Starting phenix.real_space_refine on Thu Mar 5 17:30:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e95_27956/03_2026/8e95_27956.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e95_27956/03_2026/8e95_27956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e95_27956/03_2026/8e95_27956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e95_27956/03_2026/8e95_27956.map" model { file = "/net/cci-nas-00/data/ceres_data/8e95_27956/03_2026/8e95_27956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e95_27956/03_2026/8e95_27956.cif" } resolution = 2.9 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= 0.003 sd= 0.143 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 68 5.49 5 Mg 1 5.21 5 S 87 5.16 5 C 14792 2.51 5 N 4255 2.21 5 O 4738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23943 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1724 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1769 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 15, 'TRANS': 221} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 8485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8485 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 1033} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 9916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1269, 9916 Classifications: {'peptide': 1269} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 57, 'TRANS': 1208} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 645 Classifications: {'peptide': 82} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 75} Chain: "P" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 666 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "Q" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 514 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 1 Chain: "R" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 221 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna3p': 9} 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 12487 SG CYS D 60 109.325 75.054 111.808 1.00 59.49 S ATOM 12505 SG CYS D 62 111.304 75.898 112.270 1.00 67.74 S ATOM 12614 SG CYS D 75 110.872 72.803 114.866 1.00 67.04 S ATOM 12640 SG CYS D 78 109.341 75.116 114.388 1.00 66.98 S ATOM 19055 SG CYS D 891 70.397 22.954 88.079 1.00 31.73 S ATOM 19622 SG CYS D 968 69.866 26.822 89.590 1.00 9.65 S ATOM 19664 SG CYS D 975 70.676 25.954 86.115 1.00 14.23 S ATOM 19682 SG CYS D 978 67.693 25.179 86.622 1.00 17.04 S Time building chain proxies: 4.87, per 1000 atoms: 0.20 Number of scatterers: 23943 At special positions: 0 Unit cell: (127.735, 134.23, 198.097, 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 87 16.00 P 68 15.00 Mg 1 11.99 O 4738 8.00 N 4255 7.00 C 14792 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 62 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 968 " Number of angles added : 12 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5346 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 38 sheets defined 39.2% alpha, 15.7% beta 29 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 203 through 219 Processing helix chain 'B' and resid 29 through 45 removed outlier: 3.558A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.239A 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 203 through 219 removed outlier: 3.690A pdb=" N ALA B 209 " --> pdb=" O ARG B 205 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 removed outlier: 3.662A pdb=" N ARG B 223 " --> pdb=" O PHE B 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 63 removed outlier: 3.900A pdb=" N PHE C 61 " --> pdb=" O GLN C 57 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C 62 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 79 removed outlier: 3.616A pdb=" N GLU C 76 " --> pdb=" O GLU C 72 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 233 through 241 removed outlier: 4.073A 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 removed outlier: 3.520A pdb=" N ARG C 259 " --> pdb=" O SER C 255 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C 262 " --> pdb=" O MET C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 288 through 300 Processing helix chain 'C' and resid 308 through 320 Processing helix chain 'C' and resid 334 through 349 removed outlier: 3.738A pdb=" N ILE C 342 " --> pdb=" O VAL C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 404 Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.514A pdb=" N LEU C 417 " --> pdb=" O THR C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 433 Processing helix chain 'C' and resid 444 through 453 removed outlier: 3.675A pdb=" N GLY C 448 " --> pdb=" O ASN C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 Processing helix chain 'C' and resid 533 through 537 Processing helix chain 'C' and resid 590 through 594 removed outlier: 3.715A pdb=" N ILE C 594 " --> pdb=" O THR C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 631 through 639 removed outlier: 3.506A pdb=" N GLY C 639 " --> pdb=" O ALA C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 779 through 784 removed outlier: 4.561A pdb=" N ASP C 783 " --> pdb=" O VAL C 780 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 858 Processing helix chain 'C' and resid 921 through 926 removed outlier: 3.681A pdb=" N ARG C 925 " --> pdb=" O GLY C 921 " (cutoff:3.500A) 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 991 Processing helix chain 'C' and resid 1036 through 1040 Processing helix chain 'C' and resid 1069 through 1079 removed outlier: 3.642A pdb=" N CYS C1073 " --> pdb=" O GLY C1069 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1091 removed outlier: 3.671A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1108 removed outlier: 3.780A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1119 through 1131 removed outlier: 3.784A pdb=" N VAL C1123 " --> pdb=" O GLU C1119 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 23 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 104 through 109 removed outlier: 3.541A pdb=" N GLY D 109 " --> pdb=" O TRP D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 141 through 186 removed outlier: 4.404A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 229 Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.664A pdb=" N TYR D 241 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.627A pdb=" N ILE D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 removed outlier: 4.069A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.582A pdb=" N LYS D 294 " --> pdb=" O LEU D 290 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.858A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 338 through 361 Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 411 through 417 Processing helix chain 'D' and resid 447 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 removed outlier: 3.513A pdb=" N ALA D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 491 removed outlier: 4.271A pdb=" N TRP D 484 " --> pdb=" O ARG D 480 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 579 through 589 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: 4.146A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.634A pdb=" N ILE D 745 " --> pdb=" O ARG D 741 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG D 752 " --> pdb=" O HIS D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 810 through 819 removed outlier: 3.654A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 3.846A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU D 860 " --> pdb=" O ALA D 856 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY D 871 " --> pdb=" O THR D 867 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR D 872 " --> pdb=" O ALA D 868 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU D 873 " --> pdb=" O ASP D 869 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 964 through 968 Processing helix chain 'D' and resid 976 through 980 Processing helix chain 'D' and resid 994 through 1005 removed outlier: 3.766A pdb=" N VAL D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1006 through 1008 No H-bonds generated for 'chain 'D' and resid 1006 through 1008' Processing helix chain 'D' and resid 1027 through 1037 Processing helix chain 'D' and resid 1117 through 1126 removed outlier: 3.729A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Processing helix chain 'D' and resid 1126 through 1145 removed outlier: 4.033A pdb=" N GLN D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1160 removed outlier: 4.311A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1196 removed outlier: 3.628A pdb=" N ALA D1195 " --> pdb=" O ARG D1191 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU D1196 " --> pdb=" O ARG D1192 " (cutoff:3.500A) Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1219 through 1225 removed outlier: 3.507A pdb=" N ALA D1224 " --> pdb=" O TRP D1220 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1228 through 1240 Processing helix chain 'D' and resid 1247 through 1254 Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 33 through 37 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 49 through 74 removed outlier: 3.830A pdb=" N GLY E 72 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU E 73 " --> pdb=" O ASN E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 removed outlier: 3.508A pdb=" N ILE E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU E 96 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE E 99 " --> pdb=" O ALA E 95 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 15 removed outlier: 6.614A pdb=" N ARG A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N PHE A 189 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA A 180 " --> pdb=" O PHE A 189 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYS