6.01: 601 6.01 - 9.01: 64 9.01 - 12.01: 5 12.01 - 15.01: 2 Bond angle restraints: 42165 Sorted by residual: angle pdb=" C ARG D 834 " pdb=" N PRO D 835 " pdb=" CA PRO D 835 " ideal model delta sigma weight residual 127.00 142.01 -15.01 2.40e+00 1.74e-01 3.91e+01 angle pdb=" C TYR A 168 " pdb=" N SER A 169 " pdb=" CA SER A 169 " ideal model delta sigma weight residual 122.26 115.41 6.85 1.10e+00 8.26e-01 3.88e+01 angle pdb=" C ASP D1070 " pdb=" N GLY D1071 " pdb=" CA GLY D1071 " ideal model delta sigma weight residual 121.70 132.70 -11.00 1.80e+00 3.09e-01 3.73e+01 angle pdb=" C ARG D 834 " pdb=" N PRO D 835 " pdb=" CD PRO D 835 " ideal model delta sigma weight residual 120.60 108.12 12.48 2.20e+00 2.07e-01 3.22e+01 angle pdb=" N GLN D 657 " pdb=" CA GLN D 657 " pdb=" C GLN D 657 " ideal model delta sigma weight residual 109.81 121.38 -11.57 2.21e+00 2.05e-01 2.74e+01 ... (remaining 42160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 17244 35.91 - 71.81: 1149 71.81 - 107.72: 19 107.72 - 143.62: 3 143.62 - 179.53: 5 Dihedral angle restraints: 18420 sinusoidal: 8348 harmonic: 10072 Sorted by residual: dihedral pdb=" CA ARG C 282 " pdb=" C ARG C 282 " pdb=" N PRO C 283 " pdb=" CA PRO C 283 " ideal model delta harmonic sigma weight residual -180.00 -129.67 -50.33 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA THR D1173 " pdb=" C THR D1173 " pdb=" N GLU D1174 " pdb=" CA GLU D1174 " ideal model delta harmonic sigma weight residual 180.00 145.98 34.02 0 5.00e+00 4.00e-02 4.63e+01 dihedral pdb=" CA THR M 145 " pdb=" C THR M 145 " pdb=" N ASP M 146 " pdb=" CA ASP M 146 " ideal model delta harmonic sigma weight residual 180.00 153.40 26.60 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 18417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4040 0.076 - 0.152: 720 0.152 - 0.228: 41 0.228 - 0.304: 3 0.304 - 0.380: 1 Chirality restraints: 4805 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 2.13 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CB ILE A 167 " pdb=" CA ILE A 167 " pdb=" CG1 ILE A 167 " pdb=" CG2 ILE A 167 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CB VAL C 587 " pdb=" CA VAL C 587 " pdb=" CG1 VAL C 587 " pdb=" CG2 VAL C 587 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 4802 not shown) Planarity restraints: 5085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 282 " -0.064 5.00e-02 4.00e+02 9.77e-02 1.53e+01 pdb=" N PRO C 283 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO C 283 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 283 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 413 " 0.050 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO C 414 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO C 414 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 414 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D1273 " -0.047 5.00e-02 4.00e+02 6.98e-02 7.80e+00 pdb=" N PRO D1274 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO D1274 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO D1274 " -0.039 5.00e-02 4.00e+02 ... (remaining 5082 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 1253 2.68 - 3.24: 27754 3.24 - 3.79: 53105 3.79 - 4.35: 61872 4.35 - 4.90: 101750 Nonbonded interactions: 245734 Sorted by model distance: nonbonded pdb=" OD1 ASP D 537 " pdb="MG MG D2002 " model vdw 2.126 2.170 nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2002 " model vdw 2.135 2.170 nonbonded pdb=" OD2 ASP D 537 " pdb="MG MG D2002 " model vdw 2.149 2.170 nonbonded pdb=" OD2 ASP D 535 " pdb="MG MG D2002 " model vdw 2.155 2.170 nonbonded pdb=" N CYS D 62 " pdb="ZN ZN D2001 " model vdw 2.184 2.310 ... (remaining 245729 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 223 o \ r (resid 224 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 25 through 226)) selection = (chain 'B' and resid 2 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 33.250 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 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 : 0.010 0.154 30723 Z= 0.450 Angle : 0.964 16.448 42171 Z= 0.526 Chirality : 0.056 0.380 4805 Planarity : 0.007 0.098 5085 Dihedral : 20.443 179.530 11940 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.89 % Favored : 92.05 % Rotamer: Outliers : 6.78 % Allowed : 24.07 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % Twisted Proline : 0.57 % 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: -3.75 (0.11), residues: 3496 helix: -2.22 (0.10), residues: 1375 sheet: -2.52 (0.25), residues: 347 loop : -2.71 (0.12), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 88 TYR 0.019 0.002 TYR D 704 PHE 0.021 0.003 PHE C 301 TRP 0.018 0.003 TRP D 656 HIS 0.009 0.002 HIS D 525 Details of bonding type rmsd covalent geometry : bond 0.00999 (30716) covalent geometry : angle 0.95100 (42165) hydrogen bonds : bond 0.15771 ( 1306) hydrogen bonds : angle 7.09963 ( 3673) metal coordination : bond 0.11131 ( 7) metal coordination : angle 13.31440 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 247 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.9341 (mppt) cc_final: 0.9119 (mtmt) REVERT: B 188 ASP cc_start: 0.7468 (t0) cc_final: 0.7267 (t70) REVERT: C 215 ASP cc_start: 0.8331 (m-30) cc_final: 0.8017 (p0) REVERT: C 279 ARG cc_start: 0.8945 (ttp80) cc_final: 0.8600 (ttp-110) REVERT: C 450 THR cc_start: 0.9393 (OUTLIER) cc_final: 0.9177 (p) REVERT: C 494 ILE cc_start: 0.9550 (OUTLIER) cc_final: 0.9320 (mm) REVERT: C 607 MET cc_start: 0.8525 (mtt) cc_final: 0.8321 (mtt) REVERT: C 661 MET cc_start: 0.8541 (mmm) cc_final: 0.8306 (tpp) REVERT: C 702 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9017 (mm) REVERT: C 814 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.8432 (mm) REVERT: C 907 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9226 (mt) REVERT: C 911 THR cc_start: 0.9403 (OUTLIER) cc_final: 0.9084 (p) REVERT: C 1119 GLU cc_start: 0.8592 (tp30) cc_final: 0.8333 (tp30) REVERT: D 34 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8519 (mt) REVERT: D 92 MET cc_start: 0.8920 (mtp) cc_final: 0.8682 (mtm) REVERT: D 110 VAL cc_start: 0.9420 (OUTLIER) cc_final: 0.8554 (t) REVERT: D 256 MET cc_start: 0.9185 (ttm) cc_final: 0.8970 (ttm) REVERT: D 533 ASN cc_start: 0.9013 (t0) cc_final: 0.8805 (t0) REVERT: D 588 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9139 (tp) REVERT: D 876 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8538 (ttm-80) REVERT: D 1148 SER cc_start: 0.9385 (OUTLIER) cc_final: 0.8934 (p) REVERT: D 1173 THR cc_start: 0.8109 (OUTLIER) cc_final: 0.5828 (t) REVERT: D 1228 GLU cc_start: 0.8601 (pm20) cc_final: 0.8397 (pm20) REVERT: D 1248 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8565 (tt) REVERT: E 29 TYR cc_start: 0.9003 (p90) cc_final: 0.8680 (p90) REVERT: E 35 ILE cc_start: 0.9620 (tp) cc_final: 0.9140 (tt) REVERT: E 70 GLN cc_start: 0.8338 (mm110) cc_final: 0.7873 (mt0) REVERT: E 89 GLU cc_start: 0.8240 (tp30) cc_final: 0.7928 (mt-10) REVERT: F 377 ASN cc_start: 0.9362 (m-40) cc_final: 0.9103 (p0) REVERT: F 422 SER cc_start: 0.9367 (OUTLIER) cc_final: 0.8415 (p) REVERT: J 86 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9195 (pp) outliers start: 198 outliers final: 56 residues