Starting phenix.real_space_refine on Fri Mar 6 04:02:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uwh_26832/03_2026/7uwh_26832.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uwh_26832/03_2026/7uwh_26832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uwh_26832/03_2026/7uwh_26832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uwh_26832/03_2026/7uwh_26832.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uwh_26832/03_2026/7uwh_26832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uwh_26832/03_2026/7uwh_26832.map" } resolution = 3.1 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 79 5.49 5 Mg 1 5.21 5 S 111 5.16 5 C 17256 2.51 5 N 4958 2.21 5 O 5520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 123 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27927 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 650 Classifications: {'DNA': 32} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 31} Chain breaks: 1 Chain: "B" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 776 Classifications: {'DNA': 37, 'RNA': 1} Modifications used: {'rna3p_pur': 1} Link IDs: {'rna3p': 37} Chain: "C" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1439 Classifications: {'peptide': 190} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 177} Chain: "G" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "H" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1772 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 219} Chain: "I" Number of atoms: 10407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1319, 10407 Classifications: {'peptide': 1319} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1263} Chain breaks: 1 Chain: "J" Number of atoms: 10272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1318, 10272 Classifications: {'peptide': 1318} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1264} Chain breaks: 4 Chain: "K" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain: "R" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 221 Classifications: {'RNA': 10} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17261 SG CYS J 70 104.775 67.238 24.091 1.00 50.10 S ATOM 17275 SG CYS J 72 103.785 67.333 20.717 1.00 40.99 S ATOM 17383 SG CYS J 85 106.993 68.686 21.222 1.00 42.62 S ATOM 17407 SG CYS J 88 103.786 70.466 22.977 1.00 39.36 S ATOM 23095 SG CYS J 814 109.407 80.418 89.464 1.00 20.28 S ATOM 23660 SG CYS J 888 106.955 80.172 86.587 1.00 14.12 S ATOM 23711 SG CYS J 895 107.844 77.071 88.554 1.00 10.63 S ATOM 23732 SG CYS J 898 105.658 79.677 90.131 1.00 10.55 S Time building chain proxies: 6.04, per 1000 atoms: 0.22 Number of scatterers: 27927 At special positions: 0 Unit cell: (143.576, 165.496, 145.768, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 111 16.00 P 79 15.00 Mg 1 11.99 O 5520 8.00 N 4958 7.00 C 17256 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: 2.17 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 88 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " Number of angles added : 12 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6212 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 50 sheets defined 38.0% alpha, 15.7% beta 16 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain 'C' and resid 50 through 65 removed outlier: 3.660A pdb=" N LEU C 57 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 81 Processing helix chain 'C' and resid 81 through 98 removed outlier: 3.515A pdb=" N HIS C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA C 86 " --> pdb=" O ASN C 82 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N THR C 87 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N MET C 88 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET C 91 " --> pdb=" O THR C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 128 removed outlier: 3.697A pdb=" N SER C 127 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 154 Processing helix chain 'C' and resid 158 through 163 removed outlier: 3.635A pdb=" N HIS C 162 " --> pdb=" O GLY C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'C' and resid 187 through 195 removed outlier: 3.592A pdb=" N LYS C 191 " --> pdb=" O PHE C 187 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 194 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 50 Processing helix chain 'G' and resid 77 through 87 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 212 through 230 Processing helix chain 'H' and resid 34 through 50 Processing helix chain 'H' and resid 77 through 88 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 230 Processing helix chain 'I' and resid 5 through 9 removed outlier: 3.565A pdb=" N LYS I 9 " --> pdb=" O THR I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 39 Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 4.323A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 280 Processing helix chain 'I' and resid 288 through 293 removed outlier: 4.355A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 288 through 293' Processing helix chain 'I' and resid 318 through 328 Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.538A pdb=" N LEU I 388 " --> pdb=" O LEU I 384 " (cutoff:3.500A) removed outlier: 4.329A 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 Processing helix chain 'I' and resid 455 through 480 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: 3.548A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 612 removed outlier: 3.736A 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 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.713A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 664 through 668' Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 689 removed outlier: 3.736A pdb=" N MET I 681 " --> pdb=" O ASN I 677 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA I 683 " --> pdb=" O ALA I 679 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 738 through 741 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 858 through 863 Processing helix chain 'I' and resid 942 through 976 removed outlier: 4.049A pdb=" N ALA I 969 " --> pdb=" O GLN I 965 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLY I 970 " --> pdb=" O ILE I 966 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU I 971 " --> pdb=" O LEU I 967 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE I 972 " --> pdb=" O GLU I 968 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER I 973 " --> pdb=" O ALA I 969 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG I 974 " --> pdb=" O GLY I 970 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE I 975 " --> pdb=" O LEU I 971 " (cutoff:3.500A) Processing helix chain 'I' and resid 1007 through 1025 removed outlier: 3.529A pdb=" N LYS I1022 " --> pdb=" O TYR I1018 " (cutoff:3.500A) Processing helix chain 'I' and resid 1025 through 1038 Processing helix chain 'I' and resid 1099 through 1103 removed outlier: 3.556A pdb=" N GLY I1102 " --> pdb=" O ASN I1099 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 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 1167 through 1177 removed outlier: 3.649A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1243 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1297 through 1310 Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.667A 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 77 through 81 Processing helix chain 'J' and resid 96 through 101 removed outlier: 3.603A pdb=" N GLU J 100 " --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 122 