Starting phenix.real_space_refine on Mon Sep 14 04:04:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uwh_26832/09_2026/7uwh_26832.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uwh_26832/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7uwh_26832/09_2026/7uwh_26832.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uwh_26832/09_2026/7uwh_26832.cif" model { file = "/net/cci-nas-00/data/ceres_data/7uwh_26832/09_2026/7uwh_26832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uwh_26832/09_2026/7uwh_26832.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uwh_26832/09_2026/7uwh_26832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uwh_26832/09_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): 0.15s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 'RNAv2': 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: {'RNAv2': 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: 5.73, per 1000 atoms: 0.21 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: 2.48 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: 4.10 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: 7.14 Time building geometry restraints manager: 3.32 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=" O3' DA A 26 " pdb=" P DC A 27 " ideal model delta sigma weight residual 1.607 1.665 -0.058 1.20e-02 6.94e+03 2.34e+01 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=" 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: 38008 2.19 - 4.38: 755 4.38 - 6.57: 79 6.57 - 8.76: 9 8.76 - 10.95: 2 Bond angle restraints: 38853 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=" C3' DA A 26 " pdb=" O3' DA A 26 " pdb=" P DC A 27 " ideal model delta sigma weight residual 119.70 125.68 -5.98 1.20e+00 6.94e-01 2.48e+01 ... (remaining 38848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 15534 18.07 - 36.14: 1172 36.14 - 54.21: 437 54.21 - 72.28: 123 72.28 - 90.35: 37 Dihedral angle restraints: 17303 sinusoidal: 7651 harmonic: 9652 Sorted by residual: dihedral pdb=" C4' C R 11 " pdb=" C3' C R 11 " pdb=" C2' C R 11 " pdb=" C1' C R 11 " ideal model delta sinusoidal sigma weight residual 36.34 -35.45 71.79 1 3.10e+00 1.04e-01 6.87e+02 dihedral pdb=" O4' C R 11 " pdb=" C4' C R 11 " pdb=" C3' C R 11 " pdb=" C2' C R 11 " ideal model delta sinusoidal sigma weight residual -35.15 24.16 -59.31 1 4.00e+00 6.25e-02 2.94e+02 dihedral pdb=" O4' C R 11 " pdb=" C2' C R 11 " pdb=" C1' C R 11 " pdb=" C3' C R 11 " ideal model delta sinusoidal sigma weight residual -94.41 -35.47 -58.94 3 3.80e+00 6.93e-02 1.48e+02 ... (remaining 17300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3969 0.078 - 0.157: 427 0.157 - 0.235: 33 0.235 - 0.313: 6 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: 2.120 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: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 33.880 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 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: 38.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 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= 0.272 Angle : 0.723 18.232 38865 Z= 0.452 Chirality : 0.050 0.392 4441 Planarity : 0.004 0.056 4806 Dihedral : 15.662 90.351 11091 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/Z covalent geometry : bond 0.00336 / 0.21 (28514) covalent geometry : angle 0.69939 / 0.45 (38853) hydrogen bonds : bond 0.16869 / 19.34 ( 1103) hydrogen bonds : angle 6.51528 / 6.73 ( 3092) metal coordination : bond 0.30241 / 28.81 ( 8) metal coordination : angle 10.45164 / 19.16 ( 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 : 1.063 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: 0.2265 time to fit residues: 178.7167 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 : 1.109 ------------------------------------------------------------------------------- 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... ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 HIS H 132 HIS I 314 ASN I 834 GLN I1257 GLN I1264 GLN J 209 ASN J 274 ASN J 489 ASN J 594 GLN J 651 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 = 0.4034 r_free = 0.4034 target = 0.144921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.094337 restraints weight = 48359.793| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.45 r_work: 0.3083 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28522 Z= 0.175 Angle : 0.636 13.463 38865 Z= 0.330 Chirality : 0.047 1.002 4441 Planarity : 0.005 0.058 4806 Dihedral : 14.018 89.543 4552 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.26 % Allowed : 9.79 % Favored : 88.95 % 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: -0.80 (0.14), residues: 3340 helix: 1.14 (0.15), residues: 1210 sheet: -0.69 (0.26), residues: 401 loop : -1.79 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 20 TYR 0.021 0.001 TYR H 177 PHE 0.018 0.001 PHE C 169 TRP 0.021 0.001 TRP J1020 HIS 0.006 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (28514) covalent geometry : angle 0.63460 / 0.33 (38853) hydrogen bonds : bond 0.04595 / 5.14 ( 1103) hydrogen bonds : angle 4.96703 / 5.18 ( 3092) metal coordination : bond 0.01637 / 1.64 ( 8) metal coordination : angle 2.69696 / 5.25 ( 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 428 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 392 time to evaluate : 1.109 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: C 57 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8982 (mt) REVERT: C 108 ASP cc_start: 0.8090 (t0) cc_final: 0.7570 (t0) REVERT: C 124 LYS cc_start: 0.9097 (tptp) cc_final: 0.8806 (tptp) REVERT: C 147 MET cc_start: 0.9097 (tpp) cc_final: 0.8773 (tpt) REVERT: C 173 LYS cc_start: 0.9694 (mmmm) cc_final: 0.9359 (mmmm) REVERT: C 182 HIS cc_start: 0.8301 (m90) cc_final: 0.7947 (m90) REVERT: G 86 LYS cc_start: 0.9423 (ttpp) cc_final: 0.9064 (tttm) REVERT: H 75 GLN cc_start: 0.8445 (tm-30) cc_final: 0.7720 (tm-30) REVERT: H 80 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8164 (mt-10) REVERT: H 186 ASN cc_start: 0.8362 (t0) cc_final: 0.7989 (t0) REVERT: I 239 MET cc_start: 0.8393 (ppp) cc_final: 0.7475 (tmm) REVERT: I 330 HIS cc_start: 0.7463 (m-70) cc_final: 0.6931 (m90) REVERT: I 545 PHE cc_start: 0.8193 (t80) cc_final: 0.7792 (t80) REVERT: I 1017 GLN cc_start: 0.8050 (tm-30) cc_final: 0.7766 (tm-30) REVERT: I 1024 GLU cc_start: 0.8315 (pt0) cc_final: 0.8089 (pt0) REVERT: I 1329 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8319 (mt-10) REVERT: J 128 LEU cc_start: 0.9382 (mt) cc_final: 0.9092 (mt) REVERT: J 802 ASP cc_start: 0.8353 (m-30) cc_final: 0.7987 (m-30) REVERT: J 1195 GLN cc_start: 0.8553 (tm-30) cc_final: 0.8286 (tm-30) REVERT: J 1199 PHE cc_start: 0.9005 (m-80) cc_final: 0.8483 (m-80) REVERT: J 1212 ASP cc_start: 0.8475 (m-30) cc_final: 0.8126 (m-30) REVERT: J 1330 ARG cc_start: 0.8738 (ttp80) cc_final: 0.8501 (ttp80) REVERT: K 43 ASN cc_start: 0.8820 (t0) cc_final: 0.8620 (t0) REVERT: K 55 GLU cc_start: 0.8458 (pt0) cc_final: 0.8196 (pt0) REVERT: K 70 GLN cc_start: 0.8613 (tm-30) cc_final: 0.8338 (tm-30) REVERT: K 73 GLN cc_start: 0.8697 (pp30) cc_final: 0.8493 (pp30) outliers start: 36 outliers final: 18 residues processed: 415 average time/residue: 0.2225 time to fit residues: 140.7779 Evaluate side-chains 369 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 350 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 50 SER Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 980 VAL 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 K residue 66 VAL 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: 10.0000 chunk 131 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 319 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 chunk 315 optimal weight: 0.0470 chunk 265 optimal weight: 7.9990 chunk 316 optimal weight: 2.9990 overall best weight: 2.