Starting phenix.real_space_refine on Mon Sep 14 10:38:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vvx_21406/09_2026/6vvx_21406.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vvx_21406/09_2026/6vvx_21406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vvx_21406/09_2026/6vvx_21406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vvx_21406/09_2026/6vvx_21406.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vvx_21406/09_2026/6vvx_21406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vvx_21406/09_2026/6vvx_21406.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6vvx_21406/09_2026/6vvx_21406.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vvx_21406/09_2026/6vvx_21406.cif" } resolution = 3.39 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= 0.011 sd= 0.113 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 128 5.49 5 Mg 1 5.21 5 S 99 5.16 5 C 18318 2.51 5 N 5328 2.21 5 O 5982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29858 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1716 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 210} Chain: "B" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1759 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 221} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 8554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8554 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1048} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 52 Chain: "D" Number of atoms: 9873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1266, 9873 Classifications: {'peptide': 1266} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 57, 'TRANS': 1205} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 76} Chain: "F" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2505 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 310} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 4, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "J" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 875 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1289 Classifications: {'DNA': 63} Link IDs: {'rna3p': 62} Chain breaks: 1 Chain: "M" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1241 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 4, 'TRANS': 154} 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: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'SRN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19093 SG CYS D 891 116.606 88.055 107.057 1.00118.55 S ATOM 19660 SG CYS D 968 113.259 89.705 105.236 1.00121.59 S ATOM 19702 SG CYS D 975 113.514 87.463 109.049 1.00113.35 S ATOM 19720 SG CYS D 978 114.981 90.774 108.855 1.00114.23 S ATOM 12535 SG CYS D 60 60.630 64.838 75.034 1.00142.86 S ATOM 12553 SG CYS D 62 59.125 65.195 71.752 1.00146.20 S ATOM 12688 SG CYS D 78 62.577 67.260 71.913 1.00142.18 S Time building chain proxies: 7.05, per 1000 atoms: 0.24 Number of scatterers: 29858 At special positions: 0 Unit cell: (143, 169.4, 195.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 99 16.00 P 128 15.00 Mg 1 11.99 O 5982 8.00 N 5328 7.00 C 18318 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: 2.98 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 968 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 62 " Number of angles added : 6 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6464 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 44 sheets defined 42.0% alpha, 14.7% beta 56 base pairs and 98 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 203 through 220 Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'B' and resid 29 through 45 removed outlier: 4.128A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 203 through 224 removed outlier: 4.698A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.579A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 76 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 242 removed outlier: 3.978A 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 Processing helix chain 'C' and resid 290 through 301 removed outlier: 3.559A pdb=" N THR C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU C 297 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 321 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 380 through 407 removed outlier: 4.031A pdb=" N ARG C 395 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.556A pdb=" N ILE C 418 " --> pdb=" O PRO C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 432 removed outlier: 3.504A pdb=" N GLY C 432 " --> pdb=" O LYS C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 452 removed outlier: 3.661A pdb=" N GLY C 448 " --> pdb=" O ASN C 444 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C 449 " --> pdb=" O PRO C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 removed outlier: 4.092A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 removed outlier: 3.793A pdb=" N HIS C 539 " --> pdb=" O GLU C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 594 removed outlier: 3.707A pdb=" N MET C 593 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 594 " --> pdb=" O THR C 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 590 through 594' Processing helix chain 'C' and resid 596 through 600 removed outlier: 3.590A pdb=" N HIS C 599 " --> pdb=" O PHE C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 630 through 637 Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 815 through 826 Processing helix chain 'C' and resid 922 through 926 Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 981 through 990 Processing helix chain 'C' and resid 1036 through 1040 removed outlier: 3.528A pdb=" N ASP C1039 " --> pdb=" O LEU C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1080 removed outlier: 3.693A pdb=" N CYS C1073 " --> pdb=" O GLY C1069 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY C1080 " --> pdb=" O MET C1076 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1091 removed outlier: 3.692A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.589A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.746A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 removed outlier: 3.595A pdb=" N SER D 24 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 removed outlier: 4.000A pdb=" N LYS D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 185 removed outlier: 3.613A pdb=" N ARG D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 Processing helix chain 'D' and resid 238 through 247 removed outlier: 3.719A pdb=" N ASP D 246 " --> pdb=" O ARG D 242 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG D 247 " --> pdb=" O GLU D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 250 No H-bonds generated for 'chain 'D' and resid 248 through 250' Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 269 through 283 removed outlier: 4.196A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 305 removed outlier: 4.333A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.926A 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 340 through 361 Processing helix chain 'D' and resid 363 through 383 removed outlier: 3.613A pdb=" N VAL D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 406 removed outlier: 3.609A pdb=" N LEU D 405 " --> pdb=" O LEU D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 419 Processing helix chain 'D' and resid 445 through 452 removed outlier: 3.971A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 482 through 492 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 578 through 590 removed outlier: 3.999A pdb=" N THR D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 668 through 675 Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 726 removed outlier: 3.689A pdb=" N VAL D 709 " --> pdb=" O PRO D 705 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 763 removed outlier: 3.670A pdb=" N ILE D 745 " --> pdb=" O ARG D 741 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY D 763 " --> pdb=" O GLN D 759 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 removed outlier: 3.554A pdb=" N ARG D 770 " --> pdb=" O ASN D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 797 through 805 removed outlier: 3.968A pdb=" N VAL D 803 " --> pdb=" O ILE D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 818 removed outlier: 4.099A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 4.202A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 removed outlier: 3.946A pdb=" N ILE D 949 " --> pdb=" O GLY D 945 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 980 Processing helix chain 'D' and resid 994 through 1005 removed outlier: 3.552A pdb=" N VAL D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1006 through 1010 Processing helix chain 'D' and resid 1027 through 1036 Processing helix chain 'D' and resid 1117 through 1143 removed outlier: 