through 128 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 169 Processing helix chain 'J' and resid 181 through 191 Processing helix chain 'J' and resid 193 through 206 removed outlier: 3.504A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 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 282 Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 389 Processing helix chain 'J' and resid 393 through 404 removed outlier: 3.712A pdb=" N ALA J 397 " --> pdb=" O THR J 393 " (cutoff:3.500A) Processing helix chain 'J' and resid 407 through 417 Processing helix chain 'J' and resid 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 540 Processing helix chain 'J' and resid 573 through 581 removed outlier: 3.804A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 592 removed outlier: 3.787A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 613 Processing helix chain 'J' and resid 614 through 636 Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 805 removed outlier: 3.906A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 840 Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 896 through 900 removed outlier: 3.786A pdb=" N GLY J 900 " --> pdb=" O ALA J 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 896 through 900' Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.737A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 930 removed outlier: 3.540A pdb=" N LEU J 930 " --> pdb=" O GLY J 927 " (cutoff:3.500A) Processing helix chain 'J' and resid 1068 through 1074 removed outlier: 3.724A pdb=" N LEU J1074 " --> pdb=" O GLY J1070 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1147 removed outlier: 3.540A pdb=" N VAL J1141 " --> pdb=" O GLY J1137 " (cutoff:3.500A) Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.320A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1308 through 1313 Processing helix chain 'J' and resid 1328 through 1339 Processing helix chain 'J' and resid 1347 through 1354 Processing helix chain 'J' and resid 1360 through 1373 Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 33 removed outlier: 3.823A pdb=" N GLY K 33 " --> pdb=" O GLN K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 57 Processing helix chain 'K' and resid 60 through 76 removed outlier: 3.867A pdb=" N GLU K 76 " --> pdb=" O GLN K 72 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 33 removed outlier: 3.582A pdb=" N VAL C 32 " --> pdb=" O GLY C 14 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY C 14 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP C 108 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA C 17 " --> pdb=" O ASP C 108 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL C 105 " --> pdb=" O MET C 120 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL C 122 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ILE C 107 " --> pdb=" O VAL C 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 12 through 17 removed outlier: 5.285A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 97 through 99 Processing sheet with id=AA4, first strand: chain 'G' and resid 97 through 99 removed outlier: 7.685A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN G 147 " --> pdb=" O ALA G 55 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA G 55 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AA6, first strand: chain 'G' and resid 108 through 111 Processing sheet with id=AA7, first strand: chain 'G' and resid 151 through 153 Processing sheet with id=AA8, first strand: chain 'H' and resid 13 through 16 removed outlier: 6.806A pdb=" N LEU H 13 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N GLU H 29 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU H 198 " --> pdb=" O ALA H 189 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA H 189 " --> pdb=" O LEU H 198 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LYS H 200 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL H 187 " --> pdb=" O LYS H 200 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL H 202 " --> pdb=" O TYR H 185 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR H 185 " --> pdb=" O VAL H 202 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 97 through 99 removed outlier: 6.367A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN H 147 " --> pdb=" O ALA H 55 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA H 55 " --> pdb=" O GLN H 147 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AB2, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AB3, first strand: chain 'H' and resid 108 through 111 Processing sheet with id=AB4, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB5, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.512A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 59 through 60 removed outlier: 5.161A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU I 100 " --> pdb=" O GLN I 120 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN I 120 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU I 102 " --> pdb=" O LYS I 118 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS I 118 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE I 104 " --> pdb=" O ASP I 116 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB8, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.214A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 154 through 158 Processing sheet with id=AC1, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AC2, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AC3, first strand: chain 'I' and resid 255 through 257 removed outlier: 7.369A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR I 262 " --> pdb=" O ILE I 255 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 296 through 297 removed outlier: 3.946A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 301 through 302 removed outlier: 6.882A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.224A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC8, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.514A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.763A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AD2, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AD3, first strand: chain 'I' and resid 1066 through 1068 removed outlier: 4.390A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET I 800 " --> pdb=" O MET I1230 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1066 through 1068 Processing sheet with id=AD5, first strand: chain 'I' and resid 846 through 847 removed outlier: 3.767A pdb=" N GLY I 846 " --> pdb=" O THR I 843 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR I 843 " --> pdb=" O GLY I 846 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ASP I 842 " --> pdb=" O VAL I1046 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL I1046 " --> pdb=" O ASP I 842 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.811A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 887 through 888 Processing sheet with id=AD8, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 6.427A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AE1, first strand: chain 'I' and resid 1335 through 1339 Processing sheet with id=AE2, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.354A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.168A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 9.851A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 159 through 160 removed outlier: 3.960A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 253 