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN I 834 GLN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J 424 ASN J 651 HIS J 951 GLN J 954 ASN J1218 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.140526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.088433 restraints weight = 48452.194| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.43 r_work: 0.2975 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 28522 Z= 0.279 Angle : 0.659 10.765 38865 Z= 0.342 Chirality : 0.046 0.477 4441 Planarity : 0.005 0.060 4806 Dihedral : 13.969 97.087 4539 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.10 % Allowed : 11.12 % Favored : 86.78 % 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: -0.81 (0.14), residues: 3340 helix: 1.19 (0.15), residues: 1203 sheet: -0.67 (0.25), residues: 429 loop : -1.85 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 378 TYR 0.029 0.002 TYR H 177 PHE 0.025 0.002 PHE G 231 TRP 0.041 0.002 TRP J1020 HIS 0.020 0.002 HIS G 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.28 (28514) covalent geometry : angle 0.65806 / 0.34 (38853) hydrogen bonds : bond 0.04660 / 5.15 ( 1103) hydrogen bonds : angle 4.78980 / 5.12 ( 3092) metal coordination : bond 0.01291 / 1.25 ( 8) metal coordination : angle 2.31587 / 4.46 ( 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 417 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 357 time to evaluate : 1.016 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: C 57 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9076 (mt) REVERT: C 88 MET cc_start: 0.8764 (tpp) cc_final: 0.8290 (tpp) REVERT: C 108 ASP cc_start: 0.8133 (t0) cc_final: 0.7598 (t0) REVERT: C 124 LYS cc_start: 0.8932 (tptp) cc_final: 0.8639 (tptp) REVERT: C 140 LYS cc_start: 0.9486 (tptp) cc_final: 0.9266 (tptp) REVERT: C 173 LYS cc_start: 0.9698 (mmmm) cc_final: 0.9416 (mmmm) REVERT: C 182 HIS cc_start: 0.8371 (m90) cc_final: 0.8066 (m90) REVERT: G 62 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7555 (p0) REVERT: G 200 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8333 (ttpt) REVERT: H 75 GLN cc_start: 0.8480 (tm-30) cc_final: 0.7745 (tm-30) REVERT: H 80 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8302 (mt-10) REVERT: H 188 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8492 (mm-30) REVERT: I 239 MET cc_start: 0.8527 (ppp) cc_final: 0.7624 (tmm) REVERT: I 315 MET cc_start: 0.8898 (tpp) cc_final: 0.8628 (tpp) REVERT: I 330 HIS cc_start: 0.7958 (m-70) cc_final: 0.7657 (m-70) REVERT: I 478 ARG cc_start: 0.8471 (ttp80) cc_final: 0.8271 (ttp80) REVERT: I 488 MET cc_start: 0.8850 (mmm) cc_final: 0.8006 (mmm) REVERT: I 545 PHE cc_start: 0.8285 (t80) cc_final: 0.7942 (t80) REVERT: I 685 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8970 (mtt) REVERT: I 1024 GLU cc_start: 0.8361 (pt0) cc_final: 0.8111 (pt0) REVERT: I 1273 MET cc_start: 0.9333 (mmm) cc_final: 0.9028 (mtt) REVERT: I 1322 SER cc_start: 0.8991 (m) cc_final: 0.8756 (m) REVERT: J 154 LEU cc_start: 0.8061 (mp) cc_final: 0.7859 (mp) REVERT: J 161 THR cc_start: 0.9500 (OUTLIER) cc_final: 0.9039 (p) REVERT: J 802 ASP cc_start: 0.8562 (m-30) cc_final: 0.7979 (m-30) REVERT: J 1199 PHE cc_start: 0.9004 (m-80) cc_final: 0.8562 (m-80) REVERT: K 18 ASP cc_start: 0.8415 (m-30) cc_final: 0.8197 (m-30) REVERT: K 43 ASN cc_start: 0.8960 (t0) cc_final: 0.8661 (t0) REVERT: K 55 GLU cc_start: 0.8554 (pt0) cc_final: 0.8260 (pt0) REVERT: K 69 ARG cc_start: 0.8996 (ttm110) cc_final: 0.8524 (tpp-160) outliers start: 60 outliers final: 35 residues processed: 397 average time/residue: 0.2076 time to fit residues: 127.7925 Evaluate side-chains 371 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 331 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 237 LEU 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 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 159 ILE Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 