3.605A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Proline residue: D1127 - end of helix removed outlier: 4.074A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN D1131 " --> pdb=" O PRO D1127 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG D1143 " --> pdb=" O GLN D1139 " (cutoff:3.500A) Processing helix chain 'D' and resid 1144 through 1146 No H-bonds generated for 'chain 'D' and resid 1144 through 1146' Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 3.991A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE D1157 " --> pdb=" O HIS D1153 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET D1161 " --> pdb=" O ILE D1157 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D1162 " --> pdb=" O VAL D1158 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1193 removed outlier: 3.695A pdb=" N ALA D1188 " --> pdb=" O ALA D1184 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG D1192 " --> pdb=" O ALA D1188 " (cutoff:3.500A) Processing helix chain 'D' and resid 1209 through 1214 Processing helix chain 'D' and resid 1219 through 1225 removed outlier: 4.012A pdb=" N SER D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1228 through 1240 removed outlier: 3.650A pdb=" N ASP D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA D1236 " --> pdb=" O VAL D1232 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1254 Processing helix chain 'D' and resid 1264 through 1269 removed outlier: 3.964A pdb=" N ASN D1269 " --> pdb=" O ASN D1265 " (cutoff:3.500A) Processing helix chain 'D' and resid 1275 through 1280 removed outlier: 3.679A pdb=" N ALA D1280 " --> pdb=" O GLU D1276 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.765A 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 69 Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'F' and resid 210 through 221 Processing helix chain 'F' and resid 226 through 236 removed outlier: 3.797A pdb=" N ALA F 230 " --> pdb=" O ASP F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 267 Processing helix chain 'F' and resid 274 through 308 removed outlier: 3.970A pdb=" N ASP F 289 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG F 290 " --> pdb=" O ARG F 286 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 334 Processing helix chain 'F' and resid 342 through 363 removed outlier: 3.890A pdb=" N TYR F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA F 363 " --> pdb=" O MET F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 391 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 437 removed outlier: 3.631A pdb=" N ASP F 437 " --> pdb=" O GLN F 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 434 through 437' Processing helix chain 'F' and resid 448 through 466 Processing helix chain 'F' and resid 468 through 480 Processing helix chain 'F' and resid 488 through 497 Processing helix chain 'F' and resid 499 through 515 Processing helix chain 'F' and resid 516 through 525 removed outlier: 5.852A pdb=" N VAL F 522 " --> pdb=" O SER F 518 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LEU F 523 " --> pdb=" O ARG F 519 " (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 74 Processing helix chain 'M' and resid 84 through 99 removed outlier: 3.767A pdb=" N ARG M 88 " --> pdb=" O ASN M 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 118 Processing helix chain 'M' and resid 121 through 144 Processing helix chain 'M' and resid 146 through 158 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 6.501A pdb=" N LYS A 191 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N VAL A 178 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE A 193 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N TYR A 176 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASP A 195 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL A 174 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLU A 197 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 51 removed outlier: 3.978A pdb=" N SER A 53 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 100 Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA5, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.763A pdb=" N GLY A 103 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.554A pdb=" N SER B 19 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 173 " --> pdb=" O GLU B 197 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 94 Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 94 removed outlier: 7.883A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AB1, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.593A pdb=" N ALA B 126 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB3, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.393A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.650A pdb=" N GLU C 138 " --> pdb=" O SER C 106 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE C 134 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N PHE C 112 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU C 133 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.650A pdb=" N GLU C 138 " --> pdb=" O SER C 106 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE C 134 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N PHE C 112 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG M 47 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA M 21 " --> pdb=" O VAL M 36 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS M 38 " --> pdb=" O VAL M 19 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL M 19 " --> pdb=" O LYS M 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB7, first strand: chain 'C' and resid 378 through 379 removed outlier: 3.715A pdb=" N SER C 177 " --> pdb=" O ARG C 454 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER C 456 " --> pdb=" O SER C 177 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.585A pdb=" N ASP C 188 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 199 " --> pdb=" O THR C 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP C 192 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS C 197 " --> pdb=" O ASP C 192 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 215 through 216 Processing sheet with id=AC1, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AC2, first strand: chain 'C' and resid 505 through 506 removed outlier: 5.046A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC4, first strand: chain 'C' and resid 559 through 562 Processing sheet with id=AC5, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.791A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 667 through 671 removed outlier: 6.683A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC8, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 7.035A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 749 through 760 removed outlier: 3.914A pdb=" N GLU C 867 " --> pdb=" O ALA C 759 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AD2, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.733A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 3.530A pdb=" N LEU D 497 " --> pdb=" O HIS D 544 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N CYS D 441 " --> pdb=" O MET D 515 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL D 517 " --> pdb=" O CYS D 441 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 7.557A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1136 through 1138 Processing sheet with id=AD6, first strand: chain 'D' and resid 93 through 102 removed outlier: 3.503A pdb=" N LEU D 97 " --> pdb=" O ASP D 315 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 11.605A pdb=" N ALA D 99 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 10.524A pdb=" N VAL D 313 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 234 through 235 removed outlier: 3.715A pdb=" N TYR D 134 " --> pdb=" O ILE D 235 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 335 through 336 removed outlier: 3.763A pdb=" N GLN D 329 " --> pdb=" O SER J 9 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N GLU F 440 " --> pdb=" O GLY J 8 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AE1, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AE2, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.690A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 929 through 930 removed outlier: 7.244A pdb=" N ALA D 929 " --> pdb=" O ILE D 937 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1053 through 1054 removed outlier: 5.437A pdb=" N ILE D1064 " --> pdb=" O ASP D1078 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ASP D1078 " --> pdb=" O ILE D1064 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE D1066 " --> pdb=" O VAL D1076 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL D1076 " --> pdb=" O ILE D1066 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 3.583A pdb=" N ARG D1204 " --> pdb=" O THR D1166 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1271 through 1274 Processing sheet with id=AE7, first strand: chain 'J' and resid 39 through 42 Processing sheet with id=AE8, first strand: chain 'M' and resid 26 through 27 removed outlier: 3.521A pdb=" N ILE M 27 " --> pdb=" O GLU M 30 " (cutoff:3.500A) 1183 hydrogen bonds defined for protein. 