through 254 removed outlier: 4.151A pdb=" N VAL J 253 " --> pdb=" O ALA J 261 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AE6, first strand: chain 'J' and resid 809 through 811 removed outlier: 5.988A pdb=" N VAL J 894 " --> pdb=" O VAL J 809 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU J 811 " --> pdb=" O VAL J 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE8, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.194A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 991 through 996 removed outlier: 3.857A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU J 981 " --> pdb=" O SER J 961 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY J 956 " --> pdb=" O VAL J1011 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AF2, first strand: chain 'J' and resid 1033 through 1034 Processing sheet with id=AF3, first strand: chain 'J' and resid 1047 through 1049 removed outlier: 4.346A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA J1105 " --> pdb=" O VAL J1061 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE J1106 " --> pdb=" O ARG J1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id=AF5, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.450A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1075 hydrogen bonds defined for protein. 3024 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 5.98 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4876 1.32 - 1.45: 7082 1.45 - 1.57: 16207 1.57 - 1.69: 156 1.69 - 1.81: 193 Bond restraints: 28514 Sorted by residual: bond pdb=" CA ARG C 143 " pdb=" C ARG C 143 " ideal model delta sigma weight residual 1.524 1.470 0.054 1.26e-02 6.30e+03 1.83e+01 bond pdb=" CA ILE I 292 " pdb=" CB ILE I 292 " ideal model delta sigma weight residual 1.540 1.594 -0.054 1.39e-02 5.18e+03 1.53e+01 bond pdb=" O3' DA A 26 " pdb=" P DC A 27 " ideal model delta sigma weight residual 1.607 1.665 -0.058 1.50e-02 4.44e+03 1.50e+01 bond pdb=" N TYR C 165 " pdb=" CA TYR C 165 " ideal model delta sigma weight residual 1.455 1.414 0.041 1.17e-02 7.31e+03 1.25e+01 bond pdb=" N GLN J 94 " pdb=" CA GLN J 94 " ideal model delta sigma weight residual 1.456 1.415 0.041 1.25e-02 6.40e+03 1.08e+01 ... (remaining 28509 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 38036 2.19 - 4.38: 737 4.38 - 6.57: 75 6.57 - 8.76: 9 8.76 - 10.95: 2 Bond angle restraints: 38859 Sorted by residual: angle pdb=" N GLY C 21 " pdb=" CA GLY C 21 " pdb=" C GLY C 21 " ideal model delta sigma weight residual 112.34 123.29 -10.95 2.04e+00 2.40e-01 2.88e+01 angle pdb=" N TRP J1193 " pdb=" CA TRP J1193 " pdb=" C TRP J1193 " ideal model delta sigma weight residual 111.28 116.95 -5.67 1.09e+00 8.42e-01 2.70e+01 angle pdb=" N ASN J 153 " pdb=" CA ASN J 153 " pdb=" C ASN J 153 " ideal model delta sigma weight residual 111.28 116.80 -5.52 1.09e+00 8.42e-01 2.57e+01 angle pdb=" N GLN J 157 " pdb=" CA GLN J 157 " pdb=" C GLN J 157 " ideal model delta sigma weight residual 110.80 121.44 -10.64 2.13e+00 2.20e-01 2.50e+01 angle pdb=" N VAL I1186 " pdb=" CA VAL I1186 " pdb=" C VAL I1186 " ideal model delta sigma weight residual 111.89 119.04 -7.15 1.44e+00 4.82e-01 2.46e+01 ... (remaining 38854 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 15566 18.07 - 36.14: 1171 36.14 - 54.21: 436 54.21 - 72.28: 140 72.28 - 90.35: 38 Dihedral angle restraints: 17351 sinusoidal: 7699 harmonic: 9652 Sorted by residual: dihedral pdb=" CA PHE J1325 " pdb=" C PHE J1325 " pdb=" N GLN J1326 " pdb=" CA GLN J1326 " ideal model delta harmonic sigma weight residual 180.00 157.52 22.48 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA GLY J 852 " pdb=" C GLY J 852 " pdb=" N THR J 853 " pdb=" CA THR J 853 " ideal model delta harmonic sigma weight residual -180.00 -159.21 -20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA SER I1295 " pdb=" C SER I1295 " pdb=" N ASP I1296 " pdb=" CA ASP I1296 " ideal model delta harmonic sigma weight residual -180.00 -159.44 -20.56 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 17348 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 4008 0.078 - 0.157: 406 0.157 - 0.235: 19 0.235 - 0.313: 2 0.313 - 0.392: 6 Chirality restraints: 4441 Sorted by residual: chirality pdb=" CB ILE I 292 " pdb=" CA ILE I 292 " pdb=" CG1 ILE I 292 " pdb=" CG2 ILE I 292 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CA ILE J1248 " pdb=" N ILE J1248 " pdb=" C ILE J1248 " pdb=" CB ILE J1248 " both_signs ideal model delta sigma weight residual False 2.43 2.78 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA ASP J 516 " pdb=" N ASP J 516 " pdb=" C ASP J 516 " pdb=" CB ASP J 516 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 4438 not shown) Planarity restraints: 4806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN J 94 " 0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C GLN J 94 " -0.073 2.00e-02 2.50e+03 pdb=" O GLN J 94 " 0.028 2.00e-02 2.50e+03 pdb=" N THR J 95 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA I 313 " -0.020 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C ALA I 313 " 0.070 2.00e-02 2.50e+03 pdb=" O ALA I 313 " -0.027 2.00e-02 2.50e+03 pdb=" N ASN I 314 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO I1185 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.08e+00 pdb=" C PRO I1185 " 0.052 2.00e-02 2.50e+03 pdb=" O PRO I1185 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL I1186 " -0.017 2.00e-02 2.50e+03 ... (remaining 4803 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 589 2.67 - 3.23: 26109 3.23 - 3.79: 43529 3.79 - 4.34: 59732 4.34 - 4.90: 98019 Nonbonded interactions: 227978 Sorted by model distance: nonbonded pdb=" O3' A R 20 " pdb="MG MG J1503 " model vdw 2.114 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1503 " model vdw 2.133 2.170 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1503 " model vdw 2.173 2.170 nonbonded pdb=" OE1 GLU I 562 " pdb=" OG SER I 662 " model vdw 2.217 3.040 nonbonded pdb=" OG SER G 49 " pdb=" OE2 GLU I1083 " model vdw 2.217 3.040 ... (remaining 227973 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 7 through 232) selection = (chain 'H' and resid 7 through 232) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 30.680 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 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 : 0.006 0.624 28522 Z= 0.269 Angle : 0.720 18.232 38871 Z= 0.447 Chirality : 0.047 0.392 4441 Planarity : 0.004 0.056 4806 Dihedral : 15.818 90.351 11139 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.54 % Favored : 94.31 % Rotamer: Outliers : 0.81 % Allowed : 2.91 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.96 (0.14), residues: 3340 helix: 0.98 (0.15), residues: 1205 sheet: -0.81 (0.27), residues: 397 loop : -1.84 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 47 TYR 0.013 0.001 TYR C 165 PHE 0.022 0.001 PHE C 154 TRP 0.003 0.000 TRP J 580 HIS 0.004 0.000 HIS J 651 Details of bonding type rmsd covalent geometry : bond 0.00349 (28514) covalent geometry : angle 0.69620 (38859) hydrogen bonds : bond 0.16869 ( 1103) hydrogen bonds : angle 6.51528 ( 3092) metal coordination : bond 0.30241 ( 8) metal coordination : angle 10.45164 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 504 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 108 ASP cc_start: 0.5746 (t0) cc_final: 0.5494 (t0) REVERT: I 151 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7276 (mtm180) REVERT: I 580 GLN cc_start: 0.7336 (mt0) cc_final: 0.7090 (mt0) REVERT: J 304 ASP cc_start: 0.6236 (m-30) cc_final: 0.6028 (m-30) REVERT: J 802 ASP cc_start: 0.6981 (m-30) cc_final: 0.6712 (m-30) outliers start: 23 outliers final: 6 residues processed: 523 average time/residue: 0.2121 time to fit residues: 166.0957 Evaluate side-chains 373 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 366 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain J residue 883 ARG Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 1173 ARG Chi-restraints excluded: chain J residue 1175 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.0980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 30.