410 ASP 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 33 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 312 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 329 optimal weight: 0.8980 chunk 184 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS G 160 HIS ** I 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1264 GLN J 266 ASN J 365 GLN J 951 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.142460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.091119 restraints weight = 47955.717| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.43 r_work: 0.3022 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28522 Z= 0.144 Angle : 0.570 8.854 38865 Z= 0.298 Chirality : 0.043 0.262 4441 Planarity : 0.004 0.057 4806 Dihedral : 13.842 131.450 4535 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.68 % Allowed : 12.63 % Favored : 85.69 % 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: -0.65 (0.14), residues: 3340 helix: 1.27 (0.15), residues: 1212 sheet: -0.58 (0.27), residues: 406 loop : -1.72 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 47 TYR 0.017 0.001 TYR H 177 PHE 0.014 0.001 PHE I1025 TRP 0.024 0.001 TRP C 68 HIS 0.007 0.001 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (28514) covalent geometry : angle 0.56877 / 0.30 (38853) hydrogen bonds : bond 0.03998 / 4.39 ( 1103) hydrogen bonds : angle 4.57583 / 4.86 ( 3092) metal coordination : bond 0.00591 / 0.56 ( 8) metal coordination : angle 2.04090 / 3.79 ( 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 413 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 365 time to evaluate : 1.054 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: C 57 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9103 (mt) REVERT: C 62 LYS cc_start: 0.9477 (tppp) cc_final: 0.9217 (tptt) REVERT: C 88 MET cc_start: 0.8495 (tpp) cc_final: 0.7660 (tpp) REVERT: C 108 ASP cc_start: 0.7985 (t0) cc_final: 0.7394 (t0) REVERT: C 124 LYS cc_start: 0.9062 (tptp) cc_final: 0.8841 (tptp) REVERT: C 147 MET cc_start: 0.8857 (tpp) cc_final: 0.8589 (tpt) REVERT: C 154 PHE cc_start: 0.9226 (m-10) cc_final: 0.8914 (m-10) REVERT: C 182 HIS cc_start: 0.8468 (m90) cc_final: 0.8006 (m90) REVERT: G 200 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8269 (ttpt) REVERT: H 41 ASN cc_start: 0.9070 (t0) cc_final: 0.8820 (t0) REVERT: H 75 GLN cc_start: 0.8445 (tm-30) cc_final: 0.7675 (tm-30) REVERT: I 202 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8746 (ptt90) REVERT: I 239 MET cc_start: 0.8681 (ppp) cc_final: 0.7957 (tmm) REVERT: I 330 HIS cc_start: 0.8053 (m-70) cc_final: 0.7701 (m-70) REVERT: I 488 MET cc_start: 0.8872 (mmm) cc_final: 0.8103 (mmm) REVERT: I 685 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8570 (mtt) REVERT: I 696 ASP cc_start: 0.7846 (t0) cc_final: 0.7636 (t0) REVERT: I 1273 MET cc_start: 0.9271 (mmm) cc_final: 0.8938 (mtt) REVERT: I 1322 SER cc_start: 0.8975 (m) cc_final: 0.8746 (m) REVERT: J 161 THR cc_start: 0.9445 (OUTLIER) cc_final: 0.9002 (p) REVERT: J 515 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.6942 (mmm-85) REVERT: J 697 MET cc_start: 0.9179 (tmm) cc_final: 0.8877 (tmm) REVERT: J 740 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8362 (mp) REVERT: J 802 ASP cc_start: 0.8535 (m-30) cc_final: 0.8026 (m-30) REVERT: J 1167 LYS cc_start: 0.9014 (tppt) cc_final: 0.8776 (tppt) REVERT: J 1199 PHE cc_start: 0.9032 (m-80) cc_final: 0.8636 (m-80) REVERT: K 43 ASN cc_start: 0.8964 (t0) cc_final: 0.8656 (t0) REVERT: K 55 GLU cc_start: 0.8525 (pt0) cc_final: 0.8249 (pt0) REVERT: K 69 ARG cc_start: 0.9005 (ttm110) cc_final: 0.8463 (tpp-160) outliers start: 48 outliers final: 27 residues processed: 393 average time/residue: 0.2131 time to fit residues: 128.1996 Evaluate side-chains 371 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 337 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain I residue 202 