3375 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 145 hydrogen bonds 290 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 98 stacking parallelities Total time for adding SS restraints: 8.76 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4943 1.31 - 1.43: 7923 1.43 - 1.56: 17313 1.56 - 1.68: 270 1.68 - 1.80: 178 Bond restraints: 30627 Sorted by residual: bond pdb=" C9 SRN C1201 " pdb=" O3 SRN C1201 " ideal model delta sigma weight residual 1.429 1.805 -0.376 2.00e-02 2.50e+03 3.53e+02 bond pdb=" C8 SRN C1201 " pdb=" O3 SRN C1201 " ideal model delta sigma weight residual 1.434 1.785 -0.351 2.00e-02 2.50e+03 3.08e+02 bond pdb=" C28 SRN C1201 " pdb=" C29 SRN C1201 " ideal model delta sigma weight residual 1.330 1.609 -0.279 2.00e-02 2.50e+03 1.95e+02 bond pdb=" C13 SRN C1201 " pdb=" C14 SRN C1201 " ideal model delta sigma weight residual 1.328 1.596 -0.268 2.00e-02 2.50e+03 1.80e+02 bond pdb=" C24 SRN C1201 " pdb=" C25 SRN C1201 " ideal model delta sigma weight residual 1.328 1.573 -0.245 2.00e-02 2.50e+03 1.50e+02 ... (remaining 30622 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.46: 41869 4.46 - 8.92: 158 8.92 - 13.39: 10 13.39 - 17.85: 2 17.85 - 22.31: 1 Bond angle restraints: 42040 Sorted by residual: angle pdb=" C8 SRN C1201 " pdb=" O3 SRN C1201 " pdb=" C9 SRN C1201 " ideal model delta sigma weight residual 108.56 86.25 22.31 3.00e+00 1.11e-01 5.53e+01 angle pdb=" O4' DG P 131 " pdb=" C1' DG P 131 " pdb=" N9 DG P 131 " ideal model delta sigma weight residual 108.00 112.94 -4.94 7.00e-01 2.04e+00 4.98e+01 angle pdb=" C ARG D 834 " pdb=" N PRO D 835 " pdb=" CA PRO D 835 " ideal model delta sigma weight residual 127.00 143.70 -16.70 2.40e+00 1.74e-01 4.84e+01 angle pdb=" C ARG D 834 " pdb=" N PRO D 835 " pdb=" CD PRO D 835 " ideal model delta sigma weight residual 120.60 107.29 13.31 2.20e+00 2.07e-01 3.66e+01 angle pdb=" CA ARG C 584 " pdb=" CB ARG C 584 " pdb=" CG ARG C 584 " ideal model delta sigma weight residual 114.10 126.00 -11.90 2.00e+00 2.50e-01 3.54e+01 ... (remaining 42035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.16: 17355 35.16 - 70.31: 1044 70.31 - 105.47: 11 105.47 - 140.63: 1 140.63 - 175.78: 5 Dihedral angle restraints: 18416 sinusoidal: 8368 harmonic: 10048 Sorted by residual: dihedral pdb=" CA ASP C 227 " pdb=" C ASP C 227 " pdb=" N ARG C 228 " pdb=" CA ARG C 228 " ideal model delta harmonic sigma weight residual 180.00 -130.50 -49.50 0 5.00e+00 4.00e-02 9.80e+01 dihedral pdb=" CA ILE C 226 " pdb=" C ILE C 226 " pdb=" N ASP C 227 " pdb=" CA ASP C 227 " ideal model delta harmonic sigma weight residual -180.00 -142.57 -37.43 0 5.00e+00 4.00e-02 5.60e+01 dihedral pdb=" CA GLU C 146 " pdb=" C GLU C 146 " pdb=" N ILE C 147 " pdb=" CA ILE C 147 " ideal model delta harmonic sigma weight residual 180.00 148.28 31.72 0 5.00e+00 4.00e-02 4.03e+01 ... (remaining 18413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3884 0.066 - 0.133: 819 0.133 - 0.199: 74 0.199 - 0.266: 12 0.266 - 0.332: 10 Chirality restraints: 4799 Sorted by residual: chirality pdb=" C12 SRN C1201 " pdb=" C10 SRN C1201 " pdb=" C13 SRN C1201 " pdb=" O8 SRN C1201 " both_signs ideal model delta sigma weight residual False 2.40 2.73 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" C35 SRN C1201 " pdb=" C34 SRN C1201 " pdb=" C8 SRN C1201 " pdb=" O8 SRN C1201 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" C32 SRN C1201 " pdb=" C33 SRN C1201 " pdb=" C36 SRN C1201 " pdb=" O7 SRN C1201 " both_signs ideal model delta sigma weight residual False 2.32 2.63 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 4796 not shown) Planarity restraints: 5075 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 320 " -0.052 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO D 321 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO D 321 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 321 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 413 " 0.046 5.00e-02 4.00e+02 6.94e-02 7.70e+00 pdb=" N PRO C 414 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 414 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 414 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 826 " -0.043 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO D 827 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 827 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 827 " -0.037 5.00e-02 4.00e+02 ... (remaining 5072 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2731 2.73 - 3.27: 27063 3.27 - 3.82: 51240 3.82 - 4.36: 56219 4.36 - 4.90: 95520 Nonbonded interactions: 232773 Sorted by model distance: nonbonded pdb=" OD1 ASP D 537 " pdb="MG MG D2002 " model vdw 2.190 2.170 nonbonded pdb=" N CYS D 62 " pdb="ZN ZN D2001 " model vdw 2.233 2.310 nonbonded pdb=" OD1 ASP D 539 " pdb="MG MG D2002 " model vdw 2.261 2.170 nonbonded pdb=" O VAL F 463 " pdb=" OG1 THR F 466 " model vdw 2.277 3.040 nonbonded pdb=" O GLN C1086 " pdb=" OG1 THR C1090 " model vdw 2.290 3.040 ... (remaining 232768 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 or (resid 186 \ and (name N or name CA or name C or name O or name CB )) or resid 187 through 2 \ 23 or (resid 224 and (name N or name CA or name C or name O or name CB )) or res \ id 225 through 226)) selection = (chain 'B' and resid 2 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.690 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 39.270 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.070 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 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 : 0.009 0.376 30634 Z= 0.493 Angle : 0.909 22.312 42046 Z= 0.549 Chirality : 0.055 0.332 4799 Planarity : 0.007 0.079 5075 Dihedral : 19.144 175.782 11952 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.99 % Allowed : 21.07 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.74 (0.11), residues: 3488 helix: -2.10 (0.10), residues: 1346 sheet: -2.29 (0.24), residues: 412 loop : -2.85 (0.12), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 228 TYR 0.017 0.002 TYR C 186 PHE 0.020 0.002 PHE C 906 TRP 0.018 0.002 TRP D 223 HIS 0.009 0.001 HIS D 854 Details of bonding type rmsd/Z covalent geometry : bond 0.00918 / 0.49 (30627) covalent geometry : angle 0.89672 / 0.55 (42040) hydrogen bonds : bond 0.16685 / 11.51 ( 1313) hydrogen bonds : angle 6.58299 / 4.63 ( 3665) metal coordination : bond 0.13747 / 6.39 ( 7) metal coordination : angle 12.32662 / 5.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 196 time to evaluate : 1.203 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: A 72 ASP cc_start: 0.8813 (OUTLIER) cc_final: 0.8493 (p0) REVERT: A 185 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8478 (tm-30) REVERT: A 215 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9227 (mm) REVERT: B 95 MET cc_start: 0.8759 (mtm) cc_final: 0.8546 (mtp) REVERT: C 238 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8820 (mm) REVERT: C 892 LYS cc_start: 0.9197 (pttt) cc_final: 0.8938 (pttp) REVERT: D 239 ASN cc_start: 0.9361 (OUTLIER) cc_final: 0.9050 (p0) REVERT: D 244 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9363 (mt) REVERT: D 337 THR cc_start: 0.9326 (p) cc_final: 0.8788 (p) REVERT: D 931 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.6601 (p0) REVERT: E 50 LYS cc_start: 0.8985 (ptpt) cc_final: 0.8754 (pttt) REVERT: E 66 ASP cc_start: 0.8864 (m-30) cc_final: 0.8465 (t0) REVERT: E 102 ASP cc_start: 0.8952 (OUTLIER) cc_final: 0.8731 (m-30) REVERT: J 16 TYR cc_start: 0.8043 (OUTLIER) cc_final: 0.7835 (p90) REVERT: J 28 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.7996 (mp10) REVERT: J 60 MET cc_start: 0.8101 (ptp) cc_final: 0.7803 (ptm) REVERT: J 68 ASP cc_start: 0.8591 (m-30) cc_final: 0.8257 (p0) REVERT: J 84 MET cc_start: 0.9200 (mpp) cc_final: 0.8923 (mpp) REVERT: M 26 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8516 (t) outliers start: 116 outliers final: 31 residues processed: 308 average time/residue: 0.1992 time to fit residues: 99.0707 Evaluate side-chains 175 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 733 ASP Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 239 ASN Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 931 ASP Chi-restraints excluded: chain D residue 1052 ARG Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 28 GLN Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 39 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 HIS B 226 ASN C 81 ASN C 141 ASN C 232 GLN C 298 ASN C 352 GLN C 415 GLN C 419 ASN