Starting phenix.real_space_refine on Sat Aug 8 10:39:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10mg_75285/08_2026/10mg_75285.cif Found real_map, /net/cci-nas-00/data/ceres_data/10mg_75285/08_2026/10mg_75285.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 { model { file = "/net/cci-nas-00/data/ceres_data/10mg_75285/08_2026/10mg_75285.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10mg_75285/08_2026/10mg_75285.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10mg_75285/08_2026/10mg_75285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10mg_75285/08_2026/10mg_75285.map" } 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= 0.001 sd= 0.011 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: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 P 62 5.49 5 Mg 1 5.21 5 S 106 5.16 5 Cl 2 4.86 5 C 16194 2.51 5 N 4615 2.21 5 O 5924 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26909 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 608 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 470 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain breaks: 1 Chain: "G" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1679 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1689 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10381 Classifications: {'peptide': 1316} Link IDs: {'PTRANS': 55, 'TRANS': 1260} Chain breaks: 1 Chain: "J" Number of atoms: 10403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10403 Classifications: {'peptide': 1337} Link IDs: {'PTRANS': 55, 'TRANS': 1281} Chain breaks: 2 Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 1, ' ZN': 2, '42T': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "K" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "R" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "H" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "I" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 369 Classifications: {'water': 369} Link IDs: {None: 368} Chain: "J" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 262 Classifications: {'water': 262} Link IDs: {None: 261} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16117 SG CYS J 70 17.877 93.821 69.265 1.00154.37 S ATOM 16131 SG CYS J 72 16.875 97.189 67.527 1.00148.52 S ATOM 16239 SG CYS J 85 16.164 94.646 65.722 1.00146.85 S ATOM 16263 SG CYS J 88 19.013 94.567 65.526 1.00141.30 S ATOM 21951 SG CYS J 814 56.948 37.506 63.506 1.00 60.53 S ATOM 22516 SG CYS J 888 57.749 41.305 63.959 1.00 42.01 S ATOM 22567 SG CYS J 895 57.028 39.116 67.071 1.00 49.67 S ATOM 22588 SG CYS J 898 59.523 39.225 66.004 1.00 45.34 S Time building chain proxies: 5.05, per 1000 atoms: 0.19 Number of scatterers: 26909 At special positions: 0 Unit cell: (140.608, 170.352, 163.592, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 Cl 2 17.00 S 106 16.00 P 62 15.00 Mg 1 11.99 F 3 9.00 O 5924 8.00 N 4615 7.00 C 16194 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 925.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " Number of angles added : 12 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5850 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 48 sheets defined 39.3% alpha, 18.2% beta 24 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 2.64 Creating SS restraints... Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 15 through 33 Processing helix chain 'K' and resid 45 through 57 Processing helix chain 'K' and resid 60 through 80 Processing helix chain 'G' and resid 34 through 48 removed outlier: 3.568A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN G 41 " --> pdb=" O HIS G 37 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.805A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 158 removed outlier: 3.667A pdb=" N ARG G 158 " --> pdb=" O ALA G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 229 Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.918A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.863A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 228 removed outlier: 3.568A pdb=" N GLN H 227 " --> pdb=" O ILE H 223 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.596A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.807A pdb=" N ALA I 51 " --> pdb=" O TYR I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.980A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 3.771A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 281 removed outlier: 3.634A pdb=" N GLN I 276 " --> pdb=" O ARG I 272 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS I 279 " --> pdb=" O ARG I 275 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP I 280 " --> pdb=" O GLN I 276 " (cutoff:3.500A) Processing helix chain 'I' and resid 288 through 295 removed outlier: 3.679A pdb=" N ALA I 293 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLY I 294 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 328 Processing helix chain 'I' and resid 345 through 354 removed outlier: 3.838A pdb=" N GLU I 349 " --> pdb=" O PRO I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 4.025A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 removed outlier: 3.555A pdb=" N ILE I 425 " --> pdb=" O SER I 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 481 removed outlier: 3.776A pdb=" N ARG I 473 " --> pdb=" O VAL I 469 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 493 removed outlier: 3.615A pdb=" N ILE I 493 " --> pdb=" O PRO I 489 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.577A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 612 removed outlier: 4.398A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 612' Processing helix chain 'I' and resid 663 through 668 removed outlier: 3.779A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 686 Processing helix chain 'I' and resid 687 through 689 No H-bonds generated for 'chain 'I' and resid 687 through 689' Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 738 through 741 removed outlier: 3.871A pdb=" N MET I 741 " --> pdb=" O GLU I 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 738 through 741' Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 859 through 863 Processing helix chain 'I' and resid 942 through 983 removed outlier: 4.461A pdb=" N ILE I 948 " --> pdb=" O ARG I 944 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLU I 949 " --> pdb=" O ALA I 945 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU I 963 " --> pdb=" O ASP I 959 " (cutoff:3.500A) Processing helix chain 'I' and resid 985 through 990 Processing helix chain 'I' and resid 993 through 1000 Processing helix chain 'I' and resid 1006 through 1038 Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.559A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1101 through 1106' Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 4.091A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.773A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1176 Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.565A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1282 Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 4.048A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS I1303 " --> pdb=" O ASN I1299 