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 HIS H 186 ASN I 314 ASN I 834 GLN I1257 GLN I1264 GLN J 209 ASN J 274 ASN ** J 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 594 GLN J 651 HIS J 777 HIS J 921 GLN J 951 GLN J1244 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.144420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.093679 restraints weight = 48339.522| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.45 r_work: 0.3077 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 28522 Z= 0.167 Angle : 0.599 11.622 38871 Z= 0.313 Chirality : 0.043 0.263 4441 Planarity : 0.005 0.058 4806 Dihedral : 14.386 87.032 4600 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.40 % Allowed : 9.58 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.14), residues: 3340 helix: 1.20 (0.15), residues: 1207 sheet: -0.63 (0.26), residues: 402 loop : -1.74 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 974 TYR 0.025 0.001 TYR H 177 PHE 0.019 0.001 PHE C 159 TRP 0.020 0.001 TRP C 68 HIS 0.006 0.001 HIS I1023 Details of bonding type rmsd covalent geometry : bond 0.00386 (28514) covalent geometry : angle 0.59759 (38859) hydrogen bonds : bond 0.04247 ( 1103) hydrogen bonds : angle 4.78898 ( 3092) metal coordination : bond 0.00764 ( 8) metal coordination : angle 2.41655 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 402 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 ARG cc_start: 0.9233 (tpm170) cc_final: 0.9013 (mmm160) REVERT: C 57 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8941 (mt) REVERT: C 108 ASP cc_start: 0.8133 (t0) cc_final: 0.7605 (t0) REVERT: C 124 LYS cc_start: 0.9049 (tptp) cc_final: 0.8658 (tptp) REVERT: C 147 MET cc_start: 0.9100 (tpp) cc_final: 0.8735 (tpt) REVERT: C 182 HIS cc_start: 0.8276 (m90) cc_final: 0.7919 (m90) REVERT: H 75 GLN cc_start: 0.8363 (tm-30) cc_final: 0.7636 (tm-30) REVERT: H 80 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8161 (mt-10) REVERT: I 239 MET cc_start: 0.8520 (ppp) cc_final: 0.7618 (tmm) REVERT: I 1024 GLU cc_start: 0.8347 (pt0) cc_final: 0.8060 (pt0) REVERT: J 128 LEU cc_start: 0.9421 (mt) cc_final: 0.9117 (mt) REVERT: J 144 TYR cc_start: 0.8634 (m-80) cc_final: 0.8350 (m-80) REVERT: J 724 MET cc_start: 0.9095 (mtm) cc_final: 0.8834 (mtm) REVERT: J 802 ASP cc_start: 0.8364 (m-30) cc_final: 0.7945 (m-30) REVERT: J 1167 LYS cc_start: 0.9014 (tppt) cc_final: 0.8798 (tppt) REVERT: J 1195 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8273 (tm-30) REVERT: J 1199 PHE cc_start: 0.9007 (m-80) cc_final: 0.8499 (m-80) REVERT: J 1212 ASP cc_start: 0.8475 (m-30) cc_final: 0.8099 (m-30) REVERT: J 1330 ARG cc_start: 0.8740 (ttp80) cc_final: 0.8474 (ttp80) REVERT: K 43 ASN cc_start: 0.8831 (t0) cc_final: 0.8561 (t0) REVERT: K 55 GLU cc_start: 0.8481 (pt0) cc_final: 0.8220 (pt0) REVERT: K 73 GLN cc_start: 0.8687 (pp30) cc_final: 0.8487 (pp30) outliers start: 40 outliers final: 23 residues processed: 426 average time/residue: 0.2146 time to fit residues: 138.6854 Evaluate side-chains 379 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 355 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 980 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1173 ARG Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1321 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 180 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 292 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 319 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 315 optimal weight: 0.3980 chunk 265 optimal weight: 2.9990 chunk 316 optimal weight: 3.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS I1264 GLN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 ASN J 365 GLN J 424 ASN J 651 HIS J 951 GLN J 954 ASN J1218 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.140216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.088089 restraints weight = 48396.036| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.44 r_work: 0.2966 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 28522 Z= 0.257 Angle : 0.623 10.267 38871 Z= 0.323 Chirality : 0.044 0.265 4441 Planarity : 0.005 0.061 4806 Dihedral : 14.175 86.043 4587 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.00 % Allowed : 11.72 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.75 (0.14), residues: 3340 helix: 1.24 (0.15), residues: 1201 sheet: -0.67 (0.25), residues: 430 loop : -1.80 (0.14), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 694 TYR 0.026 0.002 TYR H 177 PHE 0.024 0.002 PHE G 231 TRP 0.033 0.002 TRP J1020 HIS 0.029 0.002 HIS G 117 Details of bonding type rmsd covalent geometry : bond 0.00602 (28514) covalent geometry : angle 0.62174 (38859) hydrogen bonds : bond 0.04482 ( 1103) hydrogen bonds : angle 4.64551 ( 3092) metal coordination : bond 0.01193 ( 8) metal coordination : angle 2.28550 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 352 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9122 (mt) REVERT: C 62 LYS cc_start: 0.9416 (tppp) cc_final: 0.9146 (tppt) REVERT: C 88 MET cc_start: 0.8723 (tpp) cc_final: 0.8432 (tpp) REVERT: C 108 ASP cc_start: 0.8111 (t0) cc_final: 0.7669 (t0) REVERT: C 124 LYS cc_start: 0.9014 (tptp) cc_final: 0.8802 (tptp) REVERT: C 159 PHE cc_start: 0.8418 (m-10) cc_final: 0.8145 (m-10) REVERT: C 182 HIS cc_start: 0.8436 (m90) cc_final: 0.8047 (m90) REVERT: G 33 ARG cc_start: 0.7887 (mmt-90) cc_final: 0.7677 (mpt180) REVERT: H 75 GLN cc_start: 0.8486 (tm-30) cc_final: 0.7714 (tm-30) REVERT: H 80 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8280 (mt-10) REVERT: H 186 ASN cc_start: 0.8474 (t0) cc_final: 0.8227 (t0) REVERT: I 239 MET cc_start: 0.8705 (ppp) cc_final: 0.8250 (tmm) REVERT: I 351 LEU cc_start: 0.9138 (mt) cc_final: 0.8909 (mt) REVERT: I 685 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8941 (mtt) REVERT: I 1273 MET cc_start: 0.9320 (mmm) cc_final: 0.9059 (mtt) REVERT: I 1297 ASP cc_start: 0.7861 (t70) cc_final: 0.7655 (t70) REVERT: I 1322 SER cc_start: 0.8955 (m) cc_final: 0.8708 (m) REVERT: J 697 MET cc_start: 0.9157 (tmm) cc_final: 0.8744 (tmm) REVERT: J 740 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8419 (mp) REVERT: J 811 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8249 (mt-10) REVERT: J 954 ASN cc_start: 0.7917 (t0) cc_final: 0.7715 (t0) REVERT: J 1167 LYS cc_start: 0.9041 (tppt) cc_final: 0.8737 (tppt) REVERT: J 1199 PHE cc_start: 0.9029 (m-80) cc_final: 0.8589 (m-80) REVERT: K 21 LEU cc_start: 0.9172 (mt) cc_final: 0.8969 (mt) REVERT: K 43 ASN cc_start: 0.8985 (t0) cc_final: 0.8681 (t0) REVERT: K 55 GLU cc_start: 0.8586 (pt0) cc_final: 0.8273 (pt0) REVERT: K 69 ARG cc_start: 0.9012 (ttm110) cc_final: 0.8320 (tpm170) REVERT: K 74 GLU cc_start: 0.9384 (tm-30) cc_final: 0.9145 (pp20) outliers start: 57 outliers final: 33 residues processed: 392 average time/residue: 0.1969 time to fit residues: 