C 662 HIS C 751 HIS C 775 ASN D 239 ASN D 307 ASN D 368 ASN D 505 HIS D 564 ASN D 693 GLN D 797 ASN D1190 ASN E 65 ASN E 69 ASN F 353 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.055414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.036150 restraints weight = 137467.302| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 3.81 r_work: 0.2526 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2539 r_free = 0.2539 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2539 r_free = 0.2539 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30634 Z= 0.181 Angle : 0.638 9.837 42046 Z= 0.344 Chirality : 0.044 0.293 4799 Planarity : 0.005 0.054 5075 Dihedral : 18.941 173.902 5385 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.82 % Allowed : 21.24 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.13), residues: 3488 helix: -0.23 (0.13), residues: 1369 sheet: -1.98 (0.25), residues: 378 loop : -2.43 (0.13), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1060 TYR 0.016 0.001 TYR M 34 PHE 0.015 0.001 PHE D 7 TRP 0.039 0.001 TRP D 656 HIS 0.006 0.001 HIS D 854 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (30627) covalent geometry : angle 0.63790 / 0.34 (42040) hydrogen bonds : bond 0.05277 / 3.61 ( 1313) hydrogen bonds : angle 4.90616 / 3.45 ( 3665) metal coordination : bond 0.01578 / 0.70 ( 7) metal coordination : angle 2.13699 / 0.78 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 146 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8275 (tm-30) cc_final: 0.7777 (tm-30) REVERT: A 106 THR cc_start: 0.9247 (OUTLIER) cc_final: 0.8927 (t) REVERT: A 173 LYS cc_start: 0.9448 (ttmt) cc_final: 0.8903 (ttmm) REVERT: A 185 GLN cc_start: 0.9162 (mm-40) cc_final: 0.8935 (mm-40) REVERT: B 205 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8623 (tpt170) REVERT: C 154 MET cc_start: 0.9464 (mmm) cc_final: 0.8919 (mpp) REVERT: C 219 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8177 (mpp-170) REVERT: C 630 MET cc_start: 0.8614 (tpp) cc_final: 0.8287 (tpp) REVERT: C 713 MET cc_start: 0.9358 (tpp) cc_final: 0.8769 (mmt) REVERT: C 1051 MET cc_start: 0.9131 (tpp) cc_final: 0.8829 (tpp) REVERT: D 244 LEU cc_start: 0.9689 (OUTLIER) cc_final: 0.9485 (mt) REVERT: D 865 LEU cc_start: 0.8874 (mm) cc_final: 0.8423 (pp) REVERT: D 887 ARG cc_start: 0.9278 (OUTLIER) cc_final: 0.9070 (mmm-85) REVERT: D 901 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8583 (tt) REVERT: D 993 GLU cc_start: 0.7523 (mp0) cc_final: 0.7275 (mp0) REVERT: D 1204 ARG cc_start: 0.9301 (OUTLIER) cc_final: 0.9043 (tmm-80) REVERT: E 66 ASP cc_start: 0.9340 (m-30) cc_final: 0.8668 (t0) REVERT: E 102 ASP cc_start: 0.9372 (OUTLIER) cc_final: 0.9121 (m-30) REVERT: J 16 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.8283 (p90) REVERT: J 60 MET cc_start: 0.8301 (ptp) cc_final: 0.7893 (ptm) REVERT: J 68 ASP cc_start: 0.8835 (m-30) cc_final: 0.8621 (m-30) REVERT: M 115 ASP cc_start: 0.9410 (t0) cc_final: 0.8715 (p0) REVERT: M 133 GLN cc_start: 0.9456 (tm-30) cc_final: 0.9124 (pp30) REVERT: M 147 ASP cc_start: 0.9207 (p0) cc_final: 0.8511 (t0) outliers start: 111 outliers final: 36 residues processed: 252 average time/residue: 0.1943 time to fit residues: 79.2203 Evaluate side-chains 176 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 131 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 518 LYS Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 866 ASN Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 878 VAL Chi-restraints excluded: chain D residue 887 ARG Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1204 ARG Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 48 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 18 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 176 optimal weight: 20.0000 chunk 332 optimal weight: 40.0000 chunk 182 optimal weight: 6.9990 chunk 119 optimal weight: 0.7980 chunk 305 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 186 optimal weight: 9.9990 chunk 222 optimal weight: 5.9990 chunk 267 optimal weight: 2.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 HIS C 875 GLN C 920 HIS ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** 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 = 0.3336 r_free = 0.3336 target = 0.054987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.035463 restraints weight = 139781.888| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 3.88 r_work: 0.2531 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2527 r_free = 0.2527 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2527 r_free = 0.2527 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 30634 Z= 0.212 Angle : 0.626 9.884 42046 Z= 0.333 Chirality : 0.044 0.310 4799 Planarity : 0.004 0.051 5075 Dihedral : 18.833 178.273 5345 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.23 % Allowed : 21.51 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.14), residues: 3488 helix: 0.55 (0.14), residues: 1373 sheet: -1.72 (0.25), residues: 403 loop : -2.16 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D1085 TYR 0.031 0.001 TYR M 34 PHE 0.013 0.001 PHE D1186 TRP 0.042 0.001 TRP D 656 HIS 0.005 0.001 HIS D 854 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.21 (30627) covalent geometry : angle 0.62505 / 0.33 (42040) hydrogen bonds : bond 0.04921 / 3.34 ( 1313) hydrogen bonds : angle 4.61518 / 3.24 ( 3665) metal coordination : bond 0.00680 / 0.28 ( 7) metal coordination : angle 2.10623 / 0.76 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 134 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7749 (tm-30) REVERT: A 106 THR cc_start: 0.9214 (OUTLIER) cc_final: 0.8852 (t) REVERT: A 173 LYS cc_start: 0.9442 (ttmt) cc_final: 0.8898 (ttmm) REVERT: B 70 LYS cc_start: 0.9194 (tmmt) cc_final: 0.8965 (tmmt) REVERT: B 205 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8624 (tpt170) REVERT: C 106 SER cc_start: 0.8885 (OUTLIER) cc_final: 0.8543 (p) REVERT: C 154 MET cc_start: 0.9475 (mmm) cc_final: 0.8955 (mpp) REVERT: C 219 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8240 (mpp-170) REVERT: C 300 PHE cc_start: 0.9207 (OUTLIER) cc_final: 0.8774 (m-80) REVERT: C 453 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8588 (ptm160) REVERT: C 661 MET cc_start: 0.9115 (tpt) cc_final: 0.8913 (tpt) REVERT: C 713 MET cc_start: 0.9400 (tpp) cc_final: 0.8839 (mmt) REVERT: C 1051 MET cc_start: 0.9059 (tpp) cc_final: 0.8564 (tpp) REVERT: D 166 ARG cc_start: 0.5651 (OUTLIER) cc_final: 0.5403 (ptm-80) REVERT: D 273 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8793 (tt0) REVERT: D 663 MET cc_start: 0.9159 (mmm) cc_final: 0.8704 (mmm) REVERT: D 865 LEU cc_start: 0.8858 (mm) cc_final: 0.8443 (pp) REVERT: D 931 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.6961 (p0) REVERT: D 1186 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7105 (t80) REVERT: E 31 THR cc_start: 0.9536 (OUTLIER) cc_final: 0.9306 (p) REVERT: E 35 ILE cc_start: 0.9503 (tp) cc_final: 0.9258 (tt) REVERT: E 66 ASP cc_start: 0.9350 (m-30) cc_final: 0.8736 (t0) REVERT: E 102 ASP cc_start: 0.9368 (OUTLIER) cc_final: 0.9131 (m-30) REVERT: F 220 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7835 (pp20) REVERT: F 282 MET cc_start: 0.8722 (mmt) cc_final: 0.8514 (mmt) REVERT: J 16 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.8270 (p90) REVERT: J 28 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7619 (mp10) REVERT: J 60 MET cc_start: 0.8250 (ptp) cc_final: 0.8033 (ptm) REVERT: J 68 ASP cc_start: 0.8852 (m-30) cc_final: 0.8629 (m-30) REVERT: M 43 ASP cc_start: 0.9029 (t0) cc_final: 0.8638 (t0) REVERT: M 147 ASP cc_start: 0.9233 (p0) cc_final: 0.8665 (t0) outliers start: 123 outliers final: 58 residues processed: 250 average time/residue: 0.1863 time to fit residues: 76.4850 Evaluate side-chains 197 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 124 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 518 LYS Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 866 ASN Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 931 ASP Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 1041 ARG Chi-restraints excluded: chain D residue 1052 ARG Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1186 PHE Chi-restraints excluded: chain D residue 1204 ARG Chi-restraints excluded: chain D residue 1226 PHE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 28 GLN Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 60 optimal weight: 5.9990 chunk 239 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 149 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 chunk 283 optimal weight: 7.9990 chunk 232 optimal weight: 7.9990 chunk 251 optimal weight: 7.9990 chunk 141 optimal weight: 0.3980 chunk 332 optimal weight: 40.0000 chunk 260 optimal weight: 20.