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.947A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.870A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG J 98 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG J 99 " --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 173 Processing helix chain 'J' and resid 181 through 191 removed outlier: 3.600A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 removed outlier: 3.668A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 285 Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 327 through 331 removed outlier: 3.604A pdb=" N MET J 330 " --> pdb=" O LEU J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 336 through 342 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 407 through 416 Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 removed outlier: 3.573A pdb=" N ASN J 489 " --> pdb=" O SER J 486 " (cutoff:3.500A) Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 581 through 583 No H-bonds generated for 'chain 'J' and resid 581 through 583' Processing helix chain 'J' and resid 588 through 592 Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.649A pdb=" N ALA J 633 " --> pdb=" O PHE J 629 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG J 634 " --> pdb=" O ALA J 630 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER J 635 " --> pdb=" O TYR J 631 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 4.199A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 removed outlier: 3.789A pdb=" N GLN J 739 " --> pdb=" O ALA J 735 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 804 Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.812A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 884 through 888 removed outlier: 3.567A pdb=" N SER J 887 " --> pdb=" O SER J 884 " (cutoff:3.500A) Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.643A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 930 removed outlier: 3.645A pdb=" N LEU J 930 " --> pdb=" O GLY J 927 " (cutoff:3.500A) Processing helix chain 'J' and resid 1037 through 1041 removed outlier: 3.939A pdb=" N ILE J1041 " --> pdb=" O THR J1038 " (cutoff:3.500A) Processing helix chain 'J' and resid 1068 through 1072 removed outlier: 3.515A pdb=" N LYS J1072 " --> pdb=" O ALA J1069 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.513A pdb=" N ARG J1231 " --> pdb=" O HIS J1227 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1260 removed outlier: 4.370A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 removed outlier: 3.813A pdb=" N ASN J1295 " --> pdb=" O GLU J1291 " (cutoff:3.500A) Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1324 Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 removed outlier: 3.619A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1359 through 1361 No H-bonds generated for 'chain 'J' and resid 1359 through 1361' Processing helix chain 'J' and resid 1362 through 1371 removed outlier: 3.606A pdb=" N HIS J1366 " --> pdb=" O GLY J1362 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 20 removed outlier: 6.722A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLN G 18 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N HIS G 23 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 115 through 116 removed outlier: 4.224A pdb=" N THR G 101 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.632A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'H' and resid 14 through 20 removed outlier: 6.585A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU H 201 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 97 through 105 removed outlier: 6.397A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 91 through 92 Processing sheet with id=AA9, first strand: chain 'H' and resid 108 through 111 removed outlier: 3.702A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.854A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 59 through 60 removed outlier: 4.001A pdb=" N ILE I 59 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU I 68 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'I' and resid 451 through 454 removed outlier: 3.528A pdb=" N SER I 147 " --> pdb=" O ARG I 529 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 160 removed outlier: 3.540A pdb=" N LEU I 171 " --> pdb=" O ASP I 160 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 284 through 286 removed outlier: 4.849A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 256 through 257 Processing sheet with id=AB9, first strand: chain 'I' and resid 301 through 302 removed outlier: 3.608A pdb=" N CYS I 311 " --> pdb=" O TYR I 301 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.839A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC3, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.667A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.224A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC6, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.347A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.983A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY I 926 " --> pdb=" O VAL I 877 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 849 through 850 Processing sheet with id=AD1, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.807A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD3, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.615A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1335 through 1340 Processing sheet with id=AD5, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.807A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.438A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 10.075A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 159 through 160 removed outlier: 3.587A pdb=" N LYS J 179 " --> pdb=" O VAL J 145 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE J 147 " --> pdb=" O ASP J 177 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 254 through 255 Processing sheet with id=AD8, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD9, first strand: chain 'J' and resid 706 through 709 Processing sheet with id=AE1, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE2, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE3, first strand: chain 'J' and resid 825 through 827 removed outlier: 6.640A pdb=" N GLU J 827 " --> pdb=" O VAL J 831 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N VAL J 831 " --> pdb=" O GLU J 827 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.849A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.139A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 991 through 997 removed outlier: 6.658A pdb=" N LEU J 984 " --> pdb=" O LYS J 992 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER J 994 " --> pdb=" O LEU J 982 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU J 982 " --> pdb=" O SER J 994 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LYS J 996 " --> pdb=" O THR J 980 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR J 980 " --> pdb=" O LYS J 996 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 1024 through 1028 removed outlier: 3.761A pdb=" N ALA J1122 " --> pdb=" O VAL J1027 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 1098 through 1100 Processing sheet with id=AE9, first strand: chain 'J' and resid 1059 through 1060 Processing sheet with id=AF1, first strand: chain 'J' and resid 1155 through 1156 removed outlier: 6.535A pdb=" N ILE J1155 " --> pdb=" O ILE J1210 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 1186 through 1191 removed outlier: 4.698A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE J1177 " --> pdb=" O TYR J1186 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 7.045A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1081 hydrogen bonds defined for protein. 