processed: 432 average time/residue: 0.1835 time to fit residues: 129.1391 Evaluate side-chains 225 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 154 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 545 ASN Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 664 ASN Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 993 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1096 THR Chi-restraints excluded: chain D residue 3 ASP Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 603 SER Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 730 THR Chi-restraints excluded: chain D residue 732 SER Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 876 ARG Chi-restraints excluded: chain D residue 909 THR Chi-restraints excluded: chain D residue 964 SER Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1148 SER Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1234 THR Chi-restraints excluded: chain D residue 1242 SER Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain D residue 1258 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 422 SER Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 522 VAL Chi-restraints excluded: chain J residue 57 ARG Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 96 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN B 129 ASN C 141 ASN C 142 ASN C 266 ASN C 293 GLN C 419 ASN C 451 HIS C 775 ASN C 920 HIS C1054 GLN D 146 ASN D 207 GLN D 307 ASN D 351 ASN D 368 ASN D 439 HIS D 482 GLN D 499 ASN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 ASN D 606 HIS D 657 GLN D 693 GLN D 797 ASN E 69 ASN F 353 GLN F 388 GLN F 461 GLN J 58 ASN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.065619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.045509 restraints weight = 118107.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.047234 restraints weight = 54653.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.048355 restraints weight = 34524.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.049062 restraints weight = 26098.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.049435 restraints weight = 22113.624| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30723 Z= 0.141 Angle : 0.641 11.876 42171 Z= 0.336 Chirality : 0.042 0.207 4805 Planarity : 0.005 0.094 5085 Dihedral : 19.410 179.430 5377 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.63 % Allowed : 25.13 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % Twisted Proline : 0.57 % 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: -2.14 (0.13), residues: 3496 helix: -0.33 (0.13), residues: 1404 sheet: -2.23 (0.25), residues: 373 loop : -2.18 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1231 TYR 0.011 0.001 TYR D 612 PHE 0.014 0.001 PHE A 63 TRP 0.010 0.001 TRP D 723 HIS 0.005 0.001 HIS C1042 Details of bonding type rmsd covalent geometry : bond 0.00303 (30716) covalent geometry : angle 0.63994 (42165) hydrogen bonds : bond 0.04320 ( 1306) hydrogen bonds : angle 5.22044 ( 3673) metal coordination : bond 0.00661 ( 7) metal coordination : angle 3.71446 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 203 time to evaluate : 1.168 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 127 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8721 (m) REVERT: B 97 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9199 (tt) REVERT: B 179 ASP cc_start: 0.7679 (m-30) cc_final: 0.7298 (m-30) REVERT: B 188 ASP cc_start: 0.7958 (t0) cc_final: 0.7533 (t70) REVERT: C 48 LEU cc_start: 0.9375 (tp) cc_final: 0.9119 (tp) REVERT: C 103 MET cc_start: 0.9236 (ptt) cc_final: 0.7765 (ptt) REVERT: C 404 MET cc_start: 0.8725 (ptt) cc_final: 0.8296 (ptt) REVERT: C 440 MET cc_start: 0.8872 (tmm) cc_final: 0.7283 (tmm) REVERT: C 470 LEU cc_start: 0.9212 (mp) cc_final: 0.8763 (tt) REVERT: C 607 MET cc_start: 0.8397 (mtt) cc_final: 0.8120 (mtp) REVERT: C 661 MET cc_start: 0.8503 (mmm) cc_final: 0.8108 (tpp) REVERT: C 792 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8797 (mm) REVERT: C 1071 MET cc_start: 0.8888 (mtt) cc_final: 0.8579 (mtp) REVERT: C 1119 GLU cc_start: 0.8678 (tp30) cc_final: 0.8264 (tp30) REVERT: D 92 MET cc_start: 0.8877 (mtp) cc_final: 0.8564 (mtm) REVERT: D 259 GLU cc_start: 0.8602 (pt0) cc_final: 0.8273 (tp30) REVERT: D 379 ASP cc_start: 0.8937 (m-30) cc_final: 0.8540 (m-30) REVERT: D 533 ASN cc_start: 0.9253 (t0) cc_final: 0.8913 (t0) REVERT: D 541 MET cc_start: 0.8496 (mtp) cc_final: 0.8260 (ttt) REVERT: D 588 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9235 (tp) REVERT: D 663 MET cc_start: 0.7993 (tpp) cc_final: 0.7657 (tpp) REVERT: D 983 MET cc_start: 0.8630 (mmm) cc_final: 0.8406 (mmt) REVERT: E 35 ILE cc_start: 0.9459 (tp) cc_final: 0.9005 (tt) REVERT: E 66 ASP cc_start: 0.9266 (m-30) cc_final: 0.8500 (t0) REVERT: F 263 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8469 (mtt) REVERT: F 310 TYR cc_start: 0.8980 (m-80) cc_final: 0.8647 (m-80) REVERT: J 19 ASP cc_start: 0.8079 (t0) cc_final: 0.7815 (t0) REVERT: J 57 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8261 (ptp-170) REVERT: J 58 ASN cc_start: 0.8883 (OUTLIER) cc_final: 0.8550 (t0) REVERT: J 84 MET cc_start: 0.9307 (mtp) cc_final: 0.9095 (mtt) REVERT: J 86 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9162 (pp) REVERT: M 47 ARG cc_start: 0.8953 (mtt180) cc_final: 0.8749 (ttp-110) REVERT: M 68 ASP cc_start: 0.8811 (p0) cc_final: 0.8483 (p0) REVERT: M 85 TRP cc_start: 0.8308 (OUTLIER) cc_final: 0.7318 (t60) REVERT: M 133 GLN cc_start: 0.9033 (tm-30) cc_final: 0.8754 (tm-30) REVERT: M 146 ASP cc_start: 0.8858 (m-30) cc_final: 0.8641 (p0) outliers start: 106 outliers final: 35 residues processed: 298 average time/residue: 0.1874 time to fit residues: 90.4290 Evaluate side-chains 203 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 151 GLN Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 787 ARG Chi-restraints excluded: chain C residue 792 ILE Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 656 TRP Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 1055 LEU Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1232 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 422 SER Chi-restraints excluded: chain J residue 57 ARG Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain M residue 85 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 95 optimal weight: 0.4980 chunk 65 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 290 optimal weight: 5.9990 chunk 37 optimal weight: 0.2980 chunk 351 optimal weight: 7.9990 chunk 265 optimal weight: 4.9990 chunk 215 optimal weight: 0.0970 chunk 136 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 179 optimal weight: 7.9990 overall best weight: 2.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN C 298 ASN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 854 HIS D1273 GLN F 294 HIS M 13 HIS M 14 HIS ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.065210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.045082 restraints weight = 118834.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.046783 restraints weight = 55196.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.047878 restraints weight = 34928.