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 142 ASN C1055 GLN ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 HIS ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.054901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.035616 restraints weight = 137331.099| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 3.77 r_work: 0.2510 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2524 r_free = 0.2524 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2524 r_free = 0.2524 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 30634 Z= 0.214 Angle : 0.616 8.086 42046 Z= 0.327 Chirality : 0.044 0.316 4799 Planarity : 0.004 0.065 5075 Dihedral : 18.764 177.566 5342 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.96 % Allowed : 21.76 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.14), residues: 3488 helix: 0.95 (0.14), residues: 1375 sheet: -1.61 (0.25), residues: 403 loop : -1.96 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 166 TYR 0.012 0.001 TYR C 186 PHE 0.015 0.001 PHE C 431 TRP 0.047 0.002 TRP D 656 HIS 0.005 0.001 HIS D 854 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 (30627) covalent geometry : angle 0.61541 / 0.33 (42040) hydrogen bonds : bond 0.04710 / 3.20 ( 1313) hydrogen bonds : angle 4.49028 / 3.15 ( 3665) metal coordination : bond 0.00770 / 0.33 ( 7) metal coordination : angle 1.39863 / 0.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 128 time to evaluate : 1.158 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 5 GLN cc_start: 0.8272 (tm-30) cc_final: 0.7718 (tm-30) REVERT: A 173 LYS cc_start: 0.9365 (ttmt) cc_final: 0.8800 (ttmm) REVERT: B 70 LYS cc_start: 0.9249 (tmmt) cc_final: 0.8876 (tmmt) REVERT: B 205 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8631 (tpt170) REVERT: C 106 SER cc_start: 0.8741 (OUTLIER) cc_final: 0.8392 (p) REVERT: C 154 MET cc_start: 0.9471 (mmm) cc_final: 0.8994 (mpp) REVERT: C 219 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8243 (mpp-170) REVERT: C 300 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8792 (m-80) REVERT: C 453 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8584 (ptm160) REVERT: C 661 MET cc_start: 0.9108 (tpt) cc_final: 0.8707 (tpt) REVERT: C 713 MET cc_start: 0.9418 (tpp) cc_final: 0.8876 (mmt) REVERT: C 926 MET cc_start: 0.9030 (mmm) cc_final: 0.8481 (mmt) REVERT: C 1051 MET cc_start: 0.9038 (tpp) cc_final: 0.8543 (tpp) REVERT: D 273 GLU cc_start: 0.9157 (OUTLIER) cc_final: 0.8826 (tt0) REVERT: D 389 ARG cc_start: 0.9251 (OUTLIER) cc_final: 0.8938 (mmt-90) REVERT: D 663 MET cc_start: 0.9186 (mmm) cc_final: 0.8802 (mmm) REVERT: D 1186 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.7028 (t80) REVERT: E 35 ILE cc_start: 0.9506 (OUTLIER) cc_final: 0.9287 (tt) REVERT: E 66 ASP cc_start: 0.9349 (m-30) cc_final: 0.8775 (t0) REVERT: E 102 ASP cc_start: 0.9369 (OUTLIER) cc_final: 0.9132 (m-30) REVERT: F 220 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7887 (pp20) REVERT: J 16 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.8145 (p90) REVERT: J 28 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7508 (mp10) REVERT: J 60 MET cc_start: 0.8152 (ptp) cc_final: 0.7931 (ptm) REVERT: J 68 ASP cc_start: 0.8844 (m-30) cc_final: 0.8619 (m-30) REVERT: M 39 VAL cc_start: 0.8953 (OUTLIER) cc_final: 0.8678 (p) REVERT: M 43 ASP cc_start: 0.9107 (t0) cc_final: 0.8628 (t0) REVERT: M 115 ASP cc_start: 0.9321 (t0) cc_final: 0.8713 (p0) REVERT: M 147 ASP cc_start: 0.9236 (p0) cc_final: 0.8653 (t0) outliers start: 115 outliers final: 66 residues processed: 236 average time/residue: 0.1845 time to fit residues: 72.3656 Evaluate side-chains 206 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 126 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 518 LYS Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 866 ASN Chi-restraints excluded: chain C residue 942 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 389 ARG Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 918 THR Chi-restraints excluded: chain D residue 937 ILE Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 1052 ARG Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1113 GLU Chi-restraints excluded: chain D residue 1168 ILE Chi-restraints excluded: chain D residue 1186 PHE Chi-restraints excluded: chain D residue 1194 VAL Chi-restraints excluded: chain D residue 1204 ARG Chi-restraints excluded: chain D residue 1210 ILE Chi-restraints excluded: chain D residue 1226 PHE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 28 GLN Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 308 optimal weight: 9.9990 chunk 206 optimal weight: 5.9990 chunk 354 optimal weight: 40.0000 chunk 159 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 342 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 316 optimal weight: 9.9990 chunk 169 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 479 HIS ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** 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 = 0.3346 r_free = 0.3346 target = 0.055315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.036100 restraints weight = 137220.919| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 3.80 r_work: 0.2525 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2542 r_free = 0.2542 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2542 r_free = 0.2542 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30634 Z= 0.154 Angle : 0.570 9.595 42046 Z= 0.304 Chirality : 0.043 0.320 4799 Planarity : 0.004 0.051 5075 Dihedral : 18.661 173.251 5340 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.89 % Allowed : 21.93 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.14), residues: 3488 helix: 1.21 (0.14), residues: 1376 sheet: -1.49 (0.25), residues: 404 loop : -1.78 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1041 TYR 0.010 0.001 TYR D1077 PHE 0.012 0.001 PHE D1186 TRP 0.050 0.001 TRP D 656 HIS 0.006 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (30627) covalent geometry : angle 0.57038 / 0.30 (42040) hydrogen bonds : bond 0.04299 / 2.93 ( 1313) hydrogen bonds : angle 4.30141 / 3.02 ( 3665) metal coordination : bond 0.00479 / 0.21 ( 7) metal coordination : angle 0.96606 / 0.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 131 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7744 (tm-30) REVERT: B 70 LYS cc_start: 0.9288 (tmmt) cc_final: 0.8902 (tmmt) REVERT: B 205 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8611 (tpt170) REVERT: C 106 SER cc_start: 0.8629 (OUTLIER) cc_final: 0.8296 (p) REVERT: C 154 MET cc_start: 0.9435 (mmm) cc_final: 0.9225 (tpp) REVERT: C 219 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8242 (mpp-170) REVERT: C 300 PHE cc_start: 0.9196 (OUTLIER) cc_final: 0.8864 (m-80) REVERT: C 453 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8624 (ptm160) REVERT: C 713 MET cc_start: 0.9415 (tpp) cc_final: 0.8894 (mmt) REVERT: C 926 MET cc_start: 0.9070 (mmm) cc_final: 0.8466 (mmt) REVERT: C 1051 MET cc_start: 0.9081 (tpp) cc_final: 0.8570 (tpp) REVERT: C 1063 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7027 (t80) REVERT: D 273 GLU cc_start: 0.9117 (OUTLIER) cc_final: 0.8869 (tt0) REVERT: D 389 ARG cc_start: 0.9235 (OUTLIER) cc_final: 0.8947 (mmp80) REVERT: D 541 MET cc_start: 0.9054 (tpp) cc_final: 0.8674 (tpp) REVERT: D 663 MET cc_start: 0.9231 (mmm) cc_final: 0.8869 (mmm) REVERT: D 1186 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.7087 (t80) REVERT: D 1204 ARG cc_start: 0.9295 (OUTLIER) cc_final: 0.8997 (tmm-80) REVERT: E 35 ILE cc_start: 0.9486 (OUTLIER) cc_final: 0.9253 (tt) REVERT: E 66 ASP cc_start: 0.9340 (m-30) cc_final: 0.8760 (t0) REVERT: E 102 ASP cc_start: 0.9338 (OUTLIER) cc_final: 0.9107 (m-30) REVERT: F 220 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7900 (pp20) REVERT: F 282 MET cc_start: 0.8512 (mmt) cc_final: 0.8156 (mmt) REVERT: F 403 MET cc_start: 0.8867 (mtt) cc_final: 0.8530 (mtt) REVERT: J 16 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.8186 (p90) REVERT: J 60 MET cc_start: 0.8056 (ptp) cc_final: 0.7754 (ptm) REVERT: J 64 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8738 (tt) REVERT: J 68 ASP cc_start: 0.8826 (m-30) cc_final: 0.8374 (p0) REVERT: M 39 VAL cc_start: 0.8909 (OUTLIER) cc_final: 0.8610 (p) REVERT: M 43 ASP cc_start: 0.9088 (t0) cc_final: 0.8665 (t0) REVERT: M 147 ASP cc_start: 0.9230 (p0) cc_final: 0.8647 (t0) outliers start: 113 outliers final: 66 residues processed: 236 average time/residue: 0.1880 time to fit residues: 73.2316 Evaluate side-chains 204 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 122 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 518 LYS Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1011 PHE Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 389 ARG Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1052 