3024 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 116 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 6.96 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7347 1.33 - 1.45: 4036 1.45 - 1.57: 14961 1.57 - 1.69: 121 1.69 - 1.81: 186 Bond restraints: 26651 Sorted by residual: bond pdb=" C3' DT B 24 " pdb=" C2' DT B 24 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DA A 25 " pdb=" C2' DA A 25 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C3' DA B 19 " pdb=" C2' DA B 19 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.32e+00 bond pdb=" N LEU J1275 " pdb=" CA LEU J1275 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.25e-02 6.40e+03 7.93e+00 bond pdb=" N PHE J1274 " pdb=" CA PHE J1274 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.32e+00 ... (remaining 26646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 35538 1.61 - 3.23: 626 3.23 - 4.84: 71 4.84 - 6.45: 25 6.45 - 8.07: 11 Bond angle restraints: 36271 Sorted by residual: angle pdb=" N MET J 932 " pdb=" CA MET J 932 " pdb=" C MET J 932 " ideal model delta sigma weight residual 114.04 108.18 5.86 1.24e+00 6.50e-01 2.23e+01 angle pdb=" N3 DT B 12 " pdb=" C4 DT B 12 " pdb=" O4 DT B 12 " ideal model delta sigma weight residual 119.90 122.69 -2.79 6.00e-01 2.78e+00 2.16e+01 angle pdb=" O4 DT B 12 " pdb=" C4 DT B 12 " pdb=" C5 DT B 12 " ideal model delta sigma weight residual 124.90 121.86 3.04 7.00e-01 2.04e+00 1.89e+01 angle pdb=" N3 DT B 10 " pdb=" C4 DT B 10 " pdb=" O4 DT B 10 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT A 26 " pdb=" C4 DT A 26 " pdb=" O4 DT A 26 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 ... (remaining 36266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.71: 15698 27.71 - 55.43: 533 55.43 - 83.14: 86 83.14 - 110.86: 5 110.86 - 138.57: 1 Dihedral angle restraints: 16323 sinusoidal: 7229 harmonic: 9094 Sorted by residual: dihedral pdb=" CD ARG G 166 " pdb=" NE ARG G 166 " pdb=" CZ ARG G 166 " pdb=" NH1 ARG G 166 " ideal model delta sinusoidal sigma weight residual 0.00 65.24 -65.24 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CD ARG H 158 " pdb=" NE ARG H 158 " pdb=" CZ ARG H 158 " pdb=" NH1 ARG H 158 " ideal model delta sinusoidal sigma weight residual 0.00 39.52 -39.52 1 1.00e+01 1.00e-02 2.19e+01 dihedral pdb=" C4' G R 10 " pdb=" C3' G R 10 " pdb=" O3' G R 10 " pdb=" P A R 11 " ideal model delta sinusoidal sigma weight residual 220.00 81.43 138.57 1 3.50e+01 8.16e-04 1.37e+01 ... (remaining 16320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 4109 0.128 - 0.256: 32 0.256 - 0.384: 0 0.384 - 0.512: 0 0.512 - 0.640: 11 Chirality restraints: 4152 Sorted by residual: chirality pdb=" P DT A 15 " pdb=" OP1 DT A 15 " pdb=" OP2 DT A 15 " pdb=" O5' DT A 15 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" P DC B 25 " pdb=" OP1 DC B 25 " pdb=" OP2 DC B 25 " pdb=" O5' DC B 25 " both_signs ideal model delta sigma weight residual True 2.34 -2.94 -0.60 2.00e-01 2.50e+01 9.01e+00 chirality pdb=" P DT A 7 " pdb=" OP1 DT A 7 " pdb=" OP2 DT A 7 " pdb=" O5' DT A 7 " both_signs ideal model delta sigma weight residual True 2.34 -2.93 -0.60 2.00e-01 2.50e+01 8.91e+00 ... (remaining 4149 not shown) Planarity restraints: 4523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 166 " 1.001 9.50e-02 1.11e+02 4.48e-01 1.22e+02 pdb=" NE ARG G 166 " -0.060 2.00e-02 2.50e+03 pdb=" CZ ARG G 166 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG G 166 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG G 166 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 158 " 0.705 9.50e-02 1.11e+02 3.16e-01 6.09e+01 pdb=" NE ARG H 158 " -0.041 2.00e-02 2.50e+03 pdb=" CZ ARG H 158 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG H 158 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG H 158 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 158 " -0.424 9.50e-02 1.11e+02 1.90e-01 2.21e+01 pdb=" NE ARG G 158 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG G 158 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG G 158 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG G 158 " -0.015 2.00e-02 2.50e+03 ... (remaining 4520 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 166 2.67 - 3.22: 23875 3.22 - 3.78: 39289 3.78 - 4.34: 55754 4.34 - 4.90: 91789 Nonbonded interactions: 210873 Sorted by model distance: nonbonded pdb=" O3' U R 19 " pdb="MG MG J1501 " model vdw 2.106 2.170 nonbonded pdb=" O4 DT B 13 " pdb=" O6 DG A 19 " model vdw 2.211 2.432 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.237 2.170 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1501 " model vdw 2.245 2.170 nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1501 " model vdw 2.262 2.170 ... (remaining 210868 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 'G' and (resid 8 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 158 or resid 170 through 231)) selection = (chain 'H' and (resid 8 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 231)) } 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: 4.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 29.020 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 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 : 0.003 0.080 26659 Z= 0.210 Angle : 0.644 36.591 36283 Z= 0.348 Chirality : 0.052 0.640 4152 Planarity : 0.010 0.448 4523 Dihedral : 13.424 138.574 10473 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.64 % Favored : 97.27 % Rotamer: Outliers : 3.82 % Allowed : 5.49 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.15), residues: 3149 helix: 1.59 (0.16), residues: 1089 sheet: 0.90 (0.24), residues: 453 loop : -0.50 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 197 TYR 0.010 0.001 TYR I 555 PHE 0.011 0.001 PHE I 514 TRP 0.006 0.001 TRP J1193 HIS 0.003 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.21 (26651) covalent geometry : angle 0.55636 / 0.34 (36271) hydrogen bonds : bond 0.14777 / 14.01 ( 1139) hydrogen bonds : angle 5.70291 / 6.63 ( 3140) metal coordination : bond 0.05156 / 4.63 ( 8) metal coordination : angle 17.89537 / 28.93 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 600 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 55 GLU cc_start: 0.5784 (tt0) cc_final: 0.5002 (mm-30) REVERT: G 57 THR cc_start: 0.7366 (m) cc_final: 0.7143 (p) REVERT: H 7 GLU cc_start: 0.5708 (pm20) cc_final: 0.5102 (mp0) REVERT: I 20 GLN cc_start: 0.7445 (mt0) cc_final: 0.7031 (mt0) REVERT: I 239 MET cc_start: 0.7074 (tmm) cc_final: 0.6642 (ppp) REVERT: I 503 LYS cc_start: 0.7324 (mtmt) cc_final: 0.6956 (mmmt) REVERT: I 541 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: I 651 ASP cc_start: 0.6658 (OUTLIER) cc_final: 0.6316 (p0) REVERT: I 811 ASN cc_start: 0.6987 (p0) cc_final: 0.6742 (p0) REVERT: I 