A 191 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL A 178 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE A 193 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR A 176 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASP A 195 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL A 174 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLU A 197 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.451A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 105 Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 147 removed outlier: 3.772A pdb=" N GLY A 145 " --> pdb=" O TYR A 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 15 removed outlier: 6.138A pdb=" N ARG B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.010A pdb=" N VAL B 111 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TYR B 96 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 99 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 134 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.670A pdb=" N GLY B 103 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.552A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 96 through 97 removed outlier: 5.535A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY C 155 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL C 135 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N PHE C 153 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA C 137 " --> pdb=" O THR C 151 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N THR C 151 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE C 139 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N SER C 149 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ASN C 141 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE C 147 " --> pdb=" O ASN C 141 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB5, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.764A pdb=" N SER C 177 " --> pdb=" O ARG C 454 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 184 through 191 removed outlier: 3.912A pdb=" N LEU C 212 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 505 through 506 removed outlier: 4.154A pdb=" N LYS C 518 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 505 through 506 removed outlier: 4.616A pdb=" N VAL C 541 " --> pdb=" O ARG C 562 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG C 562 " --> pdb=" O VAL C 541 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL C 559 " --> pdb=" O VAL C 571 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL C 571 " --> pdb=" O VAL C 559 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.439A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 667 through 671 removed outlier: 6.952A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 676 through 677 Processing sheet with id=AC3, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC4, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 5.738A pdb=" N ILE C 735 " --> pdb=" O ILE C 895 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 749 through 756 removed outlier: 3.555A pdb=" N VAL C 873 " --> pdb=" O GLU C 753 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N LYS C 876 " --> pdb=" O GLY C 845 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N GLY C 845 " --> pdb=" O LYS C 876 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 759 through 760 removed outlier: 6.897A pdb=" N ALA C 759 " --> pdb=" O ASN C 866 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 768 through 769 removed outlier: 3.653A pdb=" N GLU C 768 " --> pdb=" O VAL C 806 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1042 through 1044 Processing sheet with id=AC9, first strand: chain 'C' and resid 1067 through 1068 Processing sheet with id=AD1, first strand: chain 'C' and resid 1136 through 1138 Processing sheet with id=AD2, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.645A pdb=" N HIS D 94 " --> pdb=" O TYR D 25 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU D 27 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N GLU D 96 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 10.286A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.194A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 234 through 235 removed outlier: 3.591A pdb=" N TYR D 134 " --> pdb=" O ILE D 235 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 328 through 330 removed outlier: 4.247A pdb=" N VAL D 328 " --> pdb=" O ALA D 336 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 632 through 637 Processing sheet with id=AD6, first strand: chain 'D' and resid 822 through 825 removed outlier: 9.311A pdb=" N GLY D 822 " --> pdb=" O ARG D 834 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ARG D 834 " --> pdb=" O GLY D 822 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL D 824 " --> pdb=" O ILE D 832 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AD8, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.986A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 1051 through 1053 removed outlier: 5.561A pdb=" N TYR D1062 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS D1079 " --> pdb=" O TYR D1062 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 4.879A pdb=" N ARG D1164 " --> pdb=" O VAL D1206 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL D1206 " --> pdb=" O ARG D1164 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1271 through 1274 932 hydrogen bonds defined for protein. 2589 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 5.22 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7802 1.34 - 1.46: 3305 1.46 - 1.58: 13099 1.58 - 1.70: 132 1.70 - 1.81: 153 Bond restraints: 24491 Sorted by residual: bond pdb=" N GLY D -1 " pdb=" CA GLY D -1 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.18e+00 bond pdb=" P DG P 112 " pdb=" OP2 DG P 112 " ideal model delta sigma weight residual 1.480 1.520 -0.040 2.00e-02 2.50e+03 4.00e+00 bond pdb=" P DT P 115 " pdb=" OP2 DT P 115 " ideal model delta sigma weight residual 1.480 1.519 -0.039 2.00e-02 2.50e+03 3.90e+00 bond pdb=" P DG P 114 " pdb=" OP2 DG P 114 " ideal model delta sigma weight residual 1.480 1.518 -0.038 2.00e-02 2.50e+03 3.62e+00 bond pdb=" P DT P 117 " pdb=" OP2 DT P 117 " ideal model delta sigma weight residual 1.480 1.517 -0.037 2.00e-02 2.50e+03 3.43e+00 ... (remaining 24486 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 33227 2.75 - 5.49: 235 5.49 - 8.24: 11 8.24 - 10.98: 1 10.98 - 13.73: 1 Bond angle restraints: 33475 Sorted by residual: angle pdb=" C3' DA P 116 " pdb=" O3' DA P 116 " pdb=" P DT P 117 " ideal model delta sigma weight residual 120.20 106.47 13.73 1.50e+00 4.44e-01 8.38e+01 angle pdb=" C3' DG P 112 " pdb=" O3' DG P 112 " pdb=" P DG P 113 " ideal model delta sigma weight residual 120.20 111.03 9.17 1.50e+00 4.44e-01 3.73e+01 angle pdb=" C3' DT P 115 " pdb=" O3' DT P 115 " pdb=" P DA P 116 " ideal model delta sigma weight residual 120.20 112.08 8.12 1.50e+00 4.44e-01 2.93e+01 angle pdb=" N VAL B 183 " pdb=" CA VAL B 183 " pdb=" C VAL B 183 " ideal model delta sigma weight residual 113.71 109.62 4.09 9.50e-01 1.11e+00 1.86e+01 angle pdb=" N ARG C 584 " pdb=" CA ARG C 584 " pdb=" C ARG C 584 " ideal model delta sigma weight residual 111.71 106.56 5.15 1.34e+00 5.57e-01 1.48e+01 ... (remaining 33470 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.36: 14350 33.36 - 66.72: 458 66.72 - 100.07: 5 100.07 - 133.43: 1 133.43 - 166.79: 1 Dihedral angle restraints: 14815 sinusoidal: 6497 harmonic: 8318 Sorted by residual: dihedral pdb=" O4' C R 11 " pdb=" C1' C R 11 " pdb=" N1 C R 11 " pdb=" C2 C R 11 " ideal model delta sinusoidal sigma weight residual 200.00 33.21 166.79 1 1.50e+01 4.44e-03 8.42e+01 dihedral pdb=" CA GLU E 77 " pdb=" C GLU E 77 " pdb=" N TYR E 78 " pdb=" CA TYR E 78 " ideal model delta harmonic sigma weight residual 180.00 -158.04 -21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ASN D 5 " pdb=" C ASN D 5 " pdb=" N PHE D 6 " pdb=" CA PHE D 6 " ideal model delta harmonic sigma weight residual -180.00 -158.84 -21.16 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 14812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 3692 0.104 - 0.209: 127 0.209 - 0.313: 0 0.313 - 0.417: 0 0.417 - 0.522: 6 Chirality restraints: 3825 Sorted by residual: chirality pdb=" P DA P 116 " pdb=" OP1 DA P 116 " pdb=" OP2 DA P 116 " pdb=" O5' DA P 116 " both_signs ideal model delta sigma weight residual True 2.35 -2.87 -0.52 2.00e-01 2.50e+01 6.80e+00 chirality pdb=" P DG P 112 " pdb=" OP1 DG P 112 " pdb=" OP2 DG P 112 " pdb=" O5' DG P 112 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.51 2.00e-01 2.50e+01 6.50e+00 chirality pdb=" P DG P 114 " pdb=" OP1 DG P 114 " pdb=" OP2 DG P 114 " pdb=" O5' DG P 114 " both_signs ideal model delta sigma weight residual True 2.35 -2.81 -0.47 2.00e-01 2.50e+01 5.44e+00 ... (remaining 3822 not shown) Planarity restraints: 4169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT P 117 " -0.004 2.00e-02 2.50e+03 2.11e-02 1.11e+01 pdb=" N1 DT P 117 " 0.011 2.00e-02 2.50e+03 pdb=" C2 DT P 117 " -0.013 2.00e-02 2.50e+03 pdb=" O2 DT P 117 " -0.019 2.00e-02 2.50e+03 pdb=" N3 DT P 117 " 0.056 2.00e-02 2.50e+03 pdb=" C4 DT P 117 " -0.006 2.00e-02 2.50e+03 pdb=" O4 DT P 117 " -0.024 2.00e-02 2.50e+03 pdb=" C5 DT P 117 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT P 117 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DT P 117 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT P 115 " 0.016 2.00e-02 2.50e+03 1.29e-02 4.17e+00 pdb=" N1 DT P 115 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DT P 115 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT P 115 " -0.017 2.00e-02 2.50e+03 pdb=" N3 DT P 115 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT P 115 " -0.012 2.00e-02 2.50e+03 pdb=" O4 DT P 115 " 0.025 2.00e-02 2.50e+03 pdb=" C5 DT P 115 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT P 115 " -0.017 2.00e-02 2.50e+03 pdb=" C6 DT P 115 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 413 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO C 414 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 414 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 414 " -0.028 5.00e-02 4.00e+02 ... (remaining 4166 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 64 2.42 - 3.04: 15009 3.04 - 3.66: 33929 3.66 - 4.28: 52286 4.28 - 4.90: 88884 Nonbonded interactions: 190172 Sorted by model distance: nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2002 " model vdw 1.796 2.170 nonbonded pdb=" OE1 GLN C 150 " pdb=" OG1 THR C 413 " model vdw 1.992 3.040 nonbonded pdb=" O3' A R 20 " pdb="MG MG D2002 " model vdw 2.027 2.170 nonbonded pdb=" OD1 ASP D 539 " pdb="MG MG D2002 " model vdw 2.097 2.170 nonbonded pdb=" O SER B 45 " pdb=" NH1 ARG B 144 " model vdw 2.099 3.120 ... (remaining 190167 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 1 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 226)) \ selection = (chain 'B' and resid 1 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 25.670 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 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 : 0.004 0.248 24499 Z= 0.169 Angle : 0.772 47.946 33487 Z= 0.357 Chirality : 0.045 0.522 3825 Planarity : 0.004 0.050 4169 Dihedral : 14.082 166.790 9469 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.70 % Favored : 95.02 % Rotamer: Outliers : 4.39 % Allowed : 6.56 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.16), residues: 2893 helix: 0.83 (0.17), residues: 1011 sheet: -0.94 (0.29), residues: 316 loop : -1.40 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1067 TYR 0.010 0.001 TYR D 586 PHE 0.013 0.001 PHE C 439 TRP 0.009 0.001 TRP C 938 HIS 0.003 0.001 HIS D 689 Details of bonding type rmsd covalent geometry : bond 0.00276 (24491) covalent geometry : angle 0.59209 (33475) hydrogen bonds : bond 0.18172 ( 1007) hydrogen bonds : angle 6.74905 ( 2743) metal coordination : bond 0.14591 ( 8) metal coordination : angle 26.18530 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 496 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4486 (tpp) cc_final: 0.3594 (tmt) REVERT: A 221 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.6877 (mt) REVERT: B 24 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6485 (mt-10) REVERT: B 55 ARG cc_start: 0.7583 (ptm160) cc_final: 0.7096 (ptp90) REVERT: C 160 MET cc_start: 0.9154 (ttm) cc_final: 0.8546 (ttp) REVERT: C 215 ASP cc_start: 0.7034 (OUTLIER) cc_final: 0.6716 (m-30) REVERT: C 262 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.5859 (pp) REVERT: C 302 LYS cc_start: 0.6580 (OUTLIER) cc_final: 0.6295 (mmtt) REVERT: C 419 ASN cc_start: 0.7166 (t0) cc_final: 0.6905 (t160) REVERT: C 483 MET cc_start: 0.9033 (ttp) cc_final: 0.8796 (ttt) REVERT: C 528 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8287 (pt) REVERT: C 673 ARG cc_start: 0.8101 (ptm160) cc_final: 0.7604 (ptm-80) REVERT: C 805 LYS cc_start: 0.6057 (OUTLIER) cc_final: 0.5803 (pttt) REVERT: C 901 VAL cc_start: 0.8765 (p) cc_final: 0.8466 (t) REVERT: C 952 VAL cc_start: 0.7953 (m) cc_final: 0.7715 (t) REVERT: C 1030 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8472 (mm) REVERT: C 1138 LEU cc_start: 0.8649 (mt) cc_final: 0.8382 (mt) REVERT: D 229 LEU cc_start: 0.6501 (OUTLIER) cc_final: 0.6279 (tt) REVERT: D 403 SER cc_start: 0.8513 (t) cc_final: 0.8277 (m) REVERT: D 410 GLN cc_start: 0.8419 (mp10) cc_final: 0.8092 (mm-40) REVERT: D 423 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7591 (m-30) REVERT: D 496 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8133 (p) REVERT: D 672 MET cc_start: 0.8123 (mtt) cc_final: 0.7857 (mtt) REVERT: D 865 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7546 (mm) REVERT: D 1117 ASP cc_start: 0.7561 (p0) cc_final: 0.7325 (t0) REVERT: E 33 LEU cc_start: 0.8450 (pt) cc_final: 0.8159 (mt) REVERT: E 40 ILE cc_start: 0.8448 (tp) cc_final: 0.8076 (tp) REVERT: E 62 ARG cc_start: 0.8258 (mtt180) cc_final: 0.7787 (mmt-90) outliers start: 107 outliers final: 32 residues processed: 575 average time/residue: 0.5986 time to fit residues: 396.0812 Evaluate side-chains 335 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 291 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 805 LYS Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 947 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 79 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 443 ASN ** C 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 685 ASN C 739 ASN C 751 HIS C 755 HIS C 889 HIS D 564 ASN D 693 GLN D 748 HIS D 810 ASN D1032 GLN D1125 GLN E 65 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.197880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.149389 restraints weight = 25942.313| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.84 r_work: 0.3386 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 24499 Z= 0.246 Angle : 0.747 19.212 33487 Z= 0.383 Chirality : 0.049 0.204 3825 Planarity : 0.006 0.070 4169 Dihedral : 14.594 166.757 4018 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.15 % Favored : 93.54 % Rotamer: Outliers : 5.70 % Allowed : 13.54 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.15), residues: 2893 helix: 0.66 (0.16), residues: 1025 sheet: -0.68 (0.27), residues: 358 loop : -1.61 (0.15), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 584 TYR 0.017 0.002 TYR A 168 PHE 0.023 0.002 PHE C 906 TRP 0.015 0.002 TRP C 938 HIS 0.007 0.002 HIS D 689 Details of bonding type rmsd covalent geometry : bond 0.00605 (24491) covalent geometry : angle 0.72596 (33475) hydrogen bonds : bond 0.06457 ( 1007) hydrogen bonds : angle 5.29157 ( 2743) metal coordination : bond 0.02108 ( 8) metal coordination : angle 9.27011 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 300 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4644 (tpp) cc_final: 0.2871 (tmt) REVERT: A 99 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6921 (tttm) REVERT: A 193 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8141 (mt) REVERT: A 221 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.6988 (mt) REVERT: B 6 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.7030 (tmt170) REVERT: B 24 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6698 (mt-10) REVERT: B 55 ARG cc_start: 0.7989 (ptm160) cc_final: 0.6377 (ptp90) REVERT: B 150 VAL cc_start: 0.8185 (OUTLIER) cc_final: 0.7623 (t) REVERT: B 217 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: C 92 GLU cc_start: 0.7203 (tp30) cc_final: 0.5850 (tt0) REVERT: C 127 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7829 (ptp) REVERT: C 347 ARG cc_start: 0.6253 (mtt-85) cc_final: 0.6021 (tpt170) REVERT: C 505 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7566 (ptp-170) REVERT: C 584 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7969 (ttt180) REVERT: C 645 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7466 (tt0) REVERT: C 673 ARG cc_start: 0.8524 (ptm160) cc_final: 0.7546 (ptm-80) REVERT: C 767 GLU cc_start: 0.6634 (OUTLIER) cc_final: 0.6195 (pm20) REVERT: C 805 LYS cc_start: 0.5481 (OUTLIER) cc_final: 0.5189 (pttt) REVERT: C 870 ARG cc_start: 0.7736 (ttm-80) cc_final: 0.7529 (ttm110) REVERT: C 877 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8327 (mtm-85) REVERT: C 952 VAL cc_start: 0.7927 (m) cc_final: 0.7653 (t) REVERT: C 1028 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8423 (ttm) REVERT: C 1030 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8558 (mm) REVERT: C 1119 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7513 (tm-30) REVERT: C 1138 LEU cc_start: 0.8442 (mt) cc_final: 0.8233 (mt) REVERT: D 9 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7187 (mt-10) REVERT: D 30 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7083 (tppp) REVERT: D 92 MET cc_start: 0.8634 (mtp) cc_final: 0.8026 (mtm) REVERT: D 126 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.6804 (tt0) REVERT: D 266 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7290 (mp0) REVERT: D 275 GLU cc_start: 0.8388 (tp30) cc_final: 0.8135 (tp30) REVERT: D 410 GLN cc_start: 0.8308 (mp10) cc_final: 0.7935 (mm-40) REVERT: D 623 ASP cc_start: 0.7262 (m-30) cc_final: 0.6872 (m-30) REVERT: D 665 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7754 (pp20) REVERT: D 787 GLN cc_start: 0.7063 (tp40) cc_final: 0.6768 (tm-30) REVERT: D 790 ARG cc_start: 0.7706 (tpt-90) cc_final: 0.6809 (ttp-170) REVERT: D 824 VAL cc_start: 0.8333 (m) cc_final: 0.7737 (p) REVERT: D 865 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7192 (mm) REVERT: D 901 LEU cc_start: 0.7179 (tp) cc_final: 0.6907 (tt) REVERT: D 959 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7400 (pt0) REVERT: D 1117 ASP cc_start: 0.7553 (p0) cc_final: 0.7062 (t0) REVERT: D 1129 GLU cc_start: 0.8280 (mp0) cc_final: 0.7875 (mm-30) REVERT: D 1231 ARG cc_start: 0.8218 (ttp-170) cc_final: 0.7982 (ttm170) REVERT: E 62 ARG cc_start: 0.8349 (mtt180) cc_final: 0.7698 (mmt-90) outliers start: 139 outliers final: 63 residues processed: 403 average time/residue: 0.6087 time to fit residues: 281.6480 Evaluate side-chains 346 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 260 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 645 GLU Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 767 GLU Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 805 LYS Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1028 MET Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1076 