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.048570 restraints weight = 26490.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.048954 restraints weight = 22467.237| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30723 Z= 0.183 Angle : 0.629 12.632 42171 Z= 0.328 Chirality : 0.042 0.191 4805 Planarity : 0.005 0.088 5085 Dihedral : 19.197 179.466 5294 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.95 % Favored : 94.02 % Rotamer: Outliers : 3.39 % Allowed : 26.26 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % Twisted Proline : 0.57 % 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: -1.44 (0.14), residues: 3496 helix: 0.46 (0.14), residues: 1414 sheet: -2.02 (0.25), residues: 406 loop : -1.94 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 876 TYR 0.012 0.001 TYR M 89 PHE 0.014 0.001 PHE C 99 TRP 0.011 0.001 TRP D 723 HIS 0.006 0.001 HIS M 13 Details of bonding type rmsd covalent geometry : bond 0.00402 (30716) covalent geometry : angle 0.62843 (42165) hydrogen bonds : bond 0.04150 ( 1306) hydrogen bonds : angle 4.87544 ( 3673) metal coordination : bond 0.00779 ( 7) metal coordination : angle 3.03311 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 162 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8871 (m) REVERT: B 70 LYS cc_start: 0.9392 (tmtt) cc_final: 0.9067 (tmtt) REVERT: B 179 ASP cc_start: 0.7822 (m-30) cc_final: 0.7424 (m-30) REVERT: B 188 ASP cc_start: 0.8015 (t0) cc_final: 0.7622 (t70) REVERT: C 440 MET cc_start: 0.8658 (tmm) cc_final: 0.7406 (tmm) REVERT: C 470 LEU cc_start: 0.9200 (mp) cc_final: 0.8765 (tt) REVERT: C 561 VAL cc_start: 0.9166 (OUTLIER) cc_final: 0.8897 (p) REVERT: C 607 MET cc_start: 0.8290 (mtt) cc_final: 0.7999 (mtp) REVERT: C 611 MET cc_start: 0.8547 (mtm) cc_final: 0.8268 (ptp) REVERT: C 661 MET cc_start: 0.8428 (mmm) cc_final: 0.8083 (tpp) REVERT: C 792 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8850 (mm) REVERT: C 1119 GLU cc_start: 0.8803 (tp30) cc_final: 0.8352 (tp30) REVERT: D 92 MET cc_start: 0.8937 (mtp) cc_final: 0.8605 (mtm) REVERT: D 259 GLU cc_start: 0.8591 (pt0) cc_final: 0.8291 (tp30) REVERT: D 379 ASP cc_start: 0.8995 (m-30) cc_final: 0.8611 (m-30) REVERT: D 404 ASP cc_start: 0.8684 (t0) cc_final: 0.8464 (t0) REVERT: D 533 ASN cc_start: 0.9231 (t0) cc_final: 0.8907 (t0) REVERT: D 588 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9192 (tp) REVERT: D 667 THR cc_start: 0.9406 (OUTLIER) cc_final: 0.9058 (t) REVERT: D 693 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8282 (mt0) REVERT: D 983 MET cc_start: 0.8679 (mmm) cc_final: 0.8441 (mmt) REVERT: D 1063 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8959 (pttm) REVERT: E 30 ASP cc_start: 0.9000 (t70) cc_final: 0.8587 (t0) REVERT: E 35 ILE cc_start: 0.9462 (tp) cc_final: 0.9070 (tt) REVERT: F 263 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8303 (tpp) REVERT: F 377 ASN cc_start: 0.9532 (t0) cc_final: 0.9259 (t0) REVERT: J 60 MET cc_start: 0.8426 (mtm) cc_final: 0.8198 (mtm) REVERT: J 86 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9160 (pp) REVERT: M 47 ARG cc_start: 0.8942 (mtt180) cc_final: 0.8628 (ttm110) REVERT: M 85 TRP cc_start: 0.8289 (OUTLIER) cc_final: 0.7383 (t60) REVERT: M 133 GLN cc_start: 0.9081 (tm-30) cc_final: 0.8812 (tm-30) REVERT: M 146 ASP cc_start: 0.8786 (m-30) cc_final: 0.8560 (p0) outliers start: 99 outliers final: 49 residues processed: 252 average time/residue: 0.1749 time to fit residues: 73.5482 Evaluate side-chains 209 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 150 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 54 ILE 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 151 GLN Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 787 ARG Chi-restraints excluded: chain C residue 792 ILE Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1096 THR Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 1063 LYS Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 422 SER Chi-restraints excluded: chain F residue 448 VAL Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 522 VAL Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain M residue 85 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 2 optimal weight: 3.9990 chunk 253 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 270 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 137 optimal weight: 8.9990 chunk 97 optimal weight: 0.0870 chunk 152 optimal weight: 6.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 662 HIS ** D 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN F 325 ASN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.065282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.045211 restraints weight = 118218.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.046893 restraints weight = 55347.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.047958 restraints weight = 35099.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.048678 restraints weight = 26732.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.049054 restraints weight = 22613.455| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30723 Z= 0.151 Angle : 0.591 12.266 42171 Z= 0.307 Chirality : 0.041 0.249 4805 Planarity : 0.004 0.085 5085 Dihedral : 19.025 179.325 5288 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.83 % Allowed : 26.29 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % Twisted Proline : 0.57 % 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: -0.92 (0.14), residues: 3496 helix: 0.91 (0.14), residues: 1412 sheet: -1.76 (0.26), residues: 391 loop : -1.68 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1231 TYR 0.012 0.001 TYR D 241 PHE 0.012 0.001 PHE D 532 TRP 0.011 0.001 TRP D 656 HIS 0.004 0.001 HIS D 525 Details of bonding type rmsd covalent geometry : bond 0.00332 (30716) covalent geometry : angle 0.58996 (42165) hydrogen bonds : bond 0.03753 ( 1306) hydrogen bonds : angle 4.64866 ( 3673) metal coordination : bond 0.00585 ( 7) metal coordination : angle 2.41834 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 171 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8867 (m) REVERT: B 70 LYS cc_start: 0.9417 (tmtt) cc_final: 0.9096 (tmtt) REVERT: B 95 MET cc_start: 0.8878 (tpp) cc_final: 0.8640 (tpp) REVERT: B 177 LYS cc_start: 0.9117 (ptpp) cc_final: 0.8802 (ptmm) REVERT: B 179 ASP cc_start: 0.7849 (m-30) cc_final: 0.7487 (m-30) REVERT: B 188 ASP cc_start: 0.7988 (t0) cc_final: 0.7610 (t70) REVERT: C 160 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8185 (ttm) REVERT: C 440 MET cc_start: 0.8608 (tmm) cc_final: 0.7444 (tmm) REVERT: C 470 LEU cc_start: 0.9299 (mp) cc_final: 0.8802 (tt) REVERT: C 561 VAL cc_start: 0.9155 (OUTLIER) cc_final: 0.8876 (p) REVERT: C 607 MET cc_start: 0.8349 (mtt) cc_final: 0.8122 (mtm) REVERT: C 661 MET cc_start: 0.8297 (mmm) cc_final: 0.8004 (tpp) REVERT: C 792 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8857 (mm) REVERT: C 1119 GLU cc_start: 0.8807 (tp30) cc_final: 0.8344 (tp30) REVERT: D 92 MET cc_start: 0.8828 (mtp) cc_final: 0.8451 (mtm) REVERT: D 404 ASP cc_start: 0.8806 (t0) cc_final: 0.8541 (t0) REVERT: D 533 ASN cc_start: 0.9153 (t0) cc_final: 0.8850 (t0) REVERT: D 588 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9382 (tp) REVERT: D 667 THR cc_start: 0.9398 (OUTLIER) cc_final: 0.9094 (t) REVERT: D 693 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8356 (mt0) REVERT: D 820 MET cc_start: 0.9094 (ttm) cc_final: 0.8716 (ptm) REVERT: D 865 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8923 (tm) REVERT: D 983 MET cc_start: 0.8746 (mmm) cc_final: 0.8520 (mmt) REVERT: D 1063 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8910 (ptpp) REVERT: D 1131 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8291 (pm20) REVERT: E 30 ASP cc_start: 0.9009 (t70) cc_final: 0.8581 (t0) REVERT: E 35 ILE cc_start: 0.9482 (OUTLIER) cc_final: 0.9133 (tt) REVERT: F 263 MET cc_start: 0.8690 (ttt) cc_final: 0.8338 (tpp) REVERT: F 377 ASN cc_start: 0.9494 (t0) cc_final: 0.9227 (t0) REVERT: J 58 ASN cc_start: 0.9059 (OUTLIER) cc_final: 0.8752 (t0) REVERT: J 60 MET cc_start: 0.8384 (mtm) cc_final: 0.8134 (mtm) REVERT: J 86 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.9153 (pp) REVERT: M 133 GLN cc_start: 0.9070 (tm-30) cc_final: 0.8760 (tm-30) outliers start: 112 outliers final: 60 residues processed: 268 average time/residue: 0.1750 time to fit residues: 77.5333 Evaluate side-chains 224 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 151 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 151 GLN Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 792 ILE Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 993 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1027 TYR Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1100 VAL Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 782 THR Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 1063 LYS Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1131 GLN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain M residue 33 GLU Chi-restraints excluded: chain M residue 85 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 299 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 300 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 356 optimal weight: 20.0000 chunk 220 optimal weight: 5.9990 chunk 211 optimal weight: 8.9990 chunk 303 optimal weight: 1.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 GLN C 232 GLN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.064475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.044374 restraints weight = 119926.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.046027 restraints weight = 56398.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.047110 restraints weight = 35860.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.047780 restraints weight = 27247.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.048197 restraints weight = 23182.095| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 30723 Z= 0.208 Angle : 0.624 12.998 42171 Z= 0.323 Chirality : 0.042 0.279 4805 Planarity : 0.004 0.084 5085 Dihedral : 19.010 179.899 5286 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.42 % Allowed : 26.26 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % Twisted Proline : 0.57 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.14), residues: 3496 helix: 1.12 (0.14), residues: 1403 sheet: -1.70 (0.26), residues: 393 loop : -1.57 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 159 TYR 0.015 0.001 TYR D 704 PHE 0.013 0.001 PHE C 301 TRP 0.009 0.001 TRP D 723 HIS 0.005 0.001 HIS D1150 Details of bonding type rmsd covalent geometry : bond 0.00460 (30716) covalent geometry : angle 0.62338 (42165) hydrogen bonds : bond 0.03986 ( 1306) hydrogen bonds : angle 4.64567 ( 3673) metal coordination : bond 0.00912 ( 7) metal coordination : angle 2.47995 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 158 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 THR cc_start: 0.9152 (OUTLIER) cc_final: 0.8891 (m) REVERT: A 168 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.7945 (m-80) REVERT: B 70 LYS cc_start: 0.9406 (tmtt) cc_final: 0.9111 (tmtt) REVERT: B 177 LYS cc_start: 0.9122 (ptpp) cc_final: 0.8811 (ptmm) REVERT: B 179 ASP cc_start: 0.7945 (m-30) cc_final: 0.7569 (m-30) REVERT: B 188 ASP cc_start: 0.7998 (t0) cc_final: 0.7653 (t70) REVERT: C 103 MET cc_start: 0.9399 (OUTLIER) cc_final: 0.8768 (ppp) REVERT: C 279 ARG cc_start: 0.9165 (ttp80) cc_final: 0.8721 (mtm110) REVERT: C 396 MET cc_start: 0.9079 (ttp) cc_final: 0.8287 (tmm) REVERT: C 440 MET cc_start: 0.8621 (tmm) cc_final: 0.7459 (tmm) REVERT: C 470 LEU cc_start: 0.9295 (mp) cc_final: 0.8803 (tt) REVERT: C 561 VAL cc_start: 0.9219 (OUTLIER) cc_final: 0.8957 (p) REVERT: C 661 MET cc_start: 0.8330 (mmm) cc_final: 0.8054 (tpp) REVERT: C 792 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8942 (mm) REVERT: C 827 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: C 907 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9105 (mt) REVERT: C 1119 GLU cc_start: 0.8811 (tp30) cc_final: 0.8369 (tp30) REVERT: D 92 MET cc_start: 0.8924 (mtp) cc_final: 0.8538 (mtm) REVERT: D 114 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8995 (mt) REVERT: D 143 MET cc_start: 0.7028 (pmm) cc_final: 0.6756 (pmm) REVERT: D 187 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6557 (pm20) REVERT: D 404 ASP cc_start: 0.8817 (t0) cc_final: 0.8527 (t0) REVERT: D 533 ASN cc_start: 0.9235 (t0) cc_final: 0.8967 (t0) REVERT: D 588 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9334 (tp) REVERT: D 667 THR cc_start: 0.9413 (OUTLIER) cc_final: 0.9028 (t) REVERT: D 693 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8318 (mt0) REVERT: D 865 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8920 (tm) REVERT: D 944 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.9010 (tt) REVERT: D 983 MET cc_start: 0.8886 (mmm) cc_final: 0.8637 (mmt) REVERT: D 1131 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8303 (pm20) REVERT: E 30 ASP cc_start: 0.9054 (t70) cc_final: 0.8609 (t0) REVERT: E 35 ILE cc_start: 0.9482 (tp) cc_final: 0.9158 (tt) REVERT: E 40 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8281 (tp) REVERT: E 84 GLU cc_start: 0.8767 (tp30) cc_final: 0.8295 (tp30) REVERT: F 263 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8395 (tpp) REVERT: F 377 ASN cc_start: 0.9501 (t0) cc_final: 0.9154 (t0) REVERT: J 58 ASN cc_start: 0.9122 (OUTLIER) cc_final: 0.8913 (t0) REVERT: J 60 MET cc_start: 0.8326 (mtm) cc_final: 0.8086 (mtm) REVERT: J 86 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9145 (pp) REVERT: M 133 GLN cc_start: 0.9095 (tm-30) cc_final: 0.8794 (tm-30) outliers start: 129 outliers final: 75 residues processed: 273 average time/residue: 0.1697 time to fit residues: 78.3888 Evaluate side-chains 244 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 150 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 151 GLN Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 792 ILE Chi-restraints excluded: chain C residue 827 GLU Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 939 CYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 993 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1096 THR Chi-restraints excluded: chain C residue 1100 VAL Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 775 VAL Chi-restraints excluded: chain D residue 782 THR Chi-restraints excluded: chain D residue 805 SER Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1131 GLN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 522 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 85 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 349 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 chunk 287 optimal weight: 0.9980 chunk 263 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 336 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 291 optimal weight: 20.0000 chunk 88 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN ** D1131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN M 64 GLN ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.065566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.045577 restraints weight = 118833.