890 LYS cc_start: 0.1607 (OUTLIER) cc_final: 0.1268 (pttm) REVERT: I 1064 ASP cc_start: 0.6686 (OUTLIER) cc_final: 0.6389 (p0) REVERT: I 1114 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7566 (tt0) REVERT: I 1119 MET cc_start: 0.7174 (ttt) cc_final: 0.6864 (tpt) REVERT: I 1273 MET cc_start: 0.7147 (mtp) cc_final: 0.6940 (mtm) REVERT: J 124 ILE cc_start: 0.5598 (mt) cc_final: 0.5327 (mt) REVERT: J 301 GLU cc_start: 0.6559 (mt-10) cc_final: 0.6241 (pp20) REVERT: J 316 ILE cc_start: 0.5811 (OUTLIER) cc_final: 0.5492 (pt) REVERT: J 825 VAL cc_start: 0.7482 (OUTLIER) cc_final: 0.7080 (m) REVERT: J 1208 ASP cc_start: 0.7107 (m-30) cc_final: 0.6647 (m-30) REVERT: J 1230 THR cc_start: 0.8853 (t) cc_final: 0.8506 (m) outliers start: 103 outliers final: 17 residues processed: 677 average time/residue: 0.6236 time to fit residues: 489.9487 Evaluate side-chains 363 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 339 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 541 GLU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 890 LYS Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1114 GLU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1309 VAL Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 885 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 197 optimal weight: 0.1980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 7.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 23 HIS I 450 ASN I 613 ASN I 677 ASN I1070 HIS I1099 ASN I1116 HIS ** I1336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 430 HIS J 712 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.206168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.176792 restraints weight = 30182.313| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.18 r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 26659 Z= 0.210 Angle : 0.748 19.923 36283 Z= 0.396 Chirality : 0.049 0.377 4152 Planarity : 0.007 0.171 4523 Dihedral : 14.062 129.599 4324 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 5.42 % Allowed : 13.69 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.54 (0.15), residues: 3149 helix: 1.37 (0.16), residues: 1104 sheet: 0.85 (0.24), residues: 478 loop : -0.50 (0.15), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.001 ARG I1216 TYR 0.022 0.002 TYR H 152 PHE 0.021 0.002 PHE I1221 TRP 0.025 0.003 TRP I 807 HIS 0.011 0.002 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.21 (26651) covalent geometry : angle 0.74153 / 0.40 (36271) hydrogen bonds : bond 0.05984 / 5.27 ( 1139) hydrogen bonds : angle 4.55474 / 5.34 ( 3140) metal coordination : bond 0.00767 / 0.69 ( 8) metal coordination : angle 5.58833 / 8.65 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 378 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 57 THR cc_start: 0.7274 (m) cc_final: 0.6823 (p) REVERT: G 147 GLN cc_start: 0.8128 (pt0) cc_final: 0.7925 (pt0) REVERT: G 159 ILE cc_start: 0.2325 (OUTLIER) cc_final: 0.1764 (pp) REVERT: H 181 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6750 (mp0) REVERT: I 188 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7483 (t80) REVERT: I 359 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6398 (ttt180) REVERT: I 414 ILE cc_start: 0.8341 (pt) cc_final: 0.8122 (pt) REVERT: I 890 LYS cc_start: 0.0711 (OUTLIER) cc_final: 0.0378 (pttm) REVERT: I 1085 MET cc_start: 0.8733 (tpt) cc_final: 0.8438 (tpt) REVERT: I 1114 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: J 316 ILE cc_start: 0.7220 (OUTLIER) cc_final: 0.6969 (pt) REVERT: J 347 VAL cc_start: 0.8514 (OUTLIER) cc_final: 0.8281 (m) REVERT: J 479 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7374 (mt-10) REVERT: J 497 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7109 (mt-10) REVERT: J 526 VAL cc_start: 0.8127 (OUTLIER) cc_final: 0.7904 (t) REVERT: J 534 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.6976 (tp30) REVERT: J 627 THR cc_start: 0.8307 (t) cc_final: 0.7005 (p) REVERT: J 897 HIS cc_start: 0.8612 (OUTLIER) cc_final: 0.8198 (m90) outliers start: 146 outliers final: 41 residues processed: 479 average time/residue: 0.6392 time to fit residues: 354.0830 Evaluate side-chains 329 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 276 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 359 ARG Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 596 ASP Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 648 ASP Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 890 LYS Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1114 GLU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1252 SER Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1338 GLU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 497 GLU Chi-restraints excluded: chain J residue 499 ILE Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 534 GLU Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 660 GLU Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 897 HIS Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1320 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 87 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 257 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 chunk 242 optimal weight: 0.0870 chunk 63 optimal weight: 4.9990 chunk 294 optimal weight: 50.0000 chunk 296 optimal weight: 5.9990 chunk 317 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 103 ASN I 276 GLN I 604 HIS I 613 ASN I1070 HIS I1336 ASN J 294 ASN J 430 HIS ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1197 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.198935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.169039 restraints weight = 29563.513| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.13 r_work: 0.3045 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 26659 Z= 0.172 Angle : 0.619 16.735 36283 Z= 0.327 Chirality : 0.044 0.337 4152 Planarity : 0.005 0.066 4523 Dihedral : 13.880 134.221 4307 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.64 % Allowed : 16.32 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.69 (0.15), residues: 3149 helix: 1.59 (0.16), residues: 1115 sheet: 1.02 (0.24), residues: 456 loop : -0.53 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 542 TYR 0.016 0.001 TYR G 185 PHE 0.024 0.001 PHE I 188 TRP 0.012 0.002 TRP J 33 HIS 0.008 0.001 HIS J 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (26651) covalent geometry : angle 0.61534 / 0.33 (36271) hydrogen bonds : bond 0.05988 / 5.32 ( 1139) hydrogen bonds : angle 4.35116 / 5.25 ( 3140) metal coordination : bond 0.00714 / 0.67 ( 8) metal coordination : angle 3.53651 / 5.55 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 307 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 57 THR cc_start: 0.8022 (m) cc_final: 0.7376 (p) REVERT: G 147 GLN cc_start: 0.8717 (pt0) cc_final: 0.8466 (pt0) REVERT: G 158 ARG cc_start: 0.6394 (OUTLIER) cc_final: 0.6099 (ptt180) REVERT: H 7 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7371 (pm20) REVERT: H 80 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7098 (mm-30) REVERT: H 181 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7701 (mp0) REVERT: I 407 ARG cc_start: 0.8127 (tpm170) cc_final: 0.7823 (tpm170) REVERT: I 414 ILE cc_start: 0.8485 (pt) cc_final: 0.8230 (pt) REVERT: I 470 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7427 (mtp85) REVERT: I 496 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7916 (tppt) REVERT: I 503 LYS cc_start: 0.8187 (mtmt) cc_final: 0.7710 (mmmt) REVERT: I 694 ARG cc_start: 0.8140 (mtm180) cc_final: 0.7881 (mtt180) REVERT: I 731 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8352 (ttm170) REVERT: I 735 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7870 (tptt) REVERT: I 772 SER cc_start: 0.8392 (p) cc_final: 0.8174 (t) REVERT: I 834 GLN cc_start: 0.8563 (pt0) cc_final: 0.8307 (pt0) REVERT: I 890 LYS cc_start: 0.1495 (OUTLIER) cc_final: 0.0918 (pttp) REVERT: J 102 MET cc_start: 0.7869 (mtt) cc_final: 0.7527 (mtt) REVERT: J 479 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8235 (mt-10) REVERT: J 534 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.7865 (tp30) REVERT: J 724 MET cc_start: 0.8857 (mtt) cc_final: 0.8583 (mtt) REVERT: J 1187 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7258 (pp20) REVERT: J 1278 GLU cc_start: 0.8297 (tt0) cc_final: 0.8004 (pt0) REVERT: J 1320 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7288 (mt) REVERT: J 1334 GLU cc_start: 0.8292 (tp30) cc_final: 0.8073 (tp30) outliers start: 125 outliers final: 53 residues processed: 398 average time/residue: 0.6156 time to fit residues: 287.1668 Evaluate side-chains 328 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 265 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 158 ARG Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 470 ARG Chi-restraints excluded: chain I residue 496 LYS Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 599 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 634 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 731 ARG Chi-restraints excluded: chain I residue 735 LYS Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 890 LYS Chi-restraints excluded: chain I residue 961 SER Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1252 SER Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 499 ILE Chi-restraints excluded: chain J residue 534 GLU Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 753 SER Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1320 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 195 optimal weight: 7.9990 chunk 247 optimal weight: 4.9990 chunk 278 optimal weight: 20.0000 chunk 180 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 184 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 179 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 46 GLN I 604 HIS I1336 ASN J 430 HIS ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1197 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.191857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.154025 restraints weight = 28981.832| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.78 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.5643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 26659 Z= 0.173 Angle : 0.633 13.569 36283 Z= 0.335 Chirality : 0.045 0.261 4152 Planarity : 0.005 0.076 4523 Dihedral : 13.902 131.238 4302 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 5.27 % Allowed : 16.51 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.15), residues: 3149 helix: 1.61 (0.16), residues: 1109 sheet: 0.85 (0.24), residues: 461 loop : -0.54 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 731 TYR 0.020 0.002 TYR J 144 PHE 0.021 0.002 PHE I 188 TRP 0.010 0.001 TRP J 33 HIS 0.006 0.001 HIS J1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (26651) covalent geometry : angle 0.63063 / 0.34 (36271) hydrogen bonds : bond 0.06284 / 5.47 ( 1139) hydrogen bonds : angle 4.34302 / 5.13 ( 3140) metal coordination : bond 0.02181 / 1.63 ( 8) metal coordination : angle 2.92238 / 4.45 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 334 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 33 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7614 (ttt180) REVERT: H 181 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7228 (mp0) REVERT: I 11 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7731 (mt) REVERT: I 129 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8385 (mp) REVERT: I 407 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7495 (tpm170) REVERT: I 702 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.8436 (p) REVERT: I 731 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7783 (ttm170) REVERT: I 1042 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6951 (mt) REVERT: J 225 GLU cc_start: 0.7404 (tp30) cc_final: 0.6840 (tp30) REVERT: J 332 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8265 (pptt) REVERT: J 474 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8560 (mp) REVERT: J 479 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8148 (mt-10) REVERT: J 534 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.6873 (tp30) REVERT: J 571 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7448 (m-30) REVERT: J 1320 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7677 (mt) REVERT: J 1327 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6782 (mp0) outliers start: 142 outliers final: 56 residues processed: 442 average time/residue: 0.6061 time to fit residues: 312.6356 Evaluate side-chains 348 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 278 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 407 ARG Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 599 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 731 ARG Chi-restraints excluded: chain I residue 961 SER Chi-restraints excluded: chain I residue 1042 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1252 SER Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 39 LYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain J residue 332 LYS Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 534 GLU Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 660 GLU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 753 SER Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 768 ASN Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 850 LYS Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1151 LYS Chi-restraints excluded: chain J residue 1265 THR Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1327 GLU Chi-restraints excluded: chain J residue 1353 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 153 optimal weight: 8.9990 chunk 254 optimal weight: 5.9990 chunk 268 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 301 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 137 optimal weight: 0.8980 chunk 208 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 103 ASN I 649 GLN I 834 GLN I1299 ASN J 294 ASN J 430 HIS J 708 ASN J1197 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.193880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.163385 restraints weight = 28854.045| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.09 r_work: 0.2949 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.5896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26659 Z= 0.140 Angle : 0.578 14.539 36283 Z= 0.303 Chirality : 0.043 0.264 4152 Planarity : 0.005 0.048 4523 Dihedral : 13.879 134.057 