MET Chi-restraints excluded: chain C residue 1106 ILE Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 913 ASP Chi-restraints excluded: chain D residue 959 GLN Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1262 THR Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 79 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 90 optimal weight: 4.9990 chunk 256 optimal weight: 0.9980 chunk 274 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 288 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 chunk 204 optimal weight: 0.9980 chunk 238 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 276 optimal weight: 0.8980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.198817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.151484 restraints weight = 25933.743| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.76 r_work: 0.3403 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24499 Z= 0.177 Angle : 0.639 15.852 33487 Z= 0.328 Chirality : 0.045 0.175 3825 Planarity : 0.005 0.066 4169 Dihedral : 14.415 167.132 3996 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.25 % Favored : 94.47 % Rotamer: Outliers : 5.70 % Allowed : 15.75 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.15), residues: 2893 helix: 0.83 (0.16), residues: 1029 sheet: -0.59 (0.26), residues: 368 loop : -1.54 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 421 TYR 0.018 0.002 TYR C 344 PHE 0.022 0.002 PHE C 214 TRP 0.013 0.002 TRP C 938 HIS 0.006 0.001 HIS D 748 Details of bonding type rmsd covalent geometry : bond 0.00421 (24491) covalent geometry : angle 0.61962 (33475) hydrogen bonds : bond 0.05502 ( 1007) hydrogen bonds : angle 4.98486 ( 2743) metal coordination : bond 0.01229 ( 8) metal coordination : angle 8.24373 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 286 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4638 (tpp) cc_final: 0.3134 (tmt) REVERT: A 99 LYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6918 (tttt) REVERT: A 193 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8144 (mt) REVERT: A 202 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.7871 (tp) REVERT: A 221 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.6887 (mt) REVERT: B 6 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6973 (tmt170) REVERT: B 24 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6535 (mt-10) REVERT: B 150 VAL cc_start: 0.8163 (OUTLIER) cc_final: 0.7614 (t) REVERT: B 186 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.6905 (mtp180) REVERT: C 92 GLU cc_start: 0.7168 (tp30) cc_final: 0.5867 (tt0) REVERT: C 127 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7748 (ptp) REVERT: C 163 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.6920 (mmpt) REVERT: C 225 ARG cc_start: 0.7192 (mtp180) cc_final: 0.6988 (ttt180) REVERT: C 347 ARG cc_start: 0.6316 (mtt-85) cc_final: 0.5970 (tpt170) REVERT: C 396 MET cc_start: 0.6717 (ttp) cc_final: 0.6512 (ttp) REVERT: C 421 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6437 (mmp-170) REVERT: C 505 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7607 (ptp-170) REVERT: C 535 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7949 (mt-10) REVERT: C 570 TYR cc_start: 0.7312 (OUTLIER) cc_final: 0.7011 (m-80) REVERT: C 577 ASP cc_start: 0.8056 (m-30) cc_final: 0.7845 (m-30) REVERT: C 584 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8075 (ttt180) REVERT: C 673 ARG cc_start: 0.8511 (ptm160) cc_final: 0.7510 (ptm-80) REVERT: C 784 LEU cc_start: 0.5609 (tt) cc_final: 0.5397 (tt) REVERT: C 805 LYS cc_start: 0.5475 (OUTLIER) cc_final: 0.5190 (pttt) REVERT: C 877 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8341 (mtm-85) REVERT: C 952 VAL cc_start: 0.7865 (m) cc_final: 0.7573 (t) REVERT: C 1028 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8393 (ttm) REVERT: C 1030 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8415 (mm) REVERT: C 1062 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8019 (pt0) REVERT: C 1119 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7615 (tm-30) REVERT: D 1 MET cc_start: 0.5732 (OUTLIER) cc_final: 0.5485 (mtt) REVERT: D 16 THR cc_start: 0.7551 (OUTLIER) cc_final: 0.7287 (p) REVERT: D 19 ASP cc_start: 0.8068 (m-30) cc_final: 0.7860 (m-30) REVERT: D 92 MET cc_start: 0.8660 (mtp) cc_final: 0.8015 (mtm) REVERT: D 124 ASP cc_start: 0.7305 (m-30) cc_final: 0.7070 (m-30) REVERT: D 266 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7216 (mp0) REVERT: D 323 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7884 (tt0) REVERT: D 410 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7746 (mm-40) REVERT: D 623 ASP cc_start: 0.7407 (m-30) cc_final: 0.6986 (m-30) REVERT: D 791 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7162 (pt0) REVERT: D 824 VAL cc_start: 0.8088 (m) cc_final: 0.7500 (p) REVERT: D 865 LEU cc_start: 0.7538 (tp) cc_final: 0.7080 (mm) REVERT: D 866 ARG cc_start: 0.8059 (ttm110) cc_final: 0.7778 (ttp-110) REVERT: D 959 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7341 (pt0) REVERT: D 987 LYS cc_start: 0.8127 (mttp) cc_final: 0.7698 (mttp) REVERT: D 1117 ASP cc_start: 0.7561 (p0) cc_final: 0.7006 (t0) REVERT: E 62 ARG cc_start: 0.8145 (mtt180) cc_final: 0.7540 (mmt-90) REVERT: E 66 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7245 (t0) REVERT: E 92 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7269 (tt) outliers start: 139 outliers final: 64 residues processed: 387 average time/residue: 0.6047 time to fit residues: 269.2063 Evaluate side-chains 340 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 249 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 421 ARG Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 805 LYS Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1028 MET Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1062 GLN Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1106 ILE Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 913 ASP Chi-restraints excluded: chain D residue 959 GLN Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 92 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 171 optimal weight: 20.0000 chunk 108 optimal weight: 8.9990 chunk 218 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 198 optimal weight: 0.6980 chunk 254 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 225 optimal weight: 0.9980 chunk 261 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.199882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.152665 restraints weight = 25831.257| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.68 r_work: 0.3420 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24499 Z= 0.145 Angle : 0.594 13.056 33487 Z= 0.307 Chirality : 0.043 0.165 3825 Planarity : 0.005 0.064 4169 Dihedral : 14.270 166.560 3988 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.29 % Favored : 94.43 % Rotamer: Outliers : 5.62 % Allowed : 17.06 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.15), residues: 2893 helix: 0.98 (0.16), residues: 1035 sheet: -0.61 (0.27), residues: 361 loop : -1.42 (0.15), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 182 TYR 0.014 0.001 TYR D 61 PHE 0.026 0.002 PHE C 214 TRP 0.011 0.001 TRP C 938 HIS 0.006 0.001 HIS D 748 Details of bonding type rmsd covalent geometry : bond 0.00337 (24491) covalent geometry : angle 0.58037 (33475) hydrogen bonds : bond 0.04832 ( 1007) hydrogen bonds : angle 4.76190 ( 2743) metal coordination : bond 0.01168 ( 8) metal coordination : angle 6.67940 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 280 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4699 (tpp) cc_final: 0.3119 (tmt) REVERT: A 99 LYS cc_start: 0.7143 (OUTLIER) cc_final: 0.6907 (tttt) REVERT: A 177 LYS cc_start: 0.8292 (ptpp) cc_final: 0.7772 (ptmm) REVERT: A 193 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8025 (mt) REVERT: A 221 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.6837 (mt) REVERT: B 6 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6975 (tmt170) REVERT: B 24 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6547 (mt-10) REVERT: B 54 ILE cc_start: 0.8062 (pt) cc_final: 0.7853 (pp) REVERT: B 123 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7598 (ttt) REVERT: B 150 VAL cc_start: 0.8184 (OUTLIER) cc_final: 0.7663 (t) REVERT: C 127 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7756 (ptp) REVERT: C 163 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.6939 (mmpt) REVERT: C 347 ARG cc_start: 0.6251 (mtt-85) cc_final: 0.5904 (tpt170) REVERT: C 396 MET cc_start: 0.6605 (ttp) cc_final: 0.6365 (ttp) REVERT: C 505 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7511 (ptp-170) REVERT: C 570 TYR cc_start: 0.7242 (OUTLIER) cc_final: 0.6993 (m-80) REVERT: C 577 ASP cc_start: 0.8049 (m-30) cc_final: 0.7822 (m-30) REVERT: C 584 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8016 (ttt180) REVERT: C 653 VAL cc_start: 0.8706 (OUTLIER) cc_final: 0.8388 (t) REVERT: C 673 ARG cc_start: 0.8505 (ptm160) cc_final: 0.7489 (ptm-80) REVERT: C 756 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7924 (mt-10) REVERT: C 767 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.6287 (pm20) REVERT: C 784 LEU cc_start: 0.5553 (tt) cc_final: 0.5271 (tt) REVERT: C 952 VAL cc_start: 0.7848 (m) cc_final: 0.7573 (t) REVERT: C 1028 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8463 (ttm) REVERT: C 1030 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8371 (mm) REVERT: C 1062 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7863 (pt0) REVERT: C 1119 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7617 (tm-30) REVERT: D 16 THR cc_start: 0.7564 (OUTLIER) cc_final: 0.7278 (p) REVERT: D 19 ASP cc_start: 0.8086 (m-30) cc_final: 