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.047252 restraints weight = 55288.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.048322 restraints weight = 34906.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.049011 restraints weight = 26508.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.049436 restraints weight = 22479.891| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30723 Z= 0.143 Angle : 0.584 12.310 42171 Z= 0.303 Chirality : 0.041 0.186 4805 Planarity : 0.004 0.083 5085 Dihedral : 18.925 179.685 5286 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.90 % Allowed : 26.74 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % Twisted Proline : 0.57 % 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: -0.48 (0.15), residues: 3496 helix: 1.33 (0.14), residues: 1400 sheet: -1.60 (0.26), residues: 400 loop : -1.44 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1060 TYR 0.012 0.001 TYR D 36 PHE 0.009 0.001 PHE C 301 TRP 0.010 0.001 TRP D 656 HIS 0.004 0.001 HIS D 525 Details of bonding type rmsd covalent geometry : bond 0.00317 (30716) covalent geometry : angle 0.58316 (42165) hydrogen bonds : bond 0.03607 ( 1306) hydrogen bonds : angle 4.50642 ( 3673) metal coordination : bond 0.00529 ( 7) metal coordination : angle 2.01284 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 161 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8872 (m) REVERT: A 168 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.7960 (m-80) REVERT: B 70 LYS cc_start: 0.9390 (tmtt) cc_final: 0.9098 (tmtt) REVERT: B 177 LYS cc_start: 0.9119 (ptpp) cc_final: 0.8812 (ptmm) REVERT: B 179 ASP cc_start: 0.7899 (m-30) cc_final: 0.7504 (m-30) REVERT: B 188 ASP cc_start: 0.7964 (t0) cc_final: 0.7632 (t70) REVERT: C 103 MET cc_start: 0.9382 (OUTLIER) cc_final: 0.8722 (ppp) REVERT: C 279 ARG cc_start: 0.9133 (ttp80) cc_final: 0.8655 (mtm110) REVERT: C 396 MET cc_start: 0.9086 (ttp) cc_final: 0.8309 (tmm) REVERT: C 470 LEU cc_start: 0.9256 (mp) cc_final: 0.8612 (tt) REVERT: C 561 VAL cc_start: 0.9156 (OUTLIER) cc_final: 0.8876 (p) REVERT: C 661 MET cc_start: 0.8351 (mmm) cc_final: 0.8076 (tpp) REVERT: C 792 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8926 (mm) REVERT: C 907 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9137 (mt) REVERT: C 1119 GLU cc_start: 0.8815 (tp30) cc_final: 0.8337 (tp30) REVERT: D 187 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6525 (pm20) REVERT: D 424 TYR cc_start: 0.9295 (m-80) cc_final: 0.9007 (m-80) REVERT: D 533 ASN cc_start: 0.9213 (t0) cc_final: 0.8947 (t0) REVERT: D 588 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9371 (tp) REVERT: D 667 THR cc_start: 0.9389 (OUTLIER) cc_final: 0.9036 (t) REVERT: D 693 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8356 (mt0) REVERT: D 820 MET cc_start: 0.9098 (ttm) cc_final: 0.8750 (ptm) REVERT: D 865 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8747 (tm) REVERT: D 1131 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8298 (pm20) REVERT: E 30 ASP cc_start: 0.9062 (t70) cc_final: 0.8616 (t0) REVERT: E 35 ILE cc_start: 0.9456 (OUTLIER) cc_final: 0.9133 (tt) REVERT: E 40 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8209 (tp) REVERT: E 84 GLU cc_start: 0.8768 (tp30) cc_final: 0.8385 (tp30) REVERT: F 263 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8386 (tpp) REVERT: F 377 ASN cc_start: 0.9511 (t0) cc_final: 0.9165 (t0) REVERT: J 60 MET cc_start: 0.8256 (mtm) cc_final: 0.8000 (mtm) REVERT: J 84 MET cc_start: 0.9147 (mtp) cc_final: 0.8738 (mtt) REVERT: J 86 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9138 (pp) REVERT: M 85 TRP cc_start: 0.8116 (OUTLIER) cc_final: 0.7577 (t60) REVERT: M 133 GLN cc_start: 0.9049 (tm-30) cc_final: 0.8761 (tm-30) REVERT: M 134 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.9081 (pp) outliers start: 114 outliers final: 71 residues processed: 257 average time/residue: 0.1694 time to fit residues: 74.0241 Evaluate side-chains 240 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 151 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 124 HIS 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 B residue 198 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 792 ILE Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 939 CYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 993 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1096 THR Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 651 PHE Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 782 THR Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 1039 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1131 GLN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 522 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 134 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 35 optimal weight: 6.9990 chunk 278 optimal weight: 7.9990 chunk 289 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 340 optimal weight: 0.0670 chunk 68 optimal weight: 8.9990 chunk 288 optimal weight: 0.0030 chunk 111 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 348 optimal weight: 20.0000 chunk 159 optimal weight: 0.9980 overall best weight: 0.5728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.066497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.046942 restraints weight = 117048.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.048578 restraints weight = 55274.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.049620 restraints weight = 35206.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.050307 restraints weight = 26865.