4298 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.08 % Allowed : 18.95 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.72 (0.15), residues: 3149 helix: 1.69 (0.16), residues: 1113 sheet: 0.96 (0.25), residues: 445 loop : -0.54 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 133 TYR 0.018 0.001 TYR I 123 PHE 0.016 0.001 PHE J1319 TRP 0.006 0.001 TRP J1193 HIS 0.004 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (26651) covalent geometry : angle 0.57443 / 0.30 (36271) hydrogen bonds : bond 0.05708 / 4.99 ( 1139) hydrogen bonds : angle 4.26073 / 5.10 ( 3140) metal coordination : bond 0.01461 / 0.79 ( 8) metal coordination : angle 3.39581 / 5.31 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 287 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7462 (mtmm) REVERT: G 72 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8240 (tt0) REVERT: H 33 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7827 (ttt180) REVERT: H 181 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7770 (mp0) REVERT: I 11 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7861 (mt) REVERT: I 239 MET cc_start: 0.6965 (tmm) cc_final: 0.6366 (ppp) REVERT: I 407 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8237 (tpm170) REVERT: I 454 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.7132 (mtm-85) REVERT: I 731 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8361 (ttm170) REVERT: I 1042 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7234 (mt) REVERT: J 138 VAL cc_start: 0.7604 (p) cc_final: 0.7293 (t) REVERT: J 215 LYS cc_start: 0.8107 (ttmm) cc_final: 0.7668 (mtmm) REVERT: J 225 GLU cc_start: 0.8231 (tp30) cc_final: 0.8004 (tp30) REVERT: J 332 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8551 (pptt) REVERT: J 474 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8701 (mp) REVERT: J 479 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8534 (mt-10) REVERT: J 1320 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.7950 (mt) REVERT: J 1327 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7518 (mp0) outliers start: 110 outliers final: 54 residues processed: 369 average time/residue: 0.6444 time to fit residues: 277.6501 Evaluate side-chains 334 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 267 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 407 ARG Chi-restraints excluded: chain I residue 454 ARG Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 599 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 731 ARG Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 1042 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1252 SER Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 39 LYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 332 LYS Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 660 GLU Chi-restraints excluded: chain J residue 753 SER Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 850 LYS Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 873 GLU Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1327 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 230 optimal weight: 3.9990 chunk 178 optimal weight: 0.0170 chunk 80 optimal weight: 0.6980 chunk 151 optimal weight: 30.0000 chunk 135 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 189 optimal weight: 10.0000 chunk 310 optimal weight: 9.9990 chunk 275 optimal weight: 3.9990 overall best weight: 1.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 103 ASN J 294 ASN J 430 HIS J 708 ASN J1197 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.191512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.145560 restraints weight = 28848.655| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 3.43 r_work: 0.2903 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.6168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26659 Z= 0.149 Angle : 0.574 10.622 36283 Z= 0.303 Chirality : 0.043 0.261 4152 Planarity : 0.005 0.051 4523 Dihedral : 13.888 134.754 4298 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.49 % Allowed : 19.03 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.71 (0.15), residues: 3149 helix: 1.72 (0.16), residues: 1109 sheet: 0.92 (0.25), residues: 443 loop : -0.55 (0.15), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 779 TYR 0.019 0.001 TYR I 123 PHE 0.015 0.001 PHE J1319 TRP 0.006 0.001 TRP J1193 HIS 0.005 0.001 HIS J1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (26651) covalent geometry : angle 0.57110 / 0.30 (36271) hydrogen bonds : bond 0.05784 / 5.02 ( 1139) hydrogen bonds : angle 4.24854 / 5.05 ( 3140) metal coordination : bond 0.00700 / 0.45 ( 8) metal coordination : angle 3.01692 / 4.89 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 280 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 72 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8319 (tt0) REVERT: G 96 ASP cc_start: 0.8195 (p0) cc_final: 0.7857 (p0) REVERT: H 33 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7805 (ttt180) REVERT: H 181 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: I 11 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7984 (mt) REVERT: I 129 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8678 (mp) REVERT: I 163 LYS cc_start: 0.8658 (ttmm) cc_final: 0.8099 (mptt) REVERT: I 239 MET cc_start: 0.6946 (tmm) cc_final: 0.6439 (ppp) REVERT: I 407 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8134 (tpm170) REVERT: I 454 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.7167 (mtm-85) REVERT: I 731 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8407 (ttm170) REVERT: I 1042 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7339 (mt) REVERT: I 1066 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8460 (mmm) REVERT: J 138 VAL cc_start: 0.8042 (OUTLIER) cc_final: 0.7744 (t) REVERT: J 215 LYS cc_start: 0.8107 (ttmm) cc_final: 0.7702 (mtmm) REVERT: J 252 LEU cc_start: 0.7512 (pp) cc_final: 0.7202 (mt) REVERT: J 278 ARG cc_start: 0.7428 (mtp85) cc_final: 0.6932 (ttm170) REVERT: J 474 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8712 (mp) REVERT: J 1327 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7593 (mp0) outliers start: 121 outliers final: 62 residues processed: 372 average time/residue: 0.6171 time to fit residues: 269.9060 Evaluate side-chains 341 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 266 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 407 ARG Chi-restraints excluded: chain I residue 454 ARG Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 599 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 731 ARG Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 961 SER Chi-restraints excluded: chain I residue 1042 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1302 THR Chi-restraints excluded: chain I residue 1310 ASP Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 753 SER Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 850 LYS Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain J residue 1327 GLU Chi-restraints excluded: chain J residue 1353 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 174 optimal weight: 0.4980 chunk 205 optimal weight: 8.9990 chunk 132 optimal weight: 0.0980 chunk 112 optimal weight: 2.9990 chunk 