0.7871 (m-30) REVERT: D 92 MET cc_start: 0.8651 (mtp) cc_final: 0.7967 (mtm) REVERT: D 124 ASP cc_start: 0.7261 (m-30) cc_final: 0.6982 (m-30) REVERT: D 266 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7236 (mt-10) REVERT: D 350 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7323 (tpp-160) REVERT: D 376 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7185 (mt-10) REVERT: D 410 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8055 (mm-40) REVERT: D 623 ASP cc_start: 0.7402 (m-30) cc_final: 0.7000 (m-30) REVERT: D 688 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7580 (mmp) REVERT: D 791 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7060 (pt0) REVERT: D 865 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7047 (mm) REVERT: D 900 GLU cc_start: 0.7219 (tp30) cc_final: 0.6587 (mm-30) REVERT: D 959 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7275 (pt0) REVERT: D 987 LYS cc_start: 0.8131 (mttp) cc_final: 0.7549 (mttt) REVERT: D 1117 ASP cc_start: 0.7566 (p0) cc_final: 0.6890 (t0) REVERT: D 1129 GLU cc_start: 0.8111 (mp0) cc_final: 0.7787 (mm-30) REVERT: E 62 ARG cc_start: 0.8137 (mtt180) cc_final: 0.7548 (mmt-90) REVERT: E 92 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7093 (tt) outliers start: 137 outliers final: 68 residues processed: 378 average time/residue: 0.5790 time to fit residues: 253.3829 Evaluate side-chains 348 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 254 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 756 GLU Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 767 GLU Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1028 MET Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1062 GLN Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1106 ILE Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 350 ARG Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 688 MET Chi-restraints excluded: chain D residue 805 SER Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 913 ASP Chi-restraints excluded: chain D residue 959 GLN Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 105 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 100 optimal weight: 3.9990 chunk 280 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 252 optimal weight: 6.9990 chunk 171 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 182 optimal weight: 0.0770 chunk 235 optimal weight: 3.9990 chunk 259 optimal weight: 10.0000 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 443 ASN D 748 HIS D 759 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.196650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.148787 restraints weight = 25827.714| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.64 r_work: 0.3375 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 24499 Z= 0.233 Angle : 0.680 12.548 33487 Z= 0.352 Chirality : 0.047 0.176 3825 Planarity : 0.006 0.064 4169 Dihedral : 14.366 167.033 3979 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.98 % Favored : 93.74 % Rotamer: Outliers : 6.19 % Allowed : 17.47 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.15), residues: 2893 helix: 0.85 (0.16), residues: 1021 sheet: -0.53 (0.26), residues: 374 loop : -1.55 (0.15), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 584 TYR 0.017 0.002 TYR A 168 PHE 0.030 0.002 PHE C 214 TRP 0.016 0.002 TRP C 938 HIS 0.008 0.001 HIS D 689 Details of bonding type rmsd covalent geometry : bond 0.00577 (24491) covalent geometry : angle 0.66961 (33475) hydrogen bonds : bond 0.06052 ( 1007) hydrogen bonds : angle 4.87454 ( 2743) metal coordination : bond 0.01103 ( 8) metal coordination : angle 6.32174 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 272 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4837 (tpp) cc_final: 0.3213 (tmt) REVERT: A 99 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.7016 (tttt) REVERT: A 193 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8151 (mt) REVERT: A 200 ASN cc_start: 0.8850 (OUTLIER) cc_final: 0.8564 (t0) REVERT: A 202 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.7921 (tp) REVERT: A 217 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: A 221 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.6733 (mt) REVERT: A 223 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.6306 (ttm-80) REVERT: B 6 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7151 (tmt170) REVERT: B 24 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6499 (mt-10) REVERT: B 75 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: B 123 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7531 (ttt) REVERT: B 150 VAL cc_start: 0.8225 (OUTLIER) cc_final: 0.7688 (t) REVERT: C 111 ARG cc_start: 0.7734 (mtm-85) cc_final: 0.7528 (mtm180) REVERT: C 127 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7785 (ptp) REVERT: C 163 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.6984 (mmpt) REVERT: C 215 ASP cc_start: 0.7410 (m-30) cc_final: 0.7198 (m-30) REVERT: C 258 MET cc_start: 0.5444 (OUTLIER) cc_final: 0.5213 (tpt) REVERT: C 347 ARG cc_start: 0.6297 (mtt-85) cc_final: 0.5929 (tpt170) REVERT: C 421 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6520 (mmp-170) REVERT: C 505 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7631 (ptp-170) REVERT: C 570 TYR cc_start: 0.7325 (OUTLIER) cc_final: 0.7001 (m-80) REVERT: C 580 ASP cc_start: 0.8683 (m-30) cc_final: 0.8295 (m-30) REVERT: C 584 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8108 (ttt180) REVERT: C 673 ARG cc_start: 0.8533 (ptm160) cc_final: 0.7466 (ptm-80) REVERT: C 756 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8093 (mt-10) REVERT: C 767 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6140 (pm20) REVERT: C 784 LEU cc_start: 0.5719 (OUTLIER) cc_final: 0.5483 (tt) REVERT: C 877 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8399 (mtm-85) REVERT: C 1028 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8359 (ttm) REVERT: C 1030 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8421 (mm) REVERT: C 1062 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8052 (pt0) REVERT: C 1119 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7658 (tm-30) REVERT: D 16 THR cc_start: 0.7591 (OUTLIER) cc_final: 0.7322 (p) REVERT: D 19 ASP cc_start: 0.8197 (m-30) cc_final: 0.7971 (m-30) REVERT: D 30 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7126 (tppp) REVERT: D 92 MET cc_start: 0.8702 (mtp) cc_final: 0.8079 (mtm) REVERT: D 124 ASP cc_start: 0.7434 (m-30) cc_final: 0.7205 (m-30) REVERT: D 127 LYS cc_start: 0.7373 (mttt) cc_final: 0.7139 (mttm) REVERT: D 266 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7219 (mt-10) REVERT: D 376 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7232 (mt-10) REVERT: D 410 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7759 (mm-40) REVERT: D 420 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8807 (mttm) REVERT: D 791 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7185 (pt0) REVERT: D 865 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7161 (mm) REVERT: D 900 GLU cc_start: 0.7354 (tp30) cc_final: 0.6615 (mm-30) REVERT: D 959 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7313 (pt0) REVERT: D 987 LYS cc_start: 0.8210 (mttp) cc_final: 0.7672 (mttt) REVERT: D 1117 ASP cc_start: 0.7644 (p0) cc_final: 0.7242 (p0) REVERT: D 1120 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7542 (mt-10) REVERT: E 62 ARG cc_start: 0.8137 (mtt180) cc_final: 0.7546 (mmt-90) REVERT: E 92 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7244 (tt) outliers start: 151 outliers final: 80 residues processed: 383 average time/residue: 0.6196 time to fit residues: 272.2386 Evaluate side-chains 364 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 250 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 421 ARG Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 756 GLU Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 767 GLU Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 787 ARG Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1028 MET Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1062 GLN Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1106 ILE Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 420 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 805 SER Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 913 ASP Chi-restraints excluded: chain D residue 959 GLN Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1262 THR Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 92 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 234 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 151 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 253 optimal weight: 0.7980 chunk 230 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 159 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 243 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 748 HIS D 759 GLN D1246 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.198587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.151352 restraints weight = 25822.066| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.74 r_work: 0.3400 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24499 Z= 0.155 Angle : 0.607 11.994 33487 Z= 0.314 Chirality : 0.043 0.176 3825 Planarity : 0.005 0.063 4169 Dihedral : 14.263 166.682 3979 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.36 % Favored : 94.37 % Rotamer: Outliers : 5.99 % Allowed : 18.25 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.15), residues: 2893 helix: 0.97 (0.17), residues: 1033 sheet: -0.53 (0.26), residues: 393 loop : -1.50 (0.15), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 584 TYR 0.014 0.002 TYR A 168 PHE 0.016 0.002 PHE C 906 TRP 0.014 