119.1676 Evaluate side-chains 367 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 331 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 85 HIS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 692 THR Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 876 GLU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1309 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1175 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 33 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 312 optimal weight: 20.0000 chunk 120 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 329 optimal weight: 0.9990 chunk 184 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS G 117 HIS G 160 HIS ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J 594 GLN J1197 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.141740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.090096 restraints weight = 47964.244| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.43 r_work: 0.3008 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28522 Z= 0.160 Angle : 0.555 10.899 38871 Z= 0.288 Chirality : 0.042 0.235 4441 Planarity : 0.004 0.060 4806 Dihedral : 13.969 83.466 4583 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.03 % Allowed : 12.98 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.61 (0.14), residues: 3340 helix: 1.33 (0.15), residues: 1204 sheet: -0.67 (0.25), residues: 421 loop : -1.68 (0.14), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 53 TYR 0.017 0.001 TYR H 177 PHE 0.016 0.001 PHE I1025 TRP 0.020 0.001 TRP C 68 HIS 0.007 0.001 HIS J 545 Details of bonding type rmsd covalent geometry : bond 0.00371 (28514) covalent geometry : angle 0.55378 (38859) hydrogen bonds : bond 0.03875 ( 1103) hydrogen bonds : angle 4.42734 ( 3092) metal coordination : bond 0.00680 ( 8) metal coordination : angle 1.93484 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 360 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 LYS cc_start: 0.9422 (tppp) cc_final: 0.9160 (tptt) REVERT: C 88 MET cc_start: 0.8655 (tpp) cc_final: 0.7632 (tpp) REVERT: C 108 ASP cc_start: 0.8108 (t0) cc_final: 0.7593 (t0) REVERT: C 124 LYS cc_start: 0.9020 (tptp) cc_final: 0.8811 (tptp) REVERT: C 154 PHE cc_start: 0.9161 (m-10) cc_final: 0.8706 (m-80) REVERT: C 159 PHE cc_start: 0.8551 (m-10) cc_final: 0.8222 (m-10) REVERT: C 182 HIS cc_start: 0.8495 (m90) cc_final: 0.7955 (m90) REVERT: H 75 GLN cc_start: 0.8430 (tm-30) cc_final: 0.7624 (tm-30) REVERT: H 188 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8507 (mp0) REVERT: I 202 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8721 (ptt90) REVERT: I 239 MET cc_start: 0.8643 (ppp) cc_final: 0.8284 (tmm) REVERT: I 330 HIS cc_start: 0.7991 (m-70) cc_final: 0.7535 (m90) REVERT: I 351 LEU cc_start: 0.9171 (mt) cc_final: 0.8890 (mt) REVERT: I 685 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8535 (mtt) REVERT: I 1273 MET cc_start: 0.9265 (mmm) cc_final: 0.8935 (mtt) REVERT: I 1322 SER cc_start: 0.8959 (m) cc_final: 0.8698 (m) REVERT: J 161 THR cc_start: 0.9386 (OUTLIER) cc_final: 0.8954 (p) REVERT: J 213 LYS cc_start: 0.9108 (tppt) cc_final: 0.8878 (tppt) REVERT: J 304 ASP cc_start: 0.8278 (m-30) cc_final: 0.8032 (m-30) REVERT: J 515 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.6892 (mmm-85) REVERT: J 697 MET cc_start: 0.9175 (tmm) cc_final: 0.8843 (tmm) REVERT: J 740 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8363 (mp) REVERT: J 802 ASP cc_start: 0.8595 (m-30) cc_final: 0.8240 (m-30) REVERT: J 873 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7999 (mt-10) REVERT: J 954 ASN cc_start: 0.7924 (t0) cc_final: 0.7665 (t0) REVERT: J 1167 LYS cc_start: 0.9060 (tppt) cc_final: 0.8778 (tppt) REVERT: J 1197 ASN cc_start: 0.8628 (OUTLIER) cc_final: 0.8219 (m-40) REVERT: J 1199 PHE cc_start: 0.8966 (m-80) cc_final: 0.8604 (m-80) REVERT: K 43 ASN cc_start: 0.9004 (t0) cc_final: 0.8680 (t0) REVERT: K 55 GLU cc_start: 0.8559 (pt0) cc_final: 0.8256 (pt0) outliers start: 58 outliers final: 26 residues processed: 395 average time/residue: 0.2039 time to fit residues: 123.9579 Evaluate side-chains 373 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 340 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 202 ARG Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 876 GLU Chi-restraints excluded: chain I residue 980 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 515 ARG Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 873 GLU Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1197 ASN Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1353 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 209 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 275 optimal weight: 1.9990 chunk 241 optimal weight: 0.6980 chunk 206 optimal weight: 4.9990 chunk 296 optimal weight: 0.9990 chunk 205 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 137 optimal weight: 0.6980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 HIS H 186 ASN ** I 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1264 GLN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 594 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.141722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.090213 restraints weight = 48035.779| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.42 r_work: 0.3009 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28522 Z= 0.152 Angle : 0.546 9.615 38871 Z= 0.284 Chirality : 0.042 0.219 4441 Planarity : 0.004 0.058 4806 Dihedral : 13.913 83.264 4583 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.17 % Allowed : 14.00 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.52 (0.15), residues: 3340 helix: 1.44 (0.15), residues: 1198 sheet: -0.61 (0.25), residues: 431 loop : -1.64 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 978 TYR 0.016 0.001 TYR J 631 PHE 0.014 0.001 PHE I1025 TRP 0.025 0.001 TRP J1020 HIS 0.006 0.001 HIS J 545 Details of bonding type rmsd covalent geometry : bond 0.00348 (28514) covalent geometry : angle 0.54466 (38859) hydrogen bonds : bond 0.03781 ( 1103) hydrogen bonds : angle 4.35472 ( 3092) metal coordination : bond 0.00795 ( 8) metal coordination : angle 1.92261 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 368 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 LYS cc_start: 0.9436 (tppp) cc_final: 0.9203 (tptt) REVERT: C 88 MET cc_start: 0.8801 (tpp) cc_final: 0.8569 (tpp) REVERT: C 104 TYR cc_start: 0.6518 (m-80) cc_final: 0.6212 (m-80) REVERT: C 108 ASP cc_start: 0.8084 (t0) cc_final: 0.7575 (t0) REVERT: C 151 ASP cc_start: 0.9466 (t0) cc_final: 0.9237 (t0) REVERT: C 154 PHE cc_start: 0.9217 (m-10) cc_final: 0.8907 (m-10) REVERT: C 159 PHE cc_start: 0.8574 (m-10) cc_final: 0.8330 (m-10) REVERT: C 182 HIS cc_start: 0.8560 (m90) cc_final: 0.8045 (m90) REVERT: G 200 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8223 (ttpp) REVERT: H 75 GLN cc_start: 0.8420 (tm-30) cc_final: 0.7611 (tm-30) REVERT: H 188 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8538 (mp0) REVERT: I 202 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8700 (ptt90) REVERT: I 239 MET cc_start: 0.8713 (ppp) cc_final: 0.8176 (tmm) REVERT: I 277 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9291 (mm) REVERT: I 351 LEU cc_start: 0.9205 (mt) cc_final: 0.8913 (mt) REVERT: I 685 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8709 (mtt) REVERT: I 1151 LEU cc_start: 0.7491 (tp) cc_final: 0.7225 (tp) REVERT: I 1273 MET cc_start: 0.9260 (mmm) cc_final: 0.8927 (mtt) REVERT: I 1322 SER cc_start: 0.8977 (m) cc_final: 0.8718 (m) REVERT: J 213 LYS cc_start: 0.9123 (tppt) cc_final: 0.8873 (tppt) REVERT: J 304 ASP cc_start: 0.8251 (m-30) cc_final: 0.8027 (m-30) REVERT: J 506 VAL cc_start: 0.9273 (t) cc_final: 0.8956 (t) REVERT: J 697 MET cc_start: 0.9164 (tmm) cc_final: 0.8861 (tmm) REVERT: J 740 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8359 (mp) REVERT: J 802 ASP cc_start: 0.8565 (m-30) cc_final: 0.8216 (m-30) REVERT: J 811 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8184 (mt-10) REVERT: J 873 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7944 (mt-10) REVERT: J 954 ASN cc_start: 0.8082 (t0) cc_final: 0.7799 (t0) REVERT: J 1167 LYS cc_start: 0.9087 (tppt) cc_final: 0.8784 (tppt) REVERT: J 1199 PHE cc_start: 0.8994 (m-80) cc_final: 0.8717 (m-80) REVERT: K 43 ASN cc_start: 0.9054 (t0) cc_final: 0.8695 (t0) REVERT: K 55 GLU cc_start: 0.8577 (pt0) cc_final: 0.8271 (pt0) outliers start: 62 outliers final: 38 residues processed: 409 average time/residue: 0.1919 time to fit residues: 121.2821 Evaluate side-chains 390 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 346 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 202 ARG Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 439 LYS Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 692 THR Chi-restraints excluded: chain I residue 876 GLU Chi-restraints excluded: chain I residue 980 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1264 GLN Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 873 GLU Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1353 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 57 optimal weight: 7.9990 chunk 227 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 214 optimal weight: 4.9990 chunk 152 optimal weight: 0.3980 chunk 136 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 63 optimal weight: 0.0980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN I 952 GLN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 335 GLN J 365 GLN ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.138420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.086163 restraints weight = 48190.119| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.41 r_work: 0.2930 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 28522 Z= 0.291 Angle : 0.630 11.021 38871 Z= 0.326 Chirality : 0.045 0.234 4441 Planarity : 0.005 0.062 4806 Dihedral : 13.984 84.546 4583 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.49 % Allowed : 14.63 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.62 (0.14), residues: 3340 helix: 1.23 (0.15), residues: 1204 sheet: -0.52 (0.26), residues: 419 loop : -1.65 (0.14), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 128 TYR 0.023 0.002 TYR J 631 PHE 0.026 0.002 PHE G 231 TRP 0.021 0.001 TRP C 68 HIS 0.006 0.001 HIS H 37 Details of bonding type rmsd covalent geometry : bond 0.00678 (28514) covalent geometry : angle 0.62927 (38859) hydrogen bonds : bond 0.04455 ( 1103) hydrogen bonds : angle 4.51351 ( 3092) metal coordination : bond 0.01208 ( 8) metal coordination : angle 1.42276 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 333 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 91 MET cc_start: 0.9547 (ppp) cc_final: 0.9174 (pmm) REVERT: C 104 TYR cc_start: 0.6298 (m-80) cc_final: 0.5980 (m-80) REVERT: C 108 ASP cc_start: 0.8261 (t0) cc_final: 0.7816 (t0) REVERT: C 154 PHE cc_start: 0.9324 (m-80) cc_final: 0.9036 (m-10) REVERT: C 159 PHE cc_start: 0.8771 (m-10) cc_final: 0.8569 (m-10) REVERT: C 182 HIS cc_start: 0.8574 (m90) cc_final: 0.8033 (m90) REVERT: G 200 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8245 (ttpp) REVERT: H 188 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8570 (mp0) REVERT: I 202 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8642 (ptt90) REVERT: I 239 MET cc_start: 0.8820 (ppp) cc_final: 0.8252 (ppp) REVERT: I 685 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8638 (mtt) REVERT: I 949 GLU cc_start: 0.9175 (tt0) cc_final: 0.8950 (tt0) REVERT: I 1034 ARG cc_start: 0.8584 (mmp80) cc_final: 0.8242 (mmp80) REVERT: I 1233 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9119 (mt) REVERT: I 1273 MET cc_start: 0.9325 (mmm) cc_final: 0.9081 (mtt) REVERT: I 1322 SER cc_start: 0.8989 (m) cc_final: 0.8716 (m) REVERT: J 213 LYS cc_start: 0.9183 (tppt) cc_final: 0.8953 (tppt) REVERT: J 304 ASP cc_start: 0.8344 (m-30) cc_final: 0.8090 (m-30) REVERT: J 515 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.7212 (mmm-85) REVERT: J 740 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8533 (mp) REVERT: J 802 ASP cc_start: 0.8565 (m-30) cc_final: 0.8067 (m-30) REVERT: J 811 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8152 (mt-10) REVERT: J 873 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8076 (mt-10) REVERT: J 954 ASN cc_start: 0.8030 (t0) cc_final: 0.7690 (t0) REVERT: J 1167 LYS cc_start: 0.9105 (tppt) cc_final: 0.8793 (tppt) REVERT: J 1199 PHE cc_start: 0.9010 (m-80) cc_final: 0.8733 (m-80) REVERT: J 1345 ARG cc_start: 0.8390 (mtp-110) cc_final: 0.8121 (ttm-80) REVERT: K 43 ASN cc_start: 0.9109 (t0) cc_final: 0.8724 (t0) REVERT: K 55 GLU cc_start: 0.8626 (pt0) cc_final: 0.8337 (pt0) REVERT: K 69 ARG cc_start: 0.8921 (ttm110) cc_final: 0.8484 (tpp-160) outliers start: 71 outliers final: 47 residues processed: 386 average time/residue: 0.1944 time to fit residues: 115.2201 Evaluate side-chains 372 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 318 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 202 ARG Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 439 LYS Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 692 THR Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 876 GLU Chi-restraints excluded: chain I residue 980 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 515 ARG Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 873 GLU Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1353 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 150 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 334 optimal weight: 0.9990 chunk 238 optimal weight: 1.9990 chunk 256 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 322 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 307 optimal weight: 40.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1264 GLN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.141192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.089743 restraints weight = 47956.853| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.42 r_work: 0.3046 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28522 Z= 0.136 Angle : 0.561 10.867 38871 Z= 0.289 Chirality : 0.041 0.199 4441 Planarity : 0.004 0.059 4806 Dihedral : 13.895 86.504 4583 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.72 % Allowed : 15.92 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.46 (0.15), residues: 3340 helix: 1.37 (0.15), residues: 1204 sheet: -0.48 (0.26), residues: 427 loop : -1.55 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 47 TYR 0.014 0.001 TYR J 631 PHE 0.008 0.001 PHE I 514 TRP 0.014 0.001 TRP C 68 HIS 0.003 0.001 HIS C 162 Details of bonding type rmsd covalent geometry : bond 0.00311 (28514) covalent geometry : angle 0.56073 (38859) hydrogen bonds : bond 0.03723 ( 1103) hydrogen bonds : angle 4.34688 ( 3092) metal coordination : bond 0.00502 ( 8) metal coordination : angle 1.06072 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 