ARG 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 539 THR 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 980 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 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 740 LEU Chi-restraints excluded: chain J residue 901 ARG 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 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: 3.9990 chunk 198 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 275 optimal weight: 0.4980 chunk 241 optimal weight: 0.7980 chunk 206 optimal weight: 1.9990 chunk 296 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 238 GLN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 594 GLN J 951 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.140799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.088816 restraints weight = 48055.587| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.42 r_work: 0.2937 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 28522 Z= 0.215 Angle : 0.593 10.848 38865 Z= 0.310 Chirality : 0.044 0.234 4441 Planarity : 0.004 0.056 4806 Dihedral : 13.787 141.592 4535 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.24 % Favored : 94.73 % Rotamer: Outliers : 2.35 % Allowed : 13.08 % Favored : 84.57 % 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: 1.33 (0.15), residues: 1200 sheet: -0.55 (0.26), residues: 425 loop : -1.72 (0.14), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 272 TYR 0.018 0.001 TYR J 631 PHE 0.018 0.001 PHE I1025 TRP 0.023 0.001 TRP C 68 HIS 0.009 0.001 HIS J 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 (28514) covalent geometry : angle 0.59188 / 0.31 (38853) hydrogen bonds : bond 0.04174 / 4.59 ( 1103) hydrogen bonds : angle 4.55315 / 4.89 ( 3092) metal coordination : bond 0.00854 / 0.81 ( 8) metal coordination : angle 2.21910 / 4.20 ( 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 406 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 339 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9139 (mt) REVERT: C 62 LYS cc_start: 0.9464 (tppp) cc_final: 0.9248 (tptt) REVERT: C 108 ASP cc_start: 0.7980 (t0) cc_final: 0.7335 (t0) REVERT: C 117 MET cc_start: 0.4350 (tmm) cc_final: 0.4096 (tmm) REVERT: C 124 LYS cc_start: 0.9076 (tptp) cc_final: 0.8815 (tptp) REVERT: C 147 MET cc_start: 0.8791 (tpp) cc_final: 0.8458 (tpt) REVERT: C 151 ASP cc_start: 0.9437 (t0) cc_final: 0.9172 (t0) REVERT: C 154 PHE cc_start: 0.9211 (m-80) cc_final: 0.8929 (m-10) REVERT: C 182 HIS cc_start: 0.8520 (m90) cc_final: 0.8029 (m90) REVERT: G 200 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8286 (ttpt) REVERT: H 41 ASN cc_start: 0.9159 (t0) cc_final: 0.8856 (t0) REVERT: H 75 GLN cc_start: 0.8463 (tm-30) cc_final: 0.7659 (tm-30) REVERT: H 186 ASN cc_start: 0.8454 (t0) cc_final: 0.8091 (t0) REVERT: H 188 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8573 (mm-30) REVERT: I 202 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8639 (ptt90) REVERT: I 239 MET cc_start: 0.8702 (ppp) cc_final: 0.8184 (tmm) REVERT: I 330 HIS cc_start: 0.8173 (m-70) cc_final: 0.7792 (m-70) REVERT: I 488 MET cc_start: 0.8942 (mmm) cc_final: 0.8211 (mmm) REVERT: I 685 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8927 (mtt) REVERT: I 1273 MET cc_start: 0.9317 (mmm) cc_final: 0.9031 (mtt) REVERT: I 1296 ASP cc_start: 0.8615 (t0) cc_final: 0.8162 (t70) REVERT: I 1322 SER cc_start: 0.8941 (m) cc_final: 0.8634 (m) REVERT: I 1327 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9179 (mt) REVERT: J 161 THR cc_start: 0.9372 (OUTLIER) cc_final: 0.8918 (p) REVERT: J 515 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.6940 (mmm-85) REVERT: J 697 MET cc_start: 0.9226 (tmm) cc_final: 0.8923 (tmm) REVERT: J 740 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8390 (mp) REVERT: J 802 ASP cc_start: 0.8649 (m-30) cc_final: 0.8107 (m-30) REVERT: J 1167 LYS cc_start: 0.9051 (tppt) cc_final: 0.8782 (tppt) REVERT: J 1199 PHE cc_start: 0.8941 (m-80) cc_final: 0.8591 (m-80) REVERT: K 43 ASN cc_start: 0.9073 (t0) cc_final: 0.8727 (t0) REVERT: K 55 GLU cc_start: 0.8568 (pt0) cc_final: 0.8290 (pt0) REVERT: K 69 ARG cc_start: 0.8990 (ttm110) cc_final: 0.8481 (tpp-160) outliers start: 67 outliers final: 41 residues processed: 384 average time/residue: 0.2004 time to fit residues: 119.2972 Evaluate side-chains 376 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 327 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 LEU 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 176 CYS Chi-restraints excluded: chain H residue 183 ILE 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 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 1075 VAL 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 1297 ASP Chi-restraints excluded: chain I residue 1327 LEU 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 161 THR Chi-restraints excluded: chain J residue 410 ASP 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 740 LEU Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 901 ARG 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 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: 10.0000 chunk 227 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 214 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 220 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 335 GLN J 365 GLN J 594 GLN ** J 954 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 = 0.3948 r_free = 0.3948 target = 0.138359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.085906 restraints weight = 48279.654| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.41 r_work: 0.2914 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 28522 Z= 0.348 Angle : 0.680 9.892 38865 Z= 0.354 Chirality : 0.047 0.245 4441 Planarity : 0.005 0.108 4806 Dihedral : 13.791 138.373 4535 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.78 % Favored : 94.19 % Rotamer: Outliers : 2.53 % Allowed : 14.03 % Favored : 83.44 % 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: -0.74 (0.14), residues: 3340 helix: 1.16 (0.15), residues: 1200 sheet: -0.52 (0.26), residues: 411 loop : -1.75 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 272 TYR 0.026 0.002 TYR H 177 PHE 0.029 0.002 PHE G 231 TRP 0.022 0.001 TRP C 68 HIS 0.013 0.001 HIS J 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00808 / 0.35 (28514) covalent geometry : angle 0.67919 / 0.35 (38853) hydrogen bonds : bond 0.04767 / 5.23 ( 1103) hydrogen bonds : angle 4.65956 / 5.09 ( 3092) metal coordination : bond 0.01444 / 1.38 ( 8) metal coordination : angle 1.49898 / 2.74 ( 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 405 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 333 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 MET cc_start: 0.9572 (ppp) cc_final: 0.9207 (pmm) REVERT: C 108 ASP cc_start: 0.8037 (t0) cc_final: 0.7496 (t0) REVERT: C 124 LYS cc_start: 0.9125 (tptp) cc_final: 0.8858 (tptp) REVERT: C 147 MET cc_start: 0.8901 (tpp) cc_final: 0.8514 (tpt) REVERT: C 151 ASP cc_start: 0.9492 (t0) cc_final: 0.9222 (t0) REVERT: C 154 PHE cc_start: 0.9344 (m-80) cc_final: 0.9086 (m-10) REVERT: C 182 HIS cc_start: 0.8641 (m90) cc_final: 0.8115 (m90) REVERT: G 200 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8357 (ttpt) REVERT: H 188 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8570 (mp0) REVERT: I 239 MET cc_start: 0.8753 (ppp) cc_final: 0.8305 (tmm) REVERT: I 330 HIS cc_start: 0.8201 (m-70) cc_final: 0.7755 (m-70) REVERT: I 488 MET cc_start: 0.9018 (mmm) cc_final: 0.8284 (mmm) REVERT: I 1233 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9167 (mt) REVERT: I 1322 SER cc_start: 0.9053 (m) cc_final: 0.8769 (m) REVERT: J 213 LYS cc_start: 0.9157 (tppt) cc_final: 0.8939 (tppt) REVERT: J 304 ASP cc_start: 0.8344 (m-30) cc_final: 0.8069 (m-30) REVERT: J 740 