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.050732 restraints weight = 22758.609| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30723 Z= 0.115 Angle : 0.571 11.332 42171 Z= 0.295 Chirality : 0.041 0.171 4805 Planarity : 0.004 0.082 5085 Dihedral : 18.792 179.746 5284 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.01 % Allowed : 27.32 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % Twisted Proline : 0.57 % 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: -0.30 (0.15), residues: 3496 helix: 1.50 (0.14), residues: 1400 sheet: -1.43 (0.26), residues: 393 loop : -1.38 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D1060 TYR 0.011 0.001 TYR D 36 PHE 0.022 0.001 PHE F 438 TRP 0.012 0.001 TRP D 656 HIS 0.009 0.001 HIS D1150 Details of bonding type rmsd covalent geometry : bond 0.00252 (30716) covalent geometry : angle 0.57110 (42165) hydrogen bonds : bond 0.03337 ( 1306) hydrogen bonds : angle 4.34259 ( 3673) metal coordination : bond 0.00245 ( 7) metal coordination : angle 1.56479 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 183 time to evaluate : 0.921 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: B 70 LYS cc_start: 0.9356 (tmtt) cc_final: 0.9075 (tmtt) REVERT: B 177 LYS cc_start: 0.9112 (ptpp) cc_final: 0.8809 (ptmm) REVERT: B 179 ASP cc_start: 0.8020 (m-30) cc_final: 0.7651 (m-30) REVERT: B 188 ASP cc_start: 0.7834 (t0) cc_final: 0.7556 (t70) REVERT: C 103 MET cc_start: 0.9329 (OUTLIER) cc_final: 0.8716 (ppp) REVERT: C 279 ARG cc_start: 0.9118 (ttp80) cc_final: 0.8680 (mtm110) REVERT: C 396 MET cc_start: 0.9064 (ttp) cc_final: 0.8307 (tmm) REVERT: C 470 LEU cc_start: 0.9222 (mp) cc_final: 0.8585 (tt) REVERT: C 561 VAL cc_start: 0.9143 (OUTLIER) cc_final: 0.8871 (p) REVERT: C 661 MET cc_start: 0.8366 (mmm) cc_final: 0.8094 (tpp) REVERT: C 672 MET cc_start: 0.8624 (mmt) cc_final: 0.8137 (mmm) REVERT: C 1076 MET cc_start: 0.8955 (mmm) cc_final: 0.8735 (mmm) REVERT: C 1119 GLU cc_start: 0.8771 (tp30) cc_final: 0.8287 (tp30) REVERT: D 92 MET cc_start: 0.8627 (mtm) cc_final: 0.8398 (mtm) REVERT: D 533 ASN cc_start: 0.9111 (t0) cc_final: 0.8881 (t0) REVERT: D 588 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9365 (tp) REVERT: D 733 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7761 (ptt) REVERT: D 865 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8715 (tm) REVERT: D 1131 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8482 (pm20) REVERT: E 30 ASP cc_start: 0.9047 (t70) cc_final: 0.8576 (t0) REVERT: E 35 ILE cc_start: 0.9454 (OUTLIER) cc_final: 0.9114 (tt) REVERT: E 40 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8215 (tt) REVERT: E 66 ASP cc_start: 0.9288 (m-30) cc_final: 0.8505 (t0) REVERT: E 69 ASN cc_start: 0.8873 (m110) cc_final: 0.8478 (m-40) REVERT: E 70 GLN cc_start: 0.8439 (mm110) cc_final: 0.7684 (mt0) REVERT: E 84 GLU cc_start: 0.8699 (tp30) cc_final: 0.8409 (tp30) REVERT: F 281 MET cc_start: 0.8393 (ttm) cc_final: 0.8134 (mmm) REVERT: F 313 ARG cc_start: 0.6761 (OUTLIER) cc_final: 0.5877 (ptp-170) REVERT: F 377 ASN cc_start: 0.9479 (t0) cc_final: 0.9110 (t0) REVERT: J 84 MET cc_start: 0.9065 (mtp) cc_final: 0.8674 (mtt) REVERT: J 86 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9189 (pp) REVERT: M 85 TRP cc_start: 0.8121 (OUTLIER) cc_final: 0.7692 (t60) REVERT: M 133 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8702 (tm-30) outliers start: 88 outliers final: 51 residues processed: 255 average time/residue: 0.1756 time to fit residues: 74.5245 Evaluate side-chains 224 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 162 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 151 GLN Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 476 HIS Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1096 THR Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1131 GLN Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 313 ARG Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 85 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 207 optimal weight: 7.9990 chunk 346 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 168 optimal weight: 1.9990 chunk 205 optimal weight: 0.7980 chunk 172 optimal weight: 0.8980 chunk 200 optimal weight: 0.8980 chunk 104 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 ASN D 693 GLN ** D1131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 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 = 0.3441 r_free = 0.3441 target = 0.066663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.046619 restraints weight = 119927.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.048305 restraints weight = 56405.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.049402 restraints weight = 35812.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.050086 restraints weight = 27182.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.050455 restraints weight = 23136.180| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30723 Z= 0.124 Angle : 0.583 11.341 42171 Z= 0.298 Chirality : 0.041 0.183 4805 Planarity : 0.004 0.082 5085 Dihedral : 18.719 179.389 5284 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.15 % Allowed : 27.49 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % Twisted Proline : 0.57 % 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: -0.17 (0.15), residues: 3496 helix: 1.58 (0.14), residues: 1407 sheet: -1.40 (0.27), residues: 377 loop : -1.28 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D1060 TYR 0.020 0.001 TYR D 36 PHE 0.017 0.001 PHE F 438 TRP 0.014 0.001 TRP D 656 HIS 0.006 0.001 HIS C1042 Details of bonding type rmsd covalent geometry : bond 0.00275 (30716) covalent geometry : angle 0.58329 (42165) hydrogen bonds : bond 0.03365 ( 1306) hydrogen bonds : angle 4.28082 ( 3673) metal coordination : bond 0.00387 ( 7) metal coordination : angle 1.37320 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 171 time to evaluate : 0.973 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: A 91 GLU cc_start: 0.8144 (pm20) cc_final: 0.7863 (pm20) REVERT: B 70 LYS cc_start: 0.9360 (tmtt) cc_final: 0.9077 (tmtt) REVERT: B 95 MET cc_start: 0.8956 (tpp) cc_final: 0.8716 (tpp) REVERT: B 177 LYS cc_start: 0.9122 (ptpp) cc_final: 0.8822 (ptmm) REVERT: B 179 ASP cc_start: 0.8004 (m-30) cc_final: 0.7632 (m-30) REVERT: B 188 ASP cc_start: 0.7926 (t0) cc_final: 0.7678 (t70) REVERT: C 103 MET cc_start: 0.9334 (OUTLIER) cc_final: 0.8724 (ppp) REVERT: C 279 ARG cc_start: 0.9119 (ttp80) cc_final: 0.8714 (mtm110) REVERT: C 396 MET cc_start: 0.9176 (ttp) cc_final: 0.8483 (tmm) REVERT: C 470 LEU cc_start: 0.9187 (mp) cc_final: 0.8597 (tt) REVERT: C 661 MET cc_start: 0.8292 (mmm) cc_final: 0.8028 (tpp) REVERT: C 672 MET cc_start: 0.8621 (mmt) cc_final: 0.8103 (mmm) REVERT: C 702 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8889 (tp) REVERT: C 907 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9143 (mt) REVERT: C 1076 MET cc_start: 0.8964 (mmm) cc_final: 0.8646 (mmm) REVERT: C 1093 SER cc_start: 0.8933 (m) cc_final: 0.8440 (p) REVERT: C 1119 GLU cc_start: 0.8788 (tp30) cc_final: 0.8305 (tp30) REVERT: D 92 MET cc_start: 0.8631 (mtm) cc_final: 0.8415 (mtm) REVERT: D 373 MET cc_start: 0.8148 (mtm) cc_final: 0.7769 (ptp) REVERT: D 533 ASN cc_start: 0.9089 (t0) cc_final: 0.8854 (t0) REVERT: D 588 LEU cc_start: 0.9617 (OUTLIER) cc_final: 0.9370 (tp) REVERT: D 693 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8299 (mt0) REVERT: D 820 MET cc_start: 0.9149 (ptm) cc_final: 0.8777 (tmm) REVERT: D 865 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8682 (tm) REVERT: D 1131 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8473 (pm20) REVERT: E 30 ASP cc_start: 0.9076 (t70) cc_final: 0.8627 (t0) REVERT: E 35 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9068 (tt) REVERT: E 69 ASN cc_start: 0.8900 (m110) cc_final: 0.8555 (m-40) REVERT: E 70 GLN cc_start: 0.8347 (mm110) cc_final: 0.7832 (mt0) REVERT: E 84 GLU cc_start: 0.8764 (tp30) cc_final: 0.8467 (tp30) REVERT: F 263 MET cc_start: 0.8905 (tpp) cc_final: 