ARG Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1113 GLU Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1168 ILE Chi-restraints excluded: chain D residue 1186 PHE Chi-restraints excluded: chain D residue 1204 ARG Chi-restraints excluded: chain D residue 1210 ILE Chi-restraints excluded: chain D residue 1226 PHE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 433 SER Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 136 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 212 optimal weight: 7.9990 chunk 356 optimal weight: 30.0000 chunk 311 optimal weight: 8.9990 chunk 266 optimal weight: 1.9990 chunk 262 optimal weight: 9.9990 chunk 206 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 265 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 476 HIS ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.054809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.035555 restraints weight = 138516.517| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 3.77 r_work: 0.2506 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2520 r_free = 0.2520 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2520 r_free = 0.2520 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 30634 Z= 0.240 Angle : 0.620 9.127 42046 Z= 0.327 Chirality : 0.043 0.319 4799 Planarity : 0.004 0.051 5075 Dihedral : 18.668 170.760 5339 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.30 % Allowed : 21.62 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.15), residues: 3488 helix: 1.36 (0.14), residues: 1377 sheet: -1.38 (0.26), residues: 394 loop : -1.73 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG D1097 TYR 0.013 0.001 TYR C 186 PHE 0.012 0.001 PHE C 301 TRP 0.050 0.002 TRP D 656 HIS 0.007 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.24 (30627) covalent geometry : angle 0.61978 / 0.33 (42040) hydrogen bonds : bond 0.04614 / 3.12 ( 1313) hydrogen bonds : angle 4.36196 / 3.05 ( 3665) metal coordination : bond 0.00959 / 0.41 ( 7) metal coordination : angle 1.47279 / 0.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 120 time to evaluate : 1.389 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 5 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7700 (tm-30) REVERT: B 70 LYS cc_start: 0.9292 (tmmt) cc_final: 0.8881 (tmmt) REVERT: B 205 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8643 (tpt170) REVERT: C 106 SER cc_start: 0.8690 (OUTLIER) cc_final: 0.8384 (p) REVERT: C 154 MET cc_start: 0.9455 (mmm) cc_final: 0.9041 (mpp) REVERT: C 219 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8269 (mpp-170) REVERT: C 300 PHE cc_start: 0.9221 (OUTLIER) cc_final: 0.8909 (m-80) REVERT: C 453 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8517 (mtp85) REVERT: C 753 GLU cc_start: 0.8245 (pm20) cc_final: 0.7900 (pm20) REVERT: C 926 MET cc_start: 0.9094 (mmm) cc_final: 0.8550 (mmt) REVERT: C 982 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8376 (mt-10) REVERT: C 1051 MET cc_start: 0.9038 (tpp) cc_final: 0.8427 (tpp) REVERT: C 1063 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.7058 (t80) REVERT: D 155 MET cc_start: 0.9157 (tmm) cc_final: 0.8717 (ppp) REVERT: D 166 ARG cc_start: 0.5625 (OUTLIER) cc_final: 0.5357 (ptm-80) REVERT: D 273 GLU cc_start: 0.9133 (OUTLIER) cc_final: 0.8904 (tt0) REVERT: D 389 ARG cc_start: 0.9237 (OUTLIER) cc_final: 0.8947 (mmp80) REVERT: D 663 MET cc_start: 0.9247 (mmm) cc_final: 0.8879 (mmm) REVERT: D 944 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9141 (tt) REVERT: D 1186 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.7011 (t80) REVERT: E 35 ILE cc_start: 0.9506 (OUTLIER) cc_final: 0.9283 (tt) REVERT: E 66 ASP cc_start: 0.9346 (m-30) cc_final: 0.8794 (t0) REVERT: E 102 ASP cc_start: 0.9329 (OUTLIER) cc_final: 0.9111 (m-30) REVERT: F 220 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7810 (pt0) REVERT: F 282 MET cc_start: 0.8624 (mmt) cc_final: 0.8241 (mmt) REVERT: F 403 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8427 (mtt) REVERT: J 6 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8649 (pp) REVERT: J 16 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.8114 (p90) REVERT: J 28 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7549 (mp10) REVERT: J 35 ASP cc_start: 0.9466 (m-30) cc_final: 0.9103 (p0) REVERT: J 68 ASP cc_start: 0.8829 (m-30) cc_final: 0.8577 (m-30) REVERT: M 39 VAL cc_start: 0.8890 (OUTLIER) cc_final: 0.8589 (p) REVERT: M 43 ASP cc_start: 0.9086 (t0) cc_final: 0.8729 (t0) REVERT: M 147 ASP cc_start: 0.9238 (p0) cc_final: 0.8650 (t0) outliers start: 125 outliers final: 91 residues processed: 236 average time/residue: 0.1828 time to fit residues: 72.6438 Evaluate side-chains 228 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 117 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 512 ILE Chi-restraints excluded: chain C residue 518 LYS Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 942 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 982 GLU Chi-restraints excluded: chain C residue 1011 PHE Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 389 ARG Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 918 THR Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1052 ARG Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1113 GLU Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1168 ILE Chi-restraints excluded: chain D residue 1186 PHE Chi-restraints excluded: chain D residue 1194 VAL Chi-restraints excluded: chain D residue 1204 ARG Chi-restraints excluded: chain D residue 1210 ILE Chi-restraints excluded: chain D residue 1226 PHE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 403 MET Chi-restraints excluded: chain F residue 433 SER Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 28 GLN Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 136 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 224 optimal weight: 7.9990 chunk 256 optimal weight: 2.9990 chunk 252 optimal weight: 0.0770 chunk 342 optimal weight: 10.0000 chunk 338 optimal weight: 0.0470 chunk 129 optimal weight: 1.9990 chunk 221 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 212 optimal weight: 5.9990 overall best weight: 1.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** 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 = 0.3350 r_free = 0.3350 target = 0.055588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.036494 restraints weight = 136719.540| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 3.77 r_work: 0.2535 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2550 r_free = 0.2550 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2550 r_free = 0.2550 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30634 Z= 0.139 Angle : 0.562 8.636 42046 Z= 0.299 Chirality : 0.043 0.323 4799 Planarity : 0.004 0.051 5075 Dihedral : 18.605 170.096 5339 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.79 % Allowed : 22.62 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.15), residues: 3488 helix: 1.51 (0.14), residues: 1380 sheet: -1.15 (0.27), residues: 379 loop : -1.63 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1085 TYR 0.009 0.001 TYR D1077 PHE 0.012 0.001 PHE C 430 TRP 0.052 0.001 TRP D 656 HIS 0.007 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (30627) covalent geometry : angle 0.56210 / 0.30 (42040) hydrogen bonds : bond 0.04076 / 2.79 ( 1313) hydrogen bonds : angle 4.15996 / 2.91 ( 3665) metal coordination : bond 0.00468 / 0.21 ( 7) metal coordination : angle 0.96132 / 0.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 122 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8386 (tm-30) cc_final: 0.7850 (tm-30) REVERT: B 70 LYS cc_start: 0.9324 (tmmt) cc_final: 0.8857 (tmmt) REVERT: B 205 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8589 (tpt170) REVERT: C 106 SER cc_start: 0.8528 (OUTLIER) cc_final: 0.8219 (p) REVERT: C 154 MET cc_start: 0.9423 (mmm) cc_final: 0.9065 (mpp) REVERT: C 219 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8263 (mpp-170) REVERT: C 300 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8897 (m-80) REVERT: C 355 MET cc_start: 0.6769 (tmm) cc_final: 0.6401 (tmm) REVERT: C 453 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8643 (ptm160) REVERT: C 926 MET cc_start: 0.9039 (mmm) cc_final: 0.8500 (mmt) REVERT: C 1051 MET cc_start: 0.9073 (tpp) cc_final: 0.8548 (tpp) REVERT: C 1063 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7034 (t80) REVERT: D 155 MET cc_start: 0.9084 (tmm) cc_final: 0.8696 (ppp) REVERT: D 310 MET cc_start: 0.9334 (mmm) cc_final: 0.9128 (tpp) REVERT: D 389 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8898 (mmp80) REVERT: D 414 ARG cc_start: 0.9243 (OUTLIER) cc_final: 0.8514 (ttm-80) REVERT: D 663 MET cc_start: 0.9256 (mmm) cc_final: 0.8885 (mmm) REVERT: D 733 MET cc_start: 0.9200 (ppp) cc_final: 0.8976 (ttp) REVERT: D 1186 