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8533 (mp) REVERT: J 802 ASP cc_start: 0.8596 (m-30) cc_final: 0.8041 (m-30) REVERT: J 873 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8102 (mt-10) REVERT: J 1167 LYS cc_start: 0.9102 (tppt) cc_final: 0.8803 (tppt) REVERT: J 1199 PHE cc_start: 0.8964 (m-80) cc_final: 0.8643 (m-80) REVERT: J 1244 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8352 (tp-100) REVERT: K 43 ASN cc_start: 0.9148 (t0) cc_final: 0.8810 (t0) REVERT: K 55 GLU cc_start: 0.8644 (pt0) cc_final: 0.8380 (pt0) outliers start: 72 outliers final: 46 residues processed: 388 average time/residue: 0.2081 time to fit residues: 124.9048 Evaluate side-chains 370 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 321 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 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 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 202 ARG 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 541 GLU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 692 THR Chi-restraints excluded: chain I residue 834 GLN 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 1309 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 210 SER Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 416 ILE 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 821 MET Chi-restraints excluded: chain J residue 901 ARG 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 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: 0.5980 chunk 49 optimal weight: 2.9990 chunk 206 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 334 optimal weight: 0.6980 chunk 238 optimal weight: 4.9990 chunk 256 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 322 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 307 optimal weight: 50.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.140596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.088931 restraints weight = 47970.703| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.42 r_work: 0.2983 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28522 Z= 0.153 Angle : 0.589 11.287 38865 Z= 0.308 Chirality : 0.043 0.225 4441 Planarity : 0.004 0.079 4806 Dihedral : 13.642 139.160 4532 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.00 % Favored : 94.97 % Rotamer: Outliers : 2.03 % Allowed : 14.80 % Favored : 83.16 % 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: -0.64 (0.14), residues: 3340 helix: 1.22 (0.15), residues: 1202 sheet: -0.53 (0.26), residues: 425 loop : -1.67 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 275 TYR 0.020 0.001 TYR H 177 PHE 0.012 0.001 PHE I 514 TRP 0.017 0.001 TRP C 68 HIS 0.006 0.001 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (28514) covalent geometry : angle 0.58821 / 0.31 (38853) hydrogen bonds : bond 0.04036 / 4.42 ( 1103) hydrogen bonds : angle 4.49451 / 4.85 ( 3092) metal coordination : bond 0.00598 / 0.56 ( 8) metal coordination : angle 1.21579 / 2.15 ( 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 407 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 349 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 104 TYR cc_start: 0.6496 (m-80) cc_final: 0.6124 (m-80) REVERT: C 108 ASP cc_start: 0.7961 (t0) cc_final: 0.7355 (t0) REVERT: C 124 LYS cc_start: 0.9099 (tptp) cc_final: 0.8837 (tptp) REVERT: C 147 MET cc_start: 0.8862 (tpp) cc_final: 0.8512 (tpt) REVERT: C 151 ASP cc_start: 0.9500 (t0) cc_final: 0.9226 (t0) REVERT: C 154 PHE cc_start: 0.9329 (m-80) cc_final: 0.9048 (m-10) REVERT: C 182 HIS cc_start: 0.8720 (m90) cc_final: 0.8194 (m90) REVERT: G 200 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8285 (ttpt) REVERT: H 41 ASN cc_start: 0.9052 (t0) cc_final: 0.8721 (t0) REVERT: H 80 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8141 (mt-10) REVERT: H 188 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8564 (mp0) REVERT: I 202 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8713 (ptt90) REVERT: I 208 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8895 (mp) REVERT: I 239 MET cc_start: 0.8687 (ppp) cc_final: 0.8261 (tmm) REVERT: I 330 HIS cc_start: 0.8264 (m-70) cc_final: 0.7825 (m-70) REVERT: I 696 ASP cc_start: 0.8036 (t0) cc_final: 0.7791 (t0) REVERT: I 949 GLU cc_start: 0.9204 (tt0) cc_final: 0.8983 (tt0) REVERT: I 1034 ARG cc_start: 0.8614 (mmp80) cc_final: 0.8308 (mmp80) REVERT: I 1322 SER cc_start: 0.8964 (m) cc_final: 0.8712 (m) REVERT: J 304 ASP cc_start: 0.8389 (m-30) cc_final: 0.8168 (m-30) REVERT: J 740 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8445 (mp) REVERT: J 802 ASP cc_start: 0.8510 (m-30) cc_final: 0.8018 (m-30) REVERT: J 811 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8137 (mt-10) REVERT: J 873 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8086 (mt-10) REVERT: J 1167 LYS cc_start: 0.9097 (tppt) cc_final: 0.8849 (tppt) REVERT: J 1199 PHE cc_start: 0.8982 (m-80) cc_final: 0.8664 (m-80) REVERT: K 43 ASN cc_start: 0.9142 (t0) cc_final: 0.8797 (t0) REVERT: K 55 GLU cc_start: 0.8556 (pt0) cc_final: 0.8290 (pt0) outliers start: 58 outliers final: 39 residues processed: 390 average time/residue: 0.2039 time to fit residues: 123.5342 Evaluate side-chains 381 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 337 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 85 HIS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 190 VAL 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 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 98 VAL Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 202 ARG Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 209 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 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 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 997 VAL 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 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: 7.9990 chunk 199 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 181 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 261 optimal weight: 0.8980 chunk 301 optimal weight: 6.9990 chunk 243 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 954 ASN ** 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 = 0.3979 r_free = 0.3979 target = 0.140960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.089413 restraints weight = 48179.050| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.42 r_work: 0.2948 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28522 Z= 0.144 Angle : 0.581 10.764 38865 Z= 0.302 Chirality : 0.043 0.221 4441 Planarity : 0.004 0.066 4806 Dihedral : 13.604 138.050 4532 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.36 % Favored : 94.61 % Rotamer: Outliers : 1.86 % Allowed : 15.26 % 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: -0.56 (0.15), residues: 3340 helix: 1.31 (0.15), residues: 1201 sheet: -0.54 (0.26), residues: 426 loop : -1.61 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 53 TYR 0.019 0.001 TYR H 177 PHE 0.009 0.001 PHE G 231 TRP 0.008 0.001 TRP C 68 HIS 0.006 0.001 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (28514) covalent geometry : angle 0.58048 / 0.30 (38853) hydrogen bonds : bond 0.03885 / 4.24 ( 1103) hydrogen bonds : angle 4.43681 / 4.78 ( 3092) metal coordination : bond 0.00560 / 0.54 ( 8) metal coordination : angle 1.05832 / 1.88 ( 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 408 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 355 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 MET cc_start: 0.8905 (tpp) cc_final: 0.8662 (tpp) REVERT: C 104 TYR cc_start: 0.6492 (m-80) cc_final: 0.6086 (m-80) REVERT: C 108 ASP cc_start: 0.7997 (t0) cc_final: 0.7344 (t0) REVERT: C 124 LYS cc_start: 0.9046 (tptp) cc_final: 0.8805 (tptp) REVERT: C 147 MET cc_start: 0.8828 (tpp) cc_final: 0.8462 (tpt) REVERT: C 151 ASP cc_start: 0.9447 (t0) cc_final: 0