0.8585 (mmt) REVERT: F 313 ARG cc_start: 0.6520 (OUTLIER) cc_final: 0.5708 (ptp-170) REVERT: F 377 ASN cc_start: 0.9485 (t0) cc_final: 0.9118 (t0) REVERT: J 84 MET cc_start: 0.9081 (mtp) cc_final: 0.8413 (ttp) REVERT: J 86 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9187 (pp) REVERT: M 85 TRP cc_start: 0.8154 (OUTLIER) cc_final: 0.7619 (t60) REVERT: M 127 MET cc_start: 0.8786 (ptm) cc_final: 0.8549 (ptm) REVERT: M 133 GLN cc_start: 0.9023 (tm-30) cc_final: 0.8723 (tm-30) REVERT: M 134 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.9059 (pp) outliers start: 92 outliers final: 62 residues processed: 248 average time/residue: 0.1709 time to fit residues: 70.8866 Evaluate side-chains 234 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 160 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 151 GLN Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 476 HIS Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 939 CYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 993 LEU Chi-restraints excluded: chain C residue 1027 TYR Chi-restraints excluded: chain C residue 1096 THR Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 651 PHE Chi-restraints excluded: chain D residue 656 TRP Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1131 GLN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 313 ARG Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 134 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 295 optimal weight: 0.8980 chunk 357 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 276 optimal weight: 10.0000 chunk 151 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 223 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN ** D1131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1133 HIS ** F 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 GLN ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.066547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.047062 restraints weight = 117327.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.048683 restraints weight = 55377.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.049737 restraints weight = 35231.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.050408 restraints weight = 26841.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.050801 restraints weight = 22757.675| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30723 Z= 0.120 Angle : 0.584 11.306 42171 Z= 0.297 Chirality : 0.041 0.183 4805 Planarity : 0.004 0.082 5085 Dihedral : 18.666 179.282 5284 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.91 % Allowed : 27.76 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % Twisted Proline : 0.57 % 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: -0.10 (0.15), residues: 3496 helix: 1.61 (0.14), residues: 1407 sheet: -1.30 (0.28), residues: 372 loop : -1.22 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG D1060 TYR 0.021 0.001 TYR F 258 PHE 0.015 0.001 PHE F 438 TRP 0.014 0.001 TRP D 656 HIS 0.006 0.001 HIS D 689 Details of bonding type rmsd covalent geometry : bond 0.00267 (30716) covalent geometry : angle 0.58399 (42165) hydrogen bonds : bond 0.03289 ( 1306) hydrogen bonds : angle 4.23183 ( 3673) metal coordination : bond 0.00350 ( 7) metal coordination : angle 1.55369 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 165 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7135 (ptp90) REVERT: A 168 TYR cc_start: 0.8331 (OUTLIER) cc_final: 0.7970 (m-80) REVERT: B 70 LYS cc_start: 0.9349 (tmtt) cc_final: 0.9065 (tmtt) REVERT: B 177 LYS cc_start: 0.9107 (ptpp) cc_final: 0.8821 (ptmm) REVERT: B 179 ASP cc_start: 0.7985 (m-30) cc_final: 0.7627 (m-30) REVERT: B 188 ASP cc_start: 0.7835 (t0) cc_final: 0.7588 (t70) REVERT: C 103 MET cc_start: 0.9301 (OUTLIER) cc_final: 0.8729 (ppp) REVERT: C 279 ARG cc_start: 0.9111 (ttp80) cc_final: 0.8707 (mtm110) REVERT: C 396 MET cc_start: 0.9178 (ttp) cc_final: 0.8487 (tmm) REVERT: C 470 LEU cc_start: 0.9174 (mp) cc_final: 0.8576 (tt) REVERT: C 661 MET cc_start: 0.8279 (mmm) cc_final: 0.8027 (tpp) REVERT: C 702 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.8900 (tp) REVERT: C 907 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9183 (mt) REVERT: C 1093 SER cc_start: 0.8702 (m) cc_final: 0.8330 (p) REVERT: C 1119 GLU cc_start: 0.8789 (tp30) cc_final: 0.8120 (tp30) REVERT: D 92 MET cc_start: 0.8601 (mtm) cc_final: 0.8372 (mtm) REVERT: D 373 MET cc_start: 0.8162 (mtm) cc_final: 0.7764 (ptp) REVERT: D 533 ASN cc_start: 0.9093 (t0) cc_final: 0.8849 (t0) REVERT: D 588 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9363 (tp) REVERT: D 733 MET cc_start: 0.8073 (ptt) cc_final: 0.7717 (ttp) REVERT: D 820 MET cc_start: 0.9161 (ptm) cc_final: 0.8762 (tmm) REVERT: D 865 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8660 (tm) REVERT: D 1131 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8577 (pm20) REVERT: E 30 ASP cc_start: 0.9058 (t70) cc_final: 0.8587 (t0) REVERT: E 35 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.8963 (tt) REVERT: E 69 ASN cc_start: 0.8844 (m110) cc_final: 0.8494 (m-40) REVERT: E 70 GLN cc_start: 0.8387 (mm110) cc_final: 0.7830 (mt0) REVERT: E 84 GLU cc_start: 0.8739 (tp30) cc_final: 0.8265 (tm-30) REVERT: F 263 MET cc_start: 0.8877 (tpp) cc_final: 0.8559 (mmt) REVERT: F 313 ARG cc_start: 0.6427 (OUTLIER) cc_final: 0.5676 (ptp-170) REVERT: F 377 ASN cc_start: 0.9467 (t0) cc_final: 0.9102 (t0) REVERT: J 84 MET cc_start: 0.9060 (mtp) cc_final: 0.8383 (ttp) REVERT: J 86 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9184 (pp) REVERT: M 68 ASP cc_start: 0.8252 (p0) cc_final: 0.8052 (p0) REVERT: M 85 TRP cc_start: 0.7944 (OUTLIER) cc_final: 0.7629 (t60) REVERT: M 127 MET cc_start: 0.8846 (ptm) cc_final: 0.8645 (ptm) REVERT: M 133 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8713 (tm-30) outliers start: 85 outliers final: 61 residues processed: 238 average time/residue: 0.1679 time to fit residues: 66.5626 Evaluate side-chains 231 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 158 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain B residue 54 ILE 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 151 GLN Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 476 HIS Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 939 CYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1027 TYR Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1096 THR Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 651 PHE Chi-restraints excluded: chain D residue 656 TRP Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 782 THR Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1131 GLN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 313 ARG Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 522 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 85 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 326 optimal weight: 4.9990 chunk 187 optimal weight: 6.9990 chunk 199 optimal weight: 6.9990 chunk 303 optimal weight: 8.9990 chunk 278 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 111 optimal weight: 8.9990 chunk 179 optimal weight: 7.9990 chunk 137 optimal weight: 4.9990 chunk 214 optimal weight: 0.8980 chunk 313 optimal weight: 0.8980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1251 ASN ** F 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.065597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.046040 restraints weight = 117475.