354 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 MET cc_start: 0.8849 (mmt) cc_final: 0.8405 (tpp) REVERT: C 104 TYR cc_start: 0.6559 (m-80) cc_final: 0.6172 (m-80) REVERT: C 108 ASP cc_start: 0.8209 (t0) cc_final: 0.7691 (t0) REVERT: C 154 PHE cc_start: 0.9328 (m-80) cc_final: 0.9010 (m-10) REVERT: C 159 PHE cc_start: 0.8783 (m-10) cc_final: 0.8434 (m-10) REVERT: C 182 HIS cc_start: 0.8658 (m90) cc_final: 0.8090 (m90) REVERT: H 188 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8493 (mp0) REVERT: I 239 MET cc_start: 0.8770 (ppp) cc_final: 0.8240 (ppp) REVERT: I 949 GLU cc_start: 0.9114 (tt0) cc_final: 0.8768 (tt0) REVERT: I 1233 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9168 (mt) REVERT: I 1322 SER cc_start: 0.8950 (m) cc_final: 0.8685 (m) REVERT: J 213 LYS cc_start: 0.9175 (tppt) cc_final: 0.8938 (tppt) REVERT: J 304 ASP cc_start: 0.8267 (m-30) cc_final: 0.8062 (m-30) REVERT: J 515 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.6923 (mmm-85) REVERT: J 802 ASP cc_start: 0.8481 (m-30) cc_final: 0.8135 (m-30) REVERT: J 811 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8184 (mt-10) REVERT: J 873 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: J 954 ASN cc_start: 0.8040 (t0) cc_final: 0.7677 (t0) REVERT: J 1167 LYS cc_start: 0.9135 (tppt) cc_final: 0.8824 (tppt) REVERT: J 1199 PHE cc_start: 0.8979 (m-80) cc_final: 0.8710 (m-80) REVERT: J 1345 ARG cc_start: 0.8189 (mtp-110) cc_final: 0.7955 (ttm-80) REVERT: K 43 ASN cc_start: 0.9048 (t0) cc_final: 0.8769 (t0) REVERT: K 74 GLU cc_start: 0.9381 (tm-30) cc_final: 0.8921 (pp20) outliers start: 49 outliers final: 36 residues processed: 384 average time/residue: 0.1948 time to fit residues: 115.0073 Evaluate side-chains 379 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 340 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 876 GLU Chi-restraints excluded: chain I residue 980 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 515 ARG Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 873 GLU Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1353 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 31 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 199 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 chunk 62 optimal weight: 0.0050 chunk 0 optimal weight: 10.0000 chunk 181 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 261 optimal weight: 0.8980 chunk 301 optimal weight: 50.0000 chunk 243 optimal weight: 0.6980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 952 GLN I1264 GLN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.141919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.090688 restraints weight = 48164.407| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.42 r_work: 0.3024 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28522 Z= 0.125 Angle : 0.559 10.888 38871 Z= 0.287 Chirality : 0.041 0.191 4441 Planarity : 0.004 0.057 4806 Dihedral : 13.817 87.940 4580 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.03 % Allowed : 15.99 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.35 (0.15), residues: 3340 helix: 1.41 (0.15), residues: 1210 sheet: -0.43 (0.26), residues: 419 loop : -1.45 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 275 TYR 0.013 0.001 TYR J 631 PHE 0.011 0.001 PHE C 159 TRP 0.013 0.001 TRP C 68 HIS 0.003 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00287 (28514) covalent geometry : angle 0.55932 (38859) hydrogen bonds : bond 0.03575 ( 1103) hydrogen bonds : angle 4.29908 ( 3092) metal coordination : bond 0.00438 ( 8) metal coordination : angle 0.89635 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 347 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 MET cc_start: 0.9540 (ppp) cc_final: 0.9064 (pmm) REVERT: C 104 TYR cc_start: 0.6579 (m-80) cc_final: 0.6230 (m-80) REVERT: C 108 ASP cc_start: 0.8200 (t0) cc_final: 0.7619 (t0) REVERT: C 154 PHE cc_start: 0.9306 (m-80) cc_final: 0.8997 (m-10) REVERT: C 182 HIS cc_start: 0.8630 (m90) cc_final: 0.8059 (m90) REVERT: G 33 ARG cc_start: 0.7649 (mpt180) cc_final: 0.7430 (mpt180) REVERT: H 188 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8561 (mp0) REVERT: I 239 MET cc_start: 0.8721 (ppp) cc_final: 0.8292 (ppp) REVERT: I 272 ARG cc_start: 0.9227 (tpt90) cc_final: 0.8967 (tpm170) REVERT: I 1210 ILE cc_start: 0.9159 (tt) cc_final: 0.8909 (pt) REVERT: I 1233 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9122 (mt) REVERT: I 1322 SER cc_start: 0.8934 (m) cc_final: 0.8642 (m) REVERT: J 213 LYS cc_start: 0.9179 (tppt) cc_final: 0.8931 (tppt) REVERT: J 304 ASP cc_start: 0.8277 (m-30) cc_final: 0.8063 (m-30) REVERT: J 515 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.6818 (mmm-85) REVERT: J 545 HIS cc_start: 0.9239 (OUTLIER) cc_final: 0.8256 (m90) REVERT: J 802 ASP cc_start: 0.8510 (m-30) cc_final: 0.8177 (m-30) REVERT: J 873 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: J 954 ASN cc_start: 0.8098 (t0) cc_final: 0.7743 (t0) REVERT: J 1167 LYS cc_start: 0.9130 (tppt) cc_final: 0.8808 (tppt) REVERT: J 1199 PHE cc_start: 0.8964 (m-80) cc_final: 0.8699 (m-80) REVERT: J 1345 ARG cc_start: 0.8176 (mtp-110) cc_final: 0.7933 (ttm-80) REVERT: K 43 ASN cc_start: 0.9107 (t0) cc_final: 0.8802 (t0) REVERT: K 74 GLU cc_start: 0.9390 (tm-30) cc_final: 0.8950 (pp20) outliers start: 58 outliers final: 36 residues processed: 385 average time/residue: 0.1904 time to fit residues: 114.1507 Evaluate side-chains 379 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 339 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 876 GLU Chi-restraints excluded: chain I residue 980 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 515 ARG Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 873 GLU Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1353 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 286 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 247 optimal weight: 0.1980 chunk 157 optimal weight: 2.9990 chunk 222 optimal weight: 0.6980 chunk 131 optimal weight: 6.9990 chunk 25 optimal weight: 0.0170 chunk 314 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.142673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.091760 restraints weight = 48026.884| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.42 r_work: 0.3042 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28522 Z= 0.116 Angle : 0.565 10.759 38871 Z= 0.288 Chirality : 0.041 0.190 4441 Planarity : 0.004 0.058 4806 Dihedral : 13.779 89.777 4580 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.72 % Allowed : 16.56 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.15), residues: 3340 helix: 1.44 (0.15), residues: 1213 sheet: -0.36 (0.26), residues: 419 loop : -1.40 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 275 TYR 0.012 0.001 TYR G 177 PHE 0.010 0.001 PHE I 35 TRP 0.012 0.001 TRP C 68 HIS 0.003 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00263 (28514) covalent geometry : angle 0.56493 (38859) hydrogen bonds : bond 0.03417 ( 1103) hydrogen bonds : angle 4.25303 ( 3092) metal coordination : bond 0.00336 ( 8) metal coordination : angle 0.84354 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 359 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 TYR cc_start: 0.6696 (m-80) cc_final: 0.6313 (m-80) REVERT: C 108 ASP cc_start: 0.8151 (t0) cc_final: 0.7539 (t0) REVERT: C 154 PHE cc_start: 0.9119 (m-80) cc_final: 0.8873 (m-10) REVERT: C 182 HIS cc_start: 0.8654 (m90) cc_final: 0.8073 (m90) REVERT: G 62 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.8000 (p0) REVERT: H 188 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8662 (mm-30) REVERT: I 239 MET cc_start: 0.8655 (ppp) cc_final: 0.8257 (ppp) REVERT: I 949 GLU cc_start: 0.9157 (tt0) cc_final: 0.8933 (tt0) REVERT: I 1034 ARG cc_start: 0.8466 (mmp80) cc_final: 0.8239 (mmp80) REVERT: I 1233 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9097 (mt) REVERT: I 1322 SER cc_start: 0.8936 (m) cc_final: 0.8623 (m) REVERT: J 213 LYS cc_start: 0.9169 (tppt) cc_final: 0.8917 (tppt) REVERT: J 304 ASP cc_start: 0.8233 (m-30) cc_final: 0.8020 (m-30) REVERT: J 515 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.6760 (mmm-85) REVERT: J 545 HIS cc_start: 0.9202 (OUTLIER) cc_final: 0.8190 (m90) REVERT: J 645 VAL cc_start: 0.9222 (m) cc_final: 0.8984 (m) REVERT: J 802 ASP cc_start: 0.8553 (m-30) cc_final: 0.8237 (m-30) REVERT: J 873 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.8054 (mt-10) REVERT: J 954 ASN cc_start: 0.8150 (t0) cc_final: 0.7801 (t0) REVERT: J 1167 LYS cc_start: 0.9124 (tppt) cc_final: 0.8801 (tppt) REVERT: J 1199 PHE cc_start: 0.8952 (m-80) cc_final: 0.8688 (m-80) REVERT: J 1345 ARG cc_start: 0.8175 (mtp-110) cc_final: 0.7912 (ttm-80) REVERT: K 43 ASN cc_start: 0.9129 (t0) cc_final: 0.8822 (t0) REVERT: K 55 GLU cc_start: 0.8509 (pt0) cc_final: 0.8305 (pt0) outliers start: 49 outliers final: 35 residues processed: 390 average time/residue: 0.1895 time to fit residues: 114.4433 Evaluate side-chains 386 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 346 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 692 THR Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 980 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 515 ARG Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 873 GLU Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1353 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 252 optimal weight: 0.9990 chunk 154 optimal weight: 6.9990 chunk 224 optimal weight: 10.0000 chunk 259 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 301 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN I 330 HIS ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.139373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.087458 restraints weight = 48114.676| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.41 r_work: 0.2959 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 28522 Z= 0.233 Angle : 0.624 13.206 38871 Z= 0.318 Chirality : 0.043 0.203 4441 Planarity : 0.004 0.058 4806 Dihedral : 13.850 88.359 4580 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.54 % Allowed : 16.84 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.15), residues: 3340 helix: 1.34 (0.15), residues: 1207 sheet: -0.37 (0.26), residues: 416 loop : -1.42 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 275 TYR 0.021 0.001 TYR J 631 PHE 0.021 0.001 PHE G 231 TRP 0.011 0.001 TRP C 68 HIS 0.009 0.001 HIS C 170 Details of bonding type rmsd covalent geometry : bond 0.00547 (28514) covalent geometry : angle 0.62370 (38859) hydrogen bonds : bond 0.04060 ( 1103) hydrogen bonds : angle 4.37946 ( 3092) metal coordination : bond 0.00932 ( 8) metal coordination : angle 0.90633 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 336 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 TYR cc_start: 0.6730 (m-80) cc_final: 0.6333 (m-80) REVERT: C 108 ASP cc_start: 0.8231 (t0) cc_final: 0.7778 (t0) REVERT: C 154 PHE cc_start: 0.9216 (m-80) cc_final: 0.8988 (m-10) REVERT: C 159 PHE cc_start: 0.9022 (m-10) cc_final: 0.8726 (m-10) REVERT: C 182 HIS cc_start: 0.8779 (m90) cc_final: 0.8193 (m90) REVERT: G 62 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.8020 (p0) REVERT: G 95 LYS cc_start: 0.8939 (mttp) cc_final: 0.8546 (mtmm) REVERT: G 200 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8187 (ttpp) REVERT: G 226 GLU cc_start: 0.8239 (pt0) cc_final: 0.7630 (pt0) REVERT: H 10 LYS cc_start: 0.9014 (mtpt) cc_final: 0.8603 (mtmm) REVERT: I 239 MET cc_start: 0.8653 (ppp) cc_final: 0.8230 (ppp) REVERT: I 315 MET cc_start: 0.8843 (ttp) cc_final: 0.7962 (mtm) REVERT: I 949 GLU cc_start: 0.9171 (tt0) cc_final: 0.8945 (tt0) REVERT: I 1233 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9085 (mt) REVERT: I 1322 SER cc_start: 0.8971 (m) cc_final: 0.8668 (m) REVERT: J 213 LYS cc_start: 0.9181 (tppt) cc_final: 0.8937 (tppt) REVERT: J 304 ASP cc_start: 0.8324 (m-30) cc_final: 0.8114 (m-30) REVERT: J 515 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.6841 (mmm-85) REVERT: J 545 HIS cc_start: 0.9337 (OUTLIER) cc_final: 0.8559 (m90) REVERT: J 802 ASP cc_start: 0.8547 (m-30) cc_final: 0.8041 (m-30) REVERT: J 811 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8240 (mt-10) REVERT: J 873 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8056 (mt-10) REVERT: J 954 ASN cc_start: 0.8195 (t0) cc_final: 0.7831 (t0) REVERT: J 1167 LYS cc_start: 0.9146 (tppt) cc_final: 0.8825 (tppt) REVERT: J 1199 PHE cc_start: 0.9006 (m-80) cc_final: 0.8741 (m-80) REVERT: J 1345 ARG cc_start: 0.8269 (mtp-110) cc_final: 0.7946 (ttm-80) REVERT: K 43 ASN cc_start: 0.9123 (t0) cc_final: 0.8827 (t0) REVERT: K 55 GLU cc_start: 0.8605 (pt0) cc_final: 0.8394 (pt0) REVERT: K 69 ARG cc_start: 0.8928 (ttm110) cc_final: 0.8450 (tpp-160) outliers start: 44 outliers final: 35 residues processed: 367 average time/residue: 0.1932 time to fit residues: 110.0249 Evaluate side-chains 368 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 327 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 692 THR Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 980 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 515 ARG Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 873 GLU Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1353 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 210 optimal weight: 0.0970 chunk 110 optimal weight: 2.9990 chunk 225 optimal weight: 1.9990 chunk 263 optimal weight: 0.0980 chunk 148 optimal weight: 0.9980 chunk 159 optimal weight: 0.6980 chunk 319 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 266 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 314 ASN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN K 15 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.142114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.091090 restraints weight = 48014.521| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.42 r_work: 0.3070 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28522 Z= 0.121 Angle : 0.581 10.977 38871 Z= 0.296 Chirality : 0.041 0.262 4441 Planarity : 0.004 0.058 4806 Dihedral : 13.764 87.047 4580 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.25 % Favored : 95.72 % Rotamer: Outliers : 1.51 % Allowed : 17.26 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.15), residues: 3340 helix: 1.39 (0.15), residues: 1212 sheet: -0.41 (0.26), residues: 415 loop : -1.33 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 67 TYR 0.013 0.001 TYR G 177 PHE 0.024 0.001 PHE C 159 TRP 0.010 0.001 TRP C 68 HIS 0.005 0.001 HIS C 162 Details of bonding type rmsd covalent geometry : bond 0.00277 (28514) covalent geometry : angle 0.58115 (38859) hydrogen bonds : bond 0.03499 ( 1103) hydrogen bonds : angle 4.27043 ( 3092) metal coordination : bond 0.00372 ( 8) metal coordination : angle 0.91691 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9332.33 seconds wall clock time: 159 minutes 30.55 seconds (9570.55 seconds total)