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7091 (t80) REVERT: D 1204 ARG cc_start: 0.9287 (OUTLIER) cc_final: 0.8962 (tmm-80) REVERT: E 35 ILE cc_start: 0.9482 (OUTLIER) cc_final: 0.9245 (tt) REVERT: E 66 ASP cc_start: 0.9337 (m-30) cc_final: 0.8760 (t0) REVERT: F 220 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7871 (pp20) REVERT: F 282 MET cc_start: 0.8662 (mmt) cc_final: 0.8347 (mmt) REVERT: F 403 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8416 (mtt) REVERT: J 6 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8675 (pp) REVERT: J 28 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7545 (mp10) REVERT: J 60 MET cc_start: 0.7811 (ptp) cc_final: 0.7464 (ptm) REVERT: J 68 ASP cc_start: 0.8803 (m-30) cc_final: 0.8315 (p0) REVERT: M 39 VAL cc_start: 0.8866 (OUTLIER) cc_final: 0.8544 (p) REVERT: M 43 ASP cc_start: 0.9068 (t0) cc_final: 0.8678 (t0) REVERT: M 133 GLN cc_start: 0.9477 (tm-30) cc_final: 0.9132 (pp30) REVERT: M 147 ASP cc_start: 0.9234 (p0) cc_final: 0.8635 (t0) outliers start: 110 outliers final: 73 residues processed: 222 average time/residue: 0.1845 time to fit residues: 68.6431 Evaluate side-chains 210 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 121 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 518 LYS Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 866 ASN Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1009 MET Chi-restraints excluded: chain C residue 1011 PHE Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 389 ARG Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 918 THR Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 1052 ARG Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1113 GLU Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1168 ILE Chi-restraints excluded: chain D residue 1186 PHE Chi-restraints excluded: chain D residue 1194 VAL Chi-restraints excluded: chain D residue 1204 ARG Chi-restraints excluded: chain D residue 1226 PHE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 403 MET Chi-restraints excluded: chain F residue 433 SER Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 28 GLN Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 84 optimal weight: 0.9990 chunk 156 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 203 optimal weight: 4.9990 chunk 266 optimal weight: 0.0570 chunk 291 optimal weight: 40.0000 chunk 267 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 2 optimal weight: 0.0000 overall best weight: 1.4108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** 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 = 0.3356 r_free = 0.3356 target = 0.055818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.036783 restraints weight = 137007.185| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 3.80 r_work: 0.2546 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30634 Z= 0.125 Angle : 0.562 13.891 42046 Z= 0.295 Chirality : 0.042 0.324 4799 Planarity : 0.004 0.051 5075 Dihedral : 18.550 169.920 5335 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.55 % Allowed : 22.62 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.15), residues: 3488 helix: 1.62 (0.14), residues: 1383 sheet: -1.01 (0.27), residues: 376 loop : -1.54 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D1085 TYR 0.009 0.001 TYR D1077 PHE 0.011 0.001 PHE C 430 TRP 0.053 0.001 TRP D 656 HIS 0.009 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (30627) covalent geometry : angle 0.56158 / 0.29 (42040) hydrogen bonds : bond 0.03926 / 2.69 ( 1313) hydrogen bonds : angle 4.06452 / 2.84 ( 3665) metal coordination : bond 0.00392 / 0.17 ( 7) metal coordination : angle 1.08957 / 0.42 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 126 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8399 (tm-30) cc_final: 0.7840 (tm-30) REVERT: B 70 LYS cc_start: 0.9341 (tmmt) cc_final: 0.8890 (tmmt) REVERT: B 205 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8538 (tpt170) REVERT: C 106 SER cc_start: 0.8466 (OUTLIER) cc_final: 0.8180 (p) REVERT: C 219 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8288 (mpp-170) REVERT: C 300 PHE cc_start: 0.9155 (OUTLIER) cc_final: 0.8909 (m-80) REVERT: C 453 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8547 (ptm160) REVERT: C 926 MET cc_start: 0.9040 (mmm) cc_final: 0.8517 (mmt) REVERT: C 1051 MET cc_start: 0.9056 (tpp) cc_final: 0.8519 (tpp) REVERT: C 1063 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.6971 (t80) REVERT: D 389 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8930 (mmp80) REVERT: D 414 ARG cc_start: 0.9243 (OUTLIER) cc_final: 0.8506 (ttm-80) REVERT: D 663 MET cc_start: 0.9257 (mmm) cc_final: 0.8871 (mmm) REVERT: D 1186 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7117 (t80) REVERT: D 1204 ARG cc_start: 0.9284 (OUTLIER) cc_final: 0.8943 (tmm-80) REVERT: E 35 ILE cc_start: 0.9462 (OUTLIER) cc_final: 0.9227 (tt) REVERT: E 66 ASP cc_start: 0.9328 (m-30) cc_final: 0.8742 (t0) REVERT: F 282 MET cc_start: 0.8619 (mmt) cc_final: 0.8328 (mmt) REVERT: J 6 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8657 (pp) REVERT: J 35 ASP cc_start: 0.9426 (m-30) cc_final: 0.9100 (p0) REVERT: J 68 ASP cc_start: 0.8748 (m-30) cc_final: 0.8297 (p0) REVERT: M 43 ASP cc_start: 0.9091 (t0) cc_final: 0.8706 (t0) REVERT: M 62 VAL cc_start: 0.9256 (OUTLIER) cc_final: 0.9041 (p) REVERT: M 147 ASP cc_start: 0.9236 (p0) cc_final: 0.8628 (t0) outliers start: 103 outliers final: 73 residues processed: 219 average time/residue: 0.1798 time to fit residues: 65.7813 Evaluate side-chains 204 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 118 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 518 LYS Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 942 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1009 MET Chi-restraints excluded: chain C residue 1011 PHE Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 389 ARG Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 918 THR Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1052 ARG Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1113 GLU Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1168 ILE Chi-restraints excluded: chain D residue 1186 PHE Chi-restraints excluded: chain D residue 1194 VAL Chi-restraints excluded: chain D residue 1204 ARG Chi-restraints excluded: chain D residue 1226 PHE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 433 SER Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 13 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 311 optimal weight: 6.9990 chunk 278 optimal weight: 6.9990 chunk 257 optimal weight: 10.0000 chunk 336 optimal weight: 50.0000 chunk 297 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 chunk 210 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 145 HIS ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1104 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.055047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.035596 restraints weight = 140101.787| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 3.83 r_work: 0.2537 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 30634 Z= 0.218 Angle : 0.616 10.861 42046 Z= 0.320 Chirality : 0.043 0.323 4799 Planarity : 0.004 0.051 5075 Dihedral : 18.579 170.812 5333 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.55 % Allowed : 22.89 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.15), residues: 3488 helix: 1.65 (0.14), residues: 1378 sheet: -1.06 (0.26), residues: 391 loop : -1.49 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 181 TYR 0.015 0.001 TYR M 55 PHE 0.010 0.001 PHE C 430 TRP 0.048 0.002 TRP D 656 HIS 0.011 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.22 (30627) covalent geometry : angle 0.61526 / 0.32 (42040) hydrogen bonds : bond 0.04360 / 2.96 ( 1313) hydrogen bonds : angle 4.18327 / 2.92 ( 3665) metal coordination : bond 0.00946 / 0.41 ( 7) metal coordination : angle 1.58182 / 0.64 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 119 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8374 (tm-30) cc_final: 0.7811 (tm-30) REVERT: B 70 LYS cc_start: 0.9357 (tmmt) cc_final: 0.8890 (tmmt) REVERT: B 205 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8584 (tpt170) REVERT: C 106 SER cc_start: 0.8546 (OUTLIER) cc_final: 0.8290 (p) REVERT: C 300 PHE cc_start: 0.9207 (OUTLIER) cc_final: 0.8919 (m-80) REVERT: C 453 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8604 (ptm160) REVERT: C 926 MET cc_start: 0.9073 (mmm) cc_final: 0.8534 (mmt) REVERT: C 1051 MET cc_start: 0.8968 (tpp) cc_final: 0.8369 (tpp) REVERT: C 1063 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7043 (t80) REVERT: D 18 GLU cc_start: 0.9381 (OUTLIER) cc_final: 0.9111 (tp30) REVERT: D 389 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8925 (mmp80) REVERT: D 414 ARG cc_start: 0.9269 (OUTLIER) cc_final: 0.8549 (ttm-80) REVERT: D 663 MET cc_start: 0.9275 (mmm) cc_final: 0.8899 (mmm) REVERT: D 1112 MET cc_start: 0.7289 (tpt) cc_final: 0.6892 (tpt) REVERT: D 1186 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.7126 (t80) REVERT: E 35 ILE cc_start: 0.9492 (OUTLIER) cc_final: 0.9263 (tt) REVERT: E 66 ASP cc_start: 0.9325 (m-30) cc_final: 0.8773 (t0) REVERT: F 220 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7821 (pp20) REVERT: F 282 MET cc_start: 0.8633 (mmt) cc_final: 0.8352 (mmt) REVERT: J 6 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8699 (pp) REVERT: J 28 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7573 (mp10) REVERT: J 35 ASP cc_start: 0.9463 (m-30) cc_final: 0.9112 (p0) REVERT: J 68 ASP cc_start: 0.8743 (m-30) cc_final: 0.8286 (p0) REVERT: M 43 ASP cc_start: 0.9093 (t0) cc_final: 0.8766 (t0) REVERT: M 62 VAL cc_start: 0.9260 (OUTLIER) cc_final: 0.9057 (p) REVERT: M 133 GLN cc_start: 0.9490 (tm-30) cc_final: 0.9105 (pp30) REVERT: M 147 ASP cc_start: 0.9235 (p0) cc_final: 0.8644 (t0) outliers start: 103 outliers final: 83 residues processed: 214 average time/residue: 0.1799 time to fit residues: 64.9752 Evaluate side-chains 214 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 117 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 518 LYS Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 738 SER Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 866 ASN Chi-restraints excluded: chain C residue 942 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1009 MET Chi-restraints excluded: chain C residue 1011 PHE Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 389 ARG Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 918 THR Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1052 ARG Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1113 GLU Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1168 ILE Chi-restraints excluded: chain D residue 1186 PHE Chi-restraints excluded: chain D residue 1194 VAL Chi-restraints excluded: chain D residue 1204 ARG Chi-restraints excluded: chain D residue 1210 ILE Chi-restraints excluded: chain D residue 1226 PHE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 433 SER Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 28 GLN Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 296 optimal weight: 20.0000 chunk 216 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 338 optimal weight: 7.9990 chunk 319 optimal weight: 10.0000 chunk 236 optimal weight: 0.0770 chunk 35 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 291 optimal weight: 0.0000 chunk 261 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 overall best weight: 1.8148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 145 HIS D 439 HIS ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** 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 = 0.3354 r_free = 0.3354 target = 0.055770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.036367 restraints weight = 139125.540| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 3.86 r_work: 0.2537 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2551 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2551 r_free = 0.2551 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2551 r_free = 0.2551 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2551 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30634 Z= 0.137 Angle : 0.574 10.723 42046 Z= 0.300 Chirality : 0.043 0.326 4799 Planarity : 0.004 0.051 5075 Dihedral : 18.549 170.353 5333 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.20 % Allowed : 23.34 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.15), residues: 3488 helix: 1.71 (0.14), residues: 1380 sheet: -0.94 (0.27), residues: 385 loop : -1.41 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 584 TYR 0.008 0.001 TYR C 186 PHE 0.011 0.001 PHE D1186 TRP 0.044 0.001 TRP D 656 HIS 0.010 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (30627) covalent geometry : angle 0.57393 / 0.30 (42040) hydrogen bonds : bond 0.03960 / 2.71 ( 1313) hydrogen bonds : angle 4.04606 / 2.83 ( 3665) metal coordination : bond 0.00448 / 0.20 ( 7) metal coordination : angle 1.15412 / 0.44 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 122 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8368 (tm-30) cc_final: 0.7793 (tm-30) REVERT: B 70 LYS cc_start: 0.9382 (tmmt) cc_final: 0.8945 (tmmt) REVERT: B 205 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8566 (tpt170) REVERT: C 106 SER cc_start: 0.8462 (OUTLIER) cc_final: 0.8204 (p) REVERT: C 300 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8898 (m-80) REVERT: C 355 MET cc_start: 0.6911 (tmm) cc_final: 0.6641 (tmm) REVERT: C 453 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8511 (ptm160) REVERT: C 926 MET cc_start: 0.9049 (mmm) cc_final: 0.8522 (mmt) REVERT: C 1051 MET cc_start: 0.9044 (tpp) cc_final: 0.8489 (tpp) REVERT: C 1063 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.6972 (t80) REVERT: D 18 GLU cc_start: 0.9355 (OUTLIER) cc_final: 0.9080 (tp30) REVERT: D 389 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8890 (mmp80) REVERT: D 414 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.8493 (ttm-80) REVERT: D 663 MET cc_start: 0.9270 (mmm) cc_final: 0.8880 (mmm) REVERT: D 1186 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7188 (t80) REVERT: E 35 ILE cc_start: 0.9464 (OUTLIER) cc_final: 0.9213 (tt) REVERT: E 66 ASP cc_start: 0.9337 (m-30) cc_final: 0.8755 (t0) REVERT: F 220 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7818 (pp20) REVERT: F 282 MET cc_start: 0.8667 (mmt) cc_final: 0.8426 (mmt) REVERT: J 6 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8653 (pp) REVERT: J 28 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7506 (mp10) REVERT: J 35 ASP cc_start: 0.9432 (m-30) cc_final: 0.9110 (p0) REVERT: J 68 ASP cc_start: 0.8756 (m-30) cc_final: 0.8301 (p0) REVERT: M 43 ASP cc_start: 0.9170 (t0) cc_final: 0.8877 (t0) REVERT: M 133 GLN cc_start: 0.9456 (tm-30) cc_final: 0.9115 (pp30) REVERT: M 147 ASP cc_start: 0.9247 (p0) cc_final: 0.8640 (t0) outliers start: 93 outliers final: 75 residues processed: 208 average time/residue: 0.1860 time to fit residues: 65.1070 Evaluate side-chains 208 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 120 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 518 LYS Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 866 ASN Chi-restraints excluded: chain C residue 942 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1009 MET Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 389 ARG Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 918 THR Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1052 ARG Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1113 GLU Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1168 ILE Chi-restraints excluded: chain D residue 1186 PHE Chi-restraints excluded: chain D residue 1194 VAL Chi-restraints excluded: chain D residue 1204 ARG Chi-restraints excluded: chain D residue 1226 PHE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 433 SER Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 28 GLN Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 65 optimal weight: 3.9990 chunk 202 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 292 optimal weight: 6.9990 chunk 215 optimal weight: 0.0470 chunk 192 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 283 optimal weight: 7.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN D 145 HIS ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** 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 = 0.3371 r_free = 0.3371 target = 0.056395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.037021 restraints weight = 140058.228| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 3.89 r_work: 0.2559 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30634 Z= 0.111 Angle : 0.565 11.387 42046 Z= 0.293 Chirality : 0.042 0.324 4799 Planarity : 0.003 0.051 5075 Dihedral : 18.448 170.114 5333 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.75 % Allowed : 23.75 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.15), residues: 3488 helix: 1.81 (0.14), residues: 1387 sheet: -0.93 (0.27), residues: 395 loop : -1.33 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 181 TYR 0.008 0.001 TYR D1077 PHE 0.011 0.001 PHE D1186 TRP 0.042 0.001 TRP D 656 HIS 0.011 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (30627) covalent geometry : angle 0.56525 / 0.29 (42040) hydrogen bonds : bond 0.03633 / 2.50 ( 1313) hydrogen bonds : angle 3.93048 / 2.75 ( 3665) metal coordination : bond 0.00264 / 0.12 ( 7) metal coordination : angle 1.23840 / 0.44 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7343.37 seconds wall clock time: 126 minutes 24.48 seconds (7584.48 seconds total)