313 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 168 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 103 ASN I1220 GLN J 430 HIS J 708 ASN J1197 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.190250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.152869 restraints weight = 28680.243| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.68 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.6379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26659 Z= 0.136 Angle : 0.566 10.255 36283 Z= 0.298 Chirality : 0.043 0.259 4152 Planarity : 0.004 0.055 4523 Dihedral : 13.875 135.730 4298 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.12 % Allowed : 19.92 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.76 (0.15), residues: 3149 helix: 1.78 (0.16), residues: 1110 sheet: 0.91 (0.25), residues: 446 loop : -0.53 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 12 TYR 0.022 0.001 TYR I 73 PHE 0.016 0.001 PHE J1319 TRP 0.007 0.001 TRP J1193 HIS 0.003 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (26651) covalent geometry : angle 0.56393 / 0.30 (36271) hydrogen bonds : bond 0.05501 / 4.80 ( 1139) hydrogen bonds : angle 4.21122 / 5.04 ( 3140) metal coordination : bond 0.00807 / 0.47 ( 8) metal coordination : angle 2.79514 / 4.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 277 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7498 (mtmm) REVERT: H 33 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7623 (ttt180) REVERT: I 129 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8570 (mp) REVERT: I 407 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7581 (tpm170) REVERT: I 454 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.7023 (mtm-85) REVERT: I 1066 MET cc_start: 0.8035 (mtm) cc_final: 0.7738 (mmm) REVERT: I 1230 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8729 (ttm) REVERT: J 252 LEU cc_start: 0.7880 (pp) cc_final: 0.7598 (mt) REVERT: J 1327 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6675 (mp0) outliers start: 111 outliers final: 58 residues processed: 365 average time/residue: 0.6302 time to fit residues: 269.4729 Evaluate side-chains 329 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 264 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 407 ARG Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 454 ARG Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 961 SER Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1230 MET Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1310 ASP Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 753 SER Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 850 LYS Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain J residue 1265 THR Chi-restraints excluded: chain J residue 1327 GLU Chi-restraints excluded: chain J residue 1353 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 302 optimal weight: 9.9990 chunk 174 optimal weight: 0.9980 chunk 157 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 257 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 212 optimal weight: 10.0000 chunk 289 optimal weight: 50.0000 chunk 134 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 737 ASN I1080 ASN J 294 ASN J 430 HIS J 708 ASN J1197 ASN J1367 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.190291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.144111 restraints weight = 28850.517| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.52 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.6558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26659 Z= 0.141 Angle : 0.583 19.546 36283 Z= 0.303 Chirality : 0.043 0.259 4152 Planarity : 0.004 0.049 4523 Dihedral : 13.859 136.212 4295 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.01 % Allowed : 20.44 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.73 (0.15), residues: 3149 helix: 1.76 (0.16), residues: 1108 sheet: 0.82 (0.25), residues: 449 loop : -0.52 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 779 TYR 0.019 0.001 TYR J1363 PHE 0.015 0.001 PHE J1319 TRP 0.006 0.001 TRP J1193 HIS 0.004 0.001 HIS J1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (26651) covalent geometry : angle 0.58133 / 0.30 (36271) hydrogen bonds : bond 0.05576 / 4.85 ( 1139) hydrogen bonds : angle 4.20614 / 5.00 ( 3140) metal coordination : bond 0.00585 / 0.38 ( 8) metal coordination : angle 2.76373 / 4.56 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 276 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7605 (mtmm) REVERT: G 72 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7454 (tt0) REVERT: H 33 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7541 (ttt180) REVERT: H 80 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.7060 (mm-30) REVERT: I 129 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8798 (mp) REVERT: I 163 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8059 (mptt) REVERT: I 407 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7359 (tpm170) REVERT: I 454 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.7086 (mtm-85) REVERT: I 1066 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7810 (mmm) REVERT: I 1230 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8696 (ttm) REVERT: J 39 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7943 (mttt) REVERT: J 252 LEU cc_start: 0.7771 (pp) cc_final: 0.7498 (mt) REVERT: J 1327 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6633 (mp0) outliers start: 108 outliers final: 62 residues processed: 363 average time/residue: 0.6223 time to fit residues: 265.7701 Evaluate side-chains 338 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 264 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 163 LYS Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 407 ARG Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 441 GLU Chi-restraints excluded: chain I residue 454 ARG Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 961 SER Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1230 MET Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1302 THR Chi-restraints excluded: chain I residue 1310 ASP Chi-restraints excluded: chain J residue 39 LYS Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 753 SER Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 850 LYS Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain J residue 1327 GLU Chi-restraints excluded: chain J residue 1353 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 181 optimal weight: 0.5980 chunk 230 optimal weight: 3.9990 chunk 130 optimal weight: 0.0370 chunk 162 optimal weight: 1.9990 chunk 302 optimal weight: 8.9990 chunk 166 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 3 optimal weight: 0.0570 chunk 121 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 737 ASN J 430 HIS J 708 ASN J1197 ASN J1367 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.191884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.154280 restraints weight = 29023.638| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.74 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.6609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 26659 Z= 0.106 Angle : 0.558 14.499 36283 Z= 0.288 Chirality : 0.041 0.253 4152 Planarity : 0.004 0.057 