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.047658 restraints weight = 54976.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.048702 restraints weight = 34866.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.049377 restraints weight = 26480.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.049748 restraints weight = 22432.797| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 30723 Z= 0.166 Angle : 0.612 12.550 42171 Z= 0.311 Chirality : 0.041 0.183 4805 Planarity : 0.004 0.082 5085 Dihedral : 18.668 179.923 5284 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.77 % Allowed : 28.04 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % Twisted Proline : 0.57 % 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: -0.05 (0.15), residues: 3496 helix: 1.65 (0.14), residues: 1401 sheet: -1.39 (0.27), residues: 400 loop : -1.15 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 278 TYR 0.014 0.001 TYR D 704 PHE 0.044 0.001 PHE B 189 TRP 0.012 0.001 TRP D 656 HIS 0.007 0.001 HIS C1042 Details of bonding type rmsd covalent geometry : bond 0.00370 (30716) covalent geometry : angle 0.61163 (42165) hydrogen bonds : bond 0.03559 ( 1306) hydrogen bonds : angle 4.30029 ( 3673) metal coordination : bond 0.00766 ( 7) metal coordination : angle 1.98409 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 157 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7204 (ptp90) REVERT: A 168 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.8016 (m-80) REVERT: B 70 LYS cc_start: 0.9365 (tmtt) cc_final: 0.9100 (tmtt) REVERT: B 177 LYS cc_start: 0.9119 (ptpp) cc_final: 0.8827 (ptmm) REVERT: B 179 ASP cc_start: 0.7939 (m-30) cc_final: 0.7560 (m-30) REVERT: B 188 ASP cc_start: 0.7898 (t0) cc_final: 0.7616 (t70) REVERT: C 103 MET cc_start: 0.9286 (OUTLIER) cc_final: 0.8750 (ppp) REVERT: C 279 ARG cc_start: 0.9126 (ttp80) cc_final: 0.8754 (mtm110) REVERT: C 396 MET cc_start: 0.9130 (ttp) cc_final: 0.8256 (tmm) REVERT: C 470 LEU cc_start: 0.9189 (mp) cc_final: 0.8586 (tt) REVERT: C 630 MET cc_start: 0.8396 (tpp) cc_final: 0.8099 (tpp) REVERT: C 661 MET cc_start: 0.8228 (mmm) cc_final: 0.7995 (tpp) REVERT: C 702 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.8931 (tp) REVERT: C 907 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9057 (mt) REVERT: C 1076 MET cc_start: 0.9002 (mmm) cc_final: 0.8788 (mmm) REVERT: C 1093 SER cc_start: 0.8713 (m) cc_final: 0.8337 (p) REVERT: C 1119 GLU cc_start: 0.8783 (tp30) cc_final: 0.8318 (tp30) REVERT: D 373 MET cc_start: 0.8190 (mtm) cc_final: 0.7806 (ptp) REVERT: D 533 ASN cc_start: 0.9139 (t0) cc_final: 0.8901 (t0) REVERT: D 588 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9359 (tp) REVERT: D 706 MET cc_start: 0.6573 (tpt) cc_final: 0.6313 (tpp) REVERT: D 733 MET cc_start: 0.8135 (ptt) cc_final: 0.7850 (ttp) REVERT: D 820 MET cc_start: 0.9161 (ptm) cc_final: 0.8749 (tmm) REVERT: D 865 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8674 (tm) REVERT: D 1131 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8592 (pm20) REVERT: E 30 ASP cc_start: 0.9101 (t70) cc_final: 0.8651 (t0) REVERT: E 35 ILE cc_start: 0.9402 (OUTLIER) cc_final: 0.9012 (tt) REVERT: E 69 ASN cc_start: 0.8892 (m110) cc_final: 0.8519 (m-40) REVERT: E 70 GLN cc_start: 0.8382 (mm110) cc_final: 0.7808 (mt0) REVERT: E 84 GLU cc_start: 0.8746 (tp30) cc_final: 0.8450 (tp30) REVERT: F 263 MET cc_start: 0.8820 (tpp) cc_final: 0.8618 (mmt) REVERT: F 313 ARG cc_start: 0.6473 (OUTLIER) cc_final: 0.5605 (ptp-170) REVERT: F 377 ASN cc_start: 0.9460 (t0) cc_final: 0.9099 (t0) REVERT: J 84 MET cc_start: 0.9053 (mtp) cc_final: 0.8382 (ttp) REVERT: J 86 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9189 (pp) REVERT: M 68 ASP cc_start: 0.8231 (p0) cc_final: 0.8028 (p0) REVERT: M 85 TRP cc_start: 0.7992 (OUTLIER) cc_final: 0.7645 (t60) REVERT: M 127 MET cc_start: 0.8862 (ptm) cc_final: 0.8640 (ptm) REVERT: M 133 GLN cc_start: 0.9030 (tm-30) cc_final: 0.8741 (tm-30) outliers start: 81 outliers final: 61 residues processed: 226 average time/residue: 0.1681 time to fit residues: 64.4233 Evaluate side-chains 229 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 156 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain B residue 54 ILE 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 151 GLN Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 476 HIS Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 939 CYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 993 LEU Chi-restraints excluded: chain C residue 1096 THR Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 651 PHE Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 782 THR Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1131 GLN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 313 ARG Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 522 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 85 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 301 optimal weight: 10.0000 chunk 132 optimal weight: 0.0270 chunk 202 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 74 optimal weight: 0.0370 chunk 237 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 192 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 245 optimal weight: 4.9990 overall best weight: 2.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 510 GLN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 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 = 0.3411 r_free = 0.3411 target = 0.065189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.045548 restraints weight = 118940.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.047111 restraints weight = 56926.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.048144 restraints weight = 36522.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.048784 restraints weight = 28006.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.049106 restraints weight = 23885.772| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30723 Z= 0.187 Angle : 0.628 12.585 42171 Z= 0.318 Chirality : 0.042 0.203 4805 Planarity : 0.004 0.082 5085 Dihedral : 18.680 178.407 5284 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.81 % Allowed : 27.90 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % Twisted Proline : 0.57 % 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: -0.07 (0.15), residues: 3496 helix: 1.63 (0.14), residues: 1401 sheet: -1.40 (0.27), residues: 396 loop : -1.15 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 278 TYR 0.014 0.001 TYR F 258 PHE 0.028 0.001 PHE B 189 TRP 0.009 0.001 TRP D 656 HIS 0.004 0.001 HIS C1042 Details of bonding type rmsd covalent geometry : bond 0.00417 (30716) covalent geometry : angle 0.62781 (42165) hydrogen bonds : bond 0.03677 ( 1306) hydrogen bonds : angle 4.36041 ( 3673) metal coordination : bond 0.00914 ( 7) metal coordination : angle 2.28703 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4997.28 seconds wall clock time: 87 minutes 3.42 seconds (5223.42 seconds total)