0.001 TRP D 778 HIS 0.006 0.001 HIS D 748 Details of bonding type rmsd covalent geometry : bond 0.00367 (24491) covalent geometry : angle 0.59666 (33475) hydrogen bonds : bond 0.05009 ( 1007) hydrogen bonds : angle 4.71914 ( 2743) metal coordination : bond 0.00982 ( 8) metal coordination : angle 5.84900 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 265 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4928 (tpp) cc_final: 0.3270 (tmt) REVERT: A 99 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6986 (tttt) REVERT: A 193 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.7962 (mp) REVERT: A 221 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.6691 (mt) REVERT: B 6 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6977 (tmt170) REVERT: B 24 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6484 (mt-10) REVERT: B 75 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.7014 (mp0) REVERT: B 123 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7452 (ttt) REVERT: B 139 VAL cc_start: 0.7798 (OUTLIER) cc_final: 0.7452 (t) REVERT: B 150 VAL cc_start: 0.8162 (OUTLIER) cc_final: 0.7617 (t) REVERT: C 111 ARG cc_start: 0.7709 (mtm-85) cc_final: 0.7494 (mtm180) REVERT: C 127 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7789 (ptp) REVERT: C 163 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7027 (mmpt) REVERT: C 188 ASP cc_start: 0.8303 (p0) cc_final: 0.7979 (p0) REVERT: C 215 ASP cc_start: 0.7329 (m-30) cc_final: 0.7113 (m-30) REVERT: C 347 ARG cc_start: 0.6283 (mtt-85) cc_final: 0.5910 (tpt170) REVERT: C 421 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6491 (mmp-170) REVERT: C 505 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7539 (ptp-170) REVERT: C 570 TYR cc_start: 0.7243 (OUTLIER) cc_final: 0.6984 (m-80) REVERT: C 580 ASP cc_start: 0.8565 (m-30) cc_final: 0.8210 (m-30) REVERT: C 584 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8063 (ttt180) REVERT: C 673 ARG cc_start: 0.8514 (ptm160) cc_final: 0.7432 (ptm-80) REVERT: C 756 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8056 (mt-10) REVERT: C 767 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6089 (pm20) REVERT: C 784 LEU cc_start: 0.5617 (OUTLIER) cc_final: 0.5385 (tt) REVERT: C 877 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8372 (mtm-85) REVERT: C 1028 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8408 (ttm) REVERT: C 1030 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8336 (mm) REVERT: C 1062 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7989 (pt0) REVERT: C 1119 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7686 (tm-30) REVERT: D 16 THR cc_start: 0.7537 (OUTLIER) cc_final: 0.7264 (p) REVERT: D 19 ASP cc_start: 0.8169 (m-30) cc_final: 0.7968 (m-30) REVERT: D 92 MET cc_start: 0.8699 (mtp) cc_final: 0.8096 (mtm) REVERT: D 117 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7889 (tp) REVERT: D 124 ASP cc_start: 0.7411 (m-30) cc_final: 0.7185 (m-30) REVERT: D 127 LYS cc_start: 0.7392 (mttt) cc_final: 0.7108 (mttm) REVERT: D 266 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7285 (mt-10) REVERT: D 323 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7793 (tt0) REVERT: D 376 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7270 (mt-10) REVERT: D 386 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8382 (tpp-160) REVERT: D 410 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7758 (mm-40) REVERT: D 496 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8065 (p) REVERT: D 649 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7337 (tt0) REVERT: D 791 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7107 (pt0) REVERT: D 865 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7073 (mm) REVERT: D 900 GLU cc_start: 0.7369 (tp30) cc_final: 0.6608 (mm-30) REVERT: D 917 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7897 (mp0) REVERT: D 959 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7343 (pt0) REVERT: D 987 LYS cc_start: 0.8174 (mttp) cc_final: 0.7604 (mttt) REVERT: D 1117 ASP cc_start: 0.7582 (p0) cc_final: 0.7166 (p0) REVERT: D 1120 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7616 (mt-10) REVERT: D 1129 GLU cc_start: 0.8085 (mp0) cc_final: 0.7680 (mm-30) REVERT: E 62 ARG cc_start: 0.8085 (mtt180) cc_final: 0.7525 (mmt-90) REVERT: E 92 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7087 (tt) outliers start: 146 outliers final: 77 residues processed: 371 average time/residue: 0.5973 time to fit residues: 254.5679 Evaluate side-chains 372 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 262 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 421 ARG Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 756 GLU Chi-restraints excluded: chain C residue 767 GLU Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 787 ARG Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1028 MET Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1062 GLN Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1106 ILE Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain D residue 350 ARG Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 805 SER Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 913 ASP Chi-restraints excluded: chain D residue 917 GLU Chi-restraints excluded: chain D residue 959 GLN Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 105 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 168 optimal weight: 20.0000 chunk 264 optimal weight: 0.7980 chunk 270 optimal weight: 0.6980 chunk 293 optimal weight: 6.9990 chunk 94 optimal weight: 0.3980 chunk 259 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 188 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1062 GLN D 759 GLN D1139 GLN D1145 GLN D1246 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.201622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.153603 restraints weight = 25795.002| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.89 r_work: 0.3444 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 24499 Z= 0.111 Angle : 0.546 10.555 33487 Z= 0.284 Chirality : 0.041 0.165 3825 Planarity : 0.005 0.061 4169 Dihedral : 14.068 165.147 3977 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.70 % Favored : 95.02 % Rotamer: Outliers : 4.55 % Allowed : 19.89 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.16), residues: 2893 helix: 1.32 (0.17), residues: 1030 sheet: -0.52 (0.27), residues: 381 loop : -1.33 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 182 TYR 0.017 0.001 TYR C 344 PHE 0.015 0.001 PHE C 214 TRP 0.014 0.001 TRP D 778 HIS 0.005 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00241 (24491) covalent geometry : angle 0.53655 (33475) hydrogen bonds : bond 0.03965 ( 1007) hydrogen bonds : angle 4.51473 ( 2743) metal coordination : bond 0.00888 ( 8) metal coordination : angle 5.26163 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 284 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4936 (tpp) cc_final: 0.3259 (tmt) REVERT: A 177 LYS cc_start: 0.8195 (ptpp) cc_final: 0.7702 (ptmm) REVERT: A 221 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.6642 (mt) REVERT: B 1 MET cc_start: 0.6377 (OUTLIER) cc_final: 0.4327 (mtt) REVERT: B 24 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6470 (mt-10) REVERT: B 72 ASP cc_start: 0.7506 (m-30) cc_final: 0.6939 (m-30) REVERT: B 123 MET cc_start: 0.7598 (ttt) cc_final: 0.7311 (ttt) REVERT: B 137 GLU cc_start: 0.6250 (mt-10) cc_final: 0.5874 (tt0) REVERT: B 139 VAL cc_start: 0.7647 (OUTLIER) cc_final: 0.7439 (t) REVERT: B 150 VAL cc_start: 0.8110 (OUTLIER) cc_final: 0.7597 (t) REVERT: C 69 ARG cc_start: 0.7720 (ttp-170) cc_final: 0.7518 (ttp80) REVERT: C 111 ARG cc_start: 0.7653 (mtm-85) cc_final: 0.7430 (mtm180) REVERT: C 127 MET cc_start: 0.7995 (ptp) cc_final: 0.7702 (ptp) REVERT: C 163 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7007 (mmpt) REVERT: C 347 ARG cc_start: 0.6276 (mtt-85) cc_final: 0.5864 (tpt170) REVERT: C 505 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7394 (ptp-170) REVERT: C 584 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7963 (ttt180) REVERT: C 653 VAL cc_start: 0.8700 (OUTLIER) cc_final: 0.8387 (t) REVERT: C 673 ARG cc_start: 0.8462 (ptm160) cc_final: 0.7373 (ptm-80) REVERT: C 767 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6193 (pm20) REVERT: C 784 LEU cc_start: 0.5400 (OUTLIER) cc_final: 0.5154 (tt) REVERT: C 877 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8341 (mtm-85) REVERT: C 925 ARG cc_start: 0.8453 (mtt-85) cc_final: 0.8226 (mtt-85) REVERT: C 952 VAL cc_start: 0.7700 (m) cc_final: 0.7404 (t) REVERT: C 1030 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8376 (mm) REVERT: C 1062 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7958 (pt0) REVERT: D 16 THR cc_start: 0.7447 (OUTLIER) cc_final: 0.7159 (p) REVERT: D 92 MET cc_start: 0.8610 (mtp) cc_final: 0.8017 (mtm) REVERT: D 127 LYS cc_start: 0.7335 (mttt) cc_final: 0.7032 (mttm) REVERT: D 134 TYR cc_start: 0.7910 (m-80) cc_final: 0.7519 (m-80) REVERT: D 266 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7258 (mt-10) REVERT: D 350 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.7183 (tpp-160) REVERT: D 376 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7029 (mt-10) REVERT: D 386 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8333 (tpp-160) REVERT: D 410 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8094 (mm-40) REVERT: D 496 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8083 (p) REVERT: D 688 MET cc_start: 0.8000 (mmt) cc_final: 0.7451 (mmp) REVERT: D 791 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7052 (pt0) REVERT: D 917 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7853 (mp0) REVERT: D 987 LYS cc_start: 0.8164 (mttp) cc_final: 0.7624 (mttt) REVERT: D 1117 ASP cc_start: 0.7541 (p0) cc_final: 0.7053 (p0) REVERT: D 1120 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7767 (mt-10) REVERT: D 1129 GLU cc_start: 0.8039 (mp0) cc_final: 0.7639 (mm-30) REVERT: E 62 ARG cc_start: 0.8043 (mtt180) cc_final: 0.7502 (mmt-90) REVERT: E 92 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.6968 (tt) outliers start: 111 outliers final: 49 residues processed: 366 average time/residue: 0.6122 time to fit residues: 256.8279 Evaluate side-chains 326 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 256 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 767 GLU Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1062 GLN Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 350 ARG Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 805 SER Chi-restraints excluded: chain D residue 826 ASN Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 917 GLU Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1246 ASN Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 92 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 214 optimal weight: 0.0070 chunk 148 optimal weight: 1.9990 chunk 203 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 263 optimal weight: 0.0980 chunk 266 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 238 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 overall best weight: 0.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 748 HIS D 759 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.201321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.153670 restraints weight = 25725.043| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.71 r_work: 0.3449 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24499 Z= 0.121 Angle : 0.561 9.909 33487 Z= 0.291 Chirality : 0.042 0.163 3825 Planarity : 0.005 0.062 4169 Dihedral : 14.007 157.507 3972 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.74 % Favored : 94.99 % Rotamer: Outliers : 3.98 % Allowed : 20.51 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.16), residues: 2893 helix: 1.38 (0.17), residues: 1031 sheet: -0.40 (0.27), residues: 371 loop : -1.29 (0.15), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 834 TYR 0.015 0.001 TYR D 61 PHE 0.014 0.001 PHE A 219 TRP 0.015 0.001 TRP D 778 HIS 0.006 0.001 HIS D 748 Details of bonding type rmsd covalent geometry : bond 0.00274 (24491) covalent geometry : angle 0.55296 (33475) hydrogen bonds : bond 0.04124 ( 1007) hydrogen bonds : angle 4.47525 ( 2743) metal coordination : bond 0.00854 ( 8) metal coordination : angle 5.02921 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 263 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5007 (tpp) cc_final: 0.3370 (tmt) REVERT: A 177 LYS cc_start: 0.8206 (ptpp) cc_final: 0.7757 (ptmm) REVERT: A 221 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.6709 (mt) REVERT: B 1 MET cc_start: 0.6476 (OUTLIER) cc_final: 0.4397 (mtt) REVERT: B 24 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6445 (mt-10) REVERT: B 139 VAL cc_start: 0.7696 (OUTLIER) cc_final: 0.7495 (t) REVERT: B 150 VAL cc_start: 0.8196 (OUTLIER) cc_final: 0.7658 (t) REVERT: C 111 ARG cc_start: 0.7721 (mtm-85) cc_final: 0.7495 (mtm180) REVERT: C 127 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7725 (ptp) REVERT: C 163 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7117 (mmpt) REVERT: C 225 ARG cc_start: 0.6909 (ttt180) cc_final: 0.6613 (ttt-90) REVERT: C 347 ARG cc_start: 0.6305 (mtt-85) cc_final: 0.5886 (tpt170) REVERT: C 505 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7438 (ptp-170) REVERT: C 580 ASP cc_start: 0.8517 (m-30) cc_final: 0.8127 (m-30) REVERT: C 584 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7943 (ttt180) REVERT: C 653 VAL cc_start: 0.8713 (OUTLIER) cc_final: 0.8390 (t) REVERT: C 673 ARG cc_start: 0.8514 (ptm160) cc_final: 0.7455 (ptm-80) REVERT: C 767 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6383 (pm20) REVERT: C 784 LEU cc_start: 0.5553 (OUTLIER) cc_final: 0.5299 (tt) REVERT: C 877 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8335 (mtm-85) REVERT: C 952 VAL cc_start: 0.7733 (m) cc_final: 0.7430 (t) REVERT: C 1030 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8353 (mm) REVERT: D 16 THR cc_start: 0.7518 (OUTLIER) cc_final: 0.7236 (p) REVERT: D 19 ASP cc_start: 0.8081 (m-30) cc_final: 0.7880 (m-30) REVERT: D 92 MET cc_start: 0.8593 (mtp) cc_final: 0.7937 (mtm) REVERT: D 134 TYR cc_start: 0.7843 (m-80) cc_final: 0.7536 (m-80) REVERT: D 320 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7730 (tt) REVERT: D 350 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7204 (tpp-160) REVERT: D 376 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7164 (mt-10) REVERT: D 386 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8369 (tpp-160) REVERT: D 410 GLN cc_start: 0.8453 (mp10) cc_final: 0.8171 (mm-40) REVERT: D 420 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8829 (mttm) REVERT: D 496 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8094 (p) REVERT: D 688 MET cc_start: 0.7985 (mmt) cc_final: 0.7417 (mmp) REVERT: D 696 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8122 (mt) REVERT: D 791 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7129 (pt0) REVERT: D 917 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7878 (mp0) REVERT: D 987 LYS cc_start: 0.8219 (mttp) cc_final: 0.7708 (mttt) REVERT: D 1117 ASP cc_start: 0.7586 (p0) cc_final: 0.7078 (p0) REVERT: D 1120 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7822 (mt-10) REVERT: D 1129 GLU cc_start: 0.8123 (mp0) cc_final: 0.7742 (mm-30) REVERT: E 62 ARG cc_start: 0.8109 (mtt180) cc_final: 0.7569 (mmt-90) REVERT: E 92 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.6983 (tt) outliers start: 97 outliers final: 53 residues processed: 336 average time/residue: 0.6205 time to fit residues: 238.8011 Evaluate side-chains 327 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 251 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 767 GLU Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 350 ARG Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 420 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 714 ASP Chi-restraints excluded: chain D residue 805 SER Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 913 ASP Chi-restraints excluded: chain D residue 917 GLU Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 92 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 26 optimal weight: 7.9990 chunk 180 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 34 optimal weight: 0.0070 chunk 145 optimal weight: 2.9990 chunk 229 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 278 optimal weight: 0.7980 chunk 220 optimal weight: 0.8980 chunk 234 optimal weight: 1.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 748 HIS D 759 GLN D1246 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.201151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.153076 restraints weight = 25875.077| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.74 r_work: 0.3441 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24499 Z= 0.124 Angle : 0.560 10.489 33487 Z= 0.290 Chirality : 0.042 0.159 3825 Planarity : 0.005 0.062 4169 Dihedral : 13.989 156.889 3972 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.53 % Favored : 95.20 % Rotamer: Outliers : 4.10 % Allowed : 20.75 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.16), residues: 2893 helix: 1.37 (0.17), residues: 1034 sheet: -0.31 (0.27), residues: 367 loop : -1.27 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 584 TYR 0.016 0.001 TYR C 344 PHE 0.012 0.001 PHE C 906 TRP 0.016 0.001 TRP D 778 HIS 0.006 0.001 HIS D 748 Details of bonding type rmsd covalent geometry : bond 0.00283 (24491) covalent geometry : angle 0.55219 (33475) hydrogen bonds : bond 0.04204 ( 1007) hydrogen bonds : angle 4.43375 ( 2743) metal coordination : bond 0.00838 ( 8) metal coordination : angle 4.83212 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 252 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4995 (tpp) cc_final: 0.3395 (tmt) REVERT: A 177 LYS cc_start: 0.8205 (ptpp) cc_final: 0.7729 (ptmm) REVERT: A 221 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.6621 (mt) REVERT: B 1 MET cc_start: 0.6336 (OUTLIER) cc_final: 0.4306 (mtt) REVERT: B 24 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6444 (mt-10) REVERT: B 123 MET cc_start: 0.8256 (ttp) cc_final: 0.7849 (ttt) REVERT: B 150 VAL cc_start: 0.8126 (OUTLIER) cc_final: 0.7588 (t) REVERT: B 185 GLN cc_start: 0.6941 (OUTLIER) cc_final: 0.5977 (mp-120) REVERT: C 127 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7696 (ptp) REVERT: C 138 GLU cc_start: 0.7035 (pt0) cc_final: 0.6369 (pp20) REVERT: C 154 MET cc_start: 0.7101 (tpt) cc_final: 0.6890 (tpt) REVERT: C 163 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7057 (mmpt) REVERT: C 225 ARG cc_start: 0.6865 (ttt180) cc_final: 0.6580 (ttt-90) REVERT: C 347 ARG cc_start: 0.6376 (mtt-85) cc_final: 0.5872 (tpt170) REVERT: C 350 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6169 (tt0) REVERT: C 505 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7446 (ptp-170) REVERT: C 584 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7896 (ttt180) REVERT: C 653 VAL cc_start: 0.8705 (OUTLIER) cc_final: 0.8385 (t) REVERT: C 673 ARG cc_start: 0.8498 (ptm160) cc_final: 0.7422 (ptm-80) REVERT: C 756 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.8045 (mt-10) REVERT: C 767 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6358 (pm20) REVERT: C 784 LEU cc_start: 0.5530 (OUTLIER) cc_final: 0.5295 (tt) REVERT: C 877 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8359 (mtm-85) REVERT: C 952 VAL cc_start: 0.7709 (m) cc_final: 0.7420 (t) REVERT: C 1030 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8320 (mm) REVERT: D 16 THR cc_start: 0.7458 (OUTLIER) cc_final: 0.7163 (p) REVERT: D 19 ASP cc_start: 0.8049 (m-30) cc_final: 0.7833 (m-30) REVERT: D 92 MET cc_start: 0.8582 (mtp) cc_final: 0.7933 (mtm) REVERT: D 134 TYR cc_start: 0.7792 (m-80) cc_final: 0.7498 (m-80) REVERT: D 320 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7600 (tt) REVERT: D 350 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.7115 (tpp-160) REVERT: D 376 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7094 (mt-10) REVERT: D 386 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8297 (tpp-160) REVERT: D 410 GLN cc_start: 0.8417 (mp10) cc_final: 0.8123 (mm-40) REVERT: D 420 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8813 (mttm) REVERT: D 496 VAL cc_start: 0.8582 (OUTLIER) cc_final: 0.8153 (p) REVERT: D 688 MET cc_start: 0.8003 (mmt) cc_final: 0.7481 (mmp) REVERT: D 696 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8100 (mt) REVERT: D 791 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7066 (pt0) REVERT: D 917 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7860 (mp0) REVERT: D 987 LYS cc_start: 0.8183 (mttp) cc_final: 0.7701 (mttt) REVERT: D 1117 ASP cc_start: 0.7548 (p0) cc_final: 0.7047 (p0) REVERT: D 1120 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7740 (mt-10) REVERT: D 1129 GLU cc_start: 0.8069 (mp0) cc_final: 0.7645 (mm-30) REVERT: E 62 ARG cc_start: 0.8034 (mtt180) cc_final: 0.7476 (mmt-90) REVERT: E 92 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6745 (tt) outliers start: 100 outliers final: 62 residues processed: 329 average time/residue: 0.6002 time to fit residues: 227.4387 Evaluate side-chains 340 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 253 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 756 GLU Chi-restraints excluded: chain C residue 767 GLU Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 350 ARG Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 420 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 714 ASP Chi-restraints excluded: chain D residue 805 SER Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 913 ASP Chi-restraints excluded: chain D residue 917 GLU Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1166 THR Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 92 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 275 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 253 optimal weight: 0.0050 chunk 89 optimal weight: 0.8980 chunk 200 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 230 optimal weight: 0.9980 chunk 266 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 748 HIS D 759 GLN D1246 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.201027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.154141 restraints weight = 25980.362| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.64 r_work: 0.3437 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24499 Z= 0.125 Angle : 0.559 9.045 33487 Z= 0.290 Chirality : 0.042 0.148 3825 Planarity : 0.005 0.061 4169 Dihedral : 13.966 157.181 3971 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.56 % Favored : 95.16 % Rotamer: Outliers : 3.94 % Allowed : 21.21 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.16), residues: 2893 helix: 1.41 (0.17), residues: 1035 sheet: -0.31 (0.27), residues: 362 loop : -1.24 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 584 TYR 0.013 0.001 TYR D 61 PHE 0.013 0.001 PHE C 906 TRP 0.018 0.001 TRP D 778 HIS 0.006 0.001 HIS D 748 Details of bonding type rmsd covalent geometry : bond 0.00288 (24491) covalent geometry : angle 0.55214 (33475) hydrogen bonds : bond 0.04212 ( 1007) hydrogen bonds : angle 4.41227 ( 2743) metal coordination : bond 0.00821 ( 8) metal coordination : angle 4.67384 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 261 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4927 (tpp) cc_final: 0.3552 (tmt) REVERT: A 99 LYS cc_start: 0.6828 (tttt) cc_final: 0.6079 (ttmt) REVERT: A 177 LYS cc_start: 0.8084 (ptpp) cc_final: 0.7649 (ptmm) REVERT: A 221 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.6684 (mt) REVERT: B 1 MET cc_start: 0.6172 (OUTLIER) cc_final: 0.4316 (mtt) REVERT: B 77 ILE cc_start: 0.8155 (mm) cc_final: 0.7934 (mt) REVERT: B 123 MET cc_start: 0.8212 (ttp) cc_final: 0.7727 (ttt) REVERT: B 150 VAL cc_start: 0.8075 (OUTLIER) cc_final: 0.7561 (t) REVERT: B 185 GLN cc_start: 0.6847 (OUTLIER) cc_final: 0.6092 (mp-120) REVERT: C 111 ARG cc_start: 0.7630 (mtm-85) cc_final: 0.7404 (mtm180) REVERT: C 127 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7625 (ptp) REVERT: C 138 GLU cc_start: 0.7011 (pt0) cc_final: 0.6365 (pp20) REVERT: C 163 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7027 (mmtt) REVERT: C 225 ARG cc_start: 0.6721 (ttt180) cc_final: 0.6407 (ttt-90) REVERT: C 347 ARG cc_start: 0.6290 (mtt-85) cc_final: 0.5814 (tpt170) REVERT: C 350 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6225 (tt0) REVERT: C 505 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7333 (ptp-170) REVERT: C 584 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7778 (ttt180) REVERT: C 653 VAL cc_start: 0.8663 (OUTLIER) cc_final: 0.8351 (t) REVERT: C 673 ARG cc_start: 0.8411 (ptm160) cc_final: 0.7375 (ptm-80) REVERT: C 756 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7936 (mt-10) REVERT: C 767 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6334 (pm20) REVERT: C 784 LEU cc_start: 0.5552 (OUTLIER) cc_final: 0.5339 (tt) REVERT: C 866 ASN cc_start: 0.5324 (p0) cc_final: 0.5119 (m110) REVERT: C 877 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8239 (mtm-85) REVERT: C 952 VAL cc_start: 0.7764 (m) cc_final: 0.7453 (t) REVERT: C 1030 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8280 (mm) REVERT: D 16 THR cc_start: 0.7347 (OUTLIER) cc_final: 0.7099 (p) REVERT: D 92 MET cc_start: 0.8456 (mtp) cc_final: 0.7875 (mtm) REVERT: D 134 TYR cc_start: 0.7679 (m-80) cc_final: 0.7456 (m-80) REVERT: D 320 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7534 (tt) REVERT: D 350 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.7028 (tpp-160) REVERT: D 376 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6977 (mt-10) REVERT: D 386 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8254 (tpp-160) REVERT: D 410 GLN cc_start: 0.8339 (mp10) cc_final: 0.8061 (mm-40) REVERT: D 420 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8851 (mttp) REVERT: D 496 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8110 (p) REVERT: D 688 MET cc_start: 0.7863 (mmt) cc_final: 0.7321 (mmp) REVERT: D 696 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.8053 (mt) REVERT: D 791 GLU cc_start: 0.7361 (tm-30) cc_final: 0.7018 (pt0) REVERT: D 917 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: D 987 LYS cc_start: 0.8117 (mttp) cc_final: 0.7656 (mttt) REVERT: D 1117 ASP cc_start: 0.7487 (p0) cc_final: 0.7148 (p0) REVERT: D 1129 GLU cc_start: 0.7897 (mp0) cc_final: 0.7523 (mm-30) REVERT: E 62 ARG cc_start: 0.7907 (mtt180) cc_final: 0.7318 (mmt-90) REVERT: E 66 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7367 (m-30) REVERT: E 92 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6619 (tt) outliers start: 96 outliers final: 59 residues processed: 333 average time/residue: 0.5883 time to fit residues: 225.6763 Evaluate side-chains 336 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 252 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 756 GLU Chi-restraints excluded: chain C residue 767 GLU Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 350 ARG Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 420 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 714 ASP Chi-restraints excluded: chain D residue 805 SER Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 913 ASP Chi-restraints excluded: chain D residue 917 GLU Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1166 THR Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 92 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 17 optimal weight: 2.9990 chunk 291 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 174 optimal weight: 8.9990 chunk 169 optimal weight: 20.0000 chunk 268 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 224 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 372 HIS D 233 GLN D 748 HIS D 759 GLN D1246 ASN E 70 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.197630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.149293 restraints weight = 25636.652| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.63 r_work: 0.3392 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 24499 Z= 0.212 Angle : 0.651 9.638 33487 Z= 0.337 Chirality : 0.046 0.195 3825 Planarity : 0.005 0.061 4169 Dihedral : 14.095 155.833 3968 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.50 % Favored : 94.26 % Rotamer: Outliers : 4.22 % Allowed : 21.37 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.16), residues: 2893 helix: 1.10 (0.17), residues: 1041 sheet: -0.43 (0.26), residues: 392 loop : -1.40 (0.15), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 584 TYR 0.016 0.002 TYR C1027 PHE 0.023 0.002 PHE C 906 TRP 0.013 0.002 TRP C 938 HIS 0.006 0.001 HIS D 689 Details of bonding type rmsd covalent geometry : bond 0.00521 (24491) covalent geometry : angle 0.64424 (33475) hydrogen bonds : bond 0.05573 ( 1007) hydrogen bonds : angle 4.58934 ( 2743) metal coordination : bond 0.00868 ( 8) metal coordination : angle 4.88618 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9312.85 seconds wall clock time: 158 minutes 35.33 seconds (9515.33 seconds total)