4523 Dihedral : 13.760 137.127 4295 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.60 % Allowed : 21.96 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.90 (0.15), residues: 3149 helix: 1.92 (0.16), residues: 1110 sheet: 0.85 (0.25), residues: 450 loop : -0.42 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG G 12 TYR 0.027 0.001 TYR J1363 PHE 0.013 0.001 PHE J1319 TRP 0.007 0.001 TRP J1193 HIS 0.003 0.000 HIS J1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 (26651) covalent geometry : angle 0.55582 / 0.29 (36271) hydrogen bonds : bond 0.04499 / 3.95 ( 1139) hydrogen bonds : angle 4.12989 / 5.03 ( 3140) metal coordination : bond 0.00440 / 0.28 ( 8) metal coordination : angle 2.61131 / 4.30 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 279 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 33 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7593 (ttt180) REVERT: H 214 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6575 (mp0) REVERT: I 129 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8581 (mp) REVERT: I 163 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7995 (mptt) REVERT: I 407 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7559 (tpm170) REVERT: I 702 THR cc_start: 0.8574 (m) cc_final: 0.8368 (p) REVERT: I 1066 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7818 (mmm) REVERT: I 1085 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8422 (mmm) REVERT: I 1230 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8687 (ttm) REVERT: J 252 LEU cc_start: 0.7866 (pp) cc_final: 0.7570 (mt) REVERT: J 278 ARG cc_start: 0.7313 (ttp-170) cc_final: 0.7074 (ttm-80) outliers start: 70 outliers final: 45 residues processed: 332 average time/residue: 0.6012 time to fit residues: 233.2821 Evaluate side-chains 315 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 262 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 163 LYS Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 407 ARG Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 441 GLU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 961 SER Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1230 MET Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 460 ASP Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 850 LYS Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1151 LYS Chi-restraints excluded: chain J residue 1265 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 1 optimal weight: 9.9990 chunk 213 optimal weight: 3.9990 chunk 310 optimal weight: 0.8980 chunk 281 optimal weight: 6.9990 chunk 250 optimal weight: 8.9990 chunk 234 optimal weight: 0.1980 chunk 147 optimal weight: 0.5980 chunk 259 optimal weight: 3.9990 chunk 255 optimal weight: 10.0000 chunk 237 optimal weight: 2.9990 chunk 80 optimal weight: 50.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 737 ASN J 430 HIS J1197 ASN J1367 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.189556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.149765 restraints weight = 28566.344| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.79 r_work: 0.3024 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.6753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26659 Z= 0.146 Angle : 0.603 15.866 36283 Z= 0.311 Chirality : 0.044 0.259 4152 Planarity : 0.005 0.058 4523 Dihedral : 13.805 137.093 4294 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.71 % Allowed : 22.22 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3149 helix: 1.80 (0.16), residues: 1118 sheet: 0.87 (0.25), residues: 447 loop : -0.47 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 12 TYR 0.022 0.002 TYR J1363 PHE 0.015 0.001 PHE J1319 TRP 0.006 0.001 TRP J1193 HIS 0.004 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (26651) covalent geometry : angle 0.60052 / 0.31 (36271) hydrogen bonds : bond 0.05572 / 4.89 ( 1139) hydrogen bonds : angle 4.20619 / 5.08 ( 3140) metal coordination : bond 0.00622 / 0.37 ( 8) metal coordination : angle 2.83770 / 4.78 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 265 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 33 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7783 (ttt180) REVERT: H 197 ASP cc_start: 0.6512 (p0) cc_final: 0.6307 (p0) REVERT: H 214 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: I 129 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8818 (mp) REVERT: I 163 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8342 (mptt) REVERT: I 407 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8255 (tpm170) REVERT: I 1066 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8410 (mmm) REVERT: I 1230 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8860 (ttm) REVERT: J 235 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.7911 (pm20) REVERT: J 252 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7465 (mt) REVERT: J 278 ARG cc_start: 0.8206 (ttp-170) cc_final: 0.7445 (ttm-80) REVERT: J 878 ASP cc_start: 0.7622 (t0) cc_final: 0.7393 (t0) outliers start: 73 outliers final: 48 residues processed: 324 average time/residue: 0.6030 time to fit residues: 229.3382 Evaluate side-chains 316 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 259 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 163 LYS Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 407 ARG Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1230 MET Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 850 LYS Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain J residue 1265 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 145 optimal weight: 6.9990 chunk 172 optimal weight: 0.8980 chunk 123 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 168 optimal weight: 0.3980 chunk 7 optimal weight: 4.9990 chunk 286 optimal weight: 50.0000 chunk 234 optimal weight: 1.9990 chunk 231 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 115 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 103 ASN J 430 HIS J1197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.190609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.152836 restraints weight = 28804.791| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.77 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.6816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26659 Z= 0.111 Angle : 0.557 14.970 36283 Z= 0.287 Chirality : 0.042 0.253 4152 Planarity : 0.004 0.059 4523 Dihedral : 13.710 137.599 4294 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.52 % Allowed : 22.59 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.90 (0.15), residues: 3149 helix: 1.90 (0.16), residues: 1116 sheet: 0.90 (0.25), residues: 447 loop : -0.42 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 12 TYR 0.025 0.001 TYR J1363 PHE 0.013 0.001 PHE J1319 TRP 0.006 0.001 TRP J1193 HIS 0.003 0.000 HIS J1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (26651) covalent geometry : angle 0.55517 / 0.29 (36271) hydrogen bonds : bond 0.04644 / 4.06 ( 1139) hydrogen bonds : angle 4.11550 / 5.01 ( 3140) metal coordination : bond 0.00372 / 0.24 ( 8) metal coordination : angle 2.45725 / 4.10 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7571.18 seconds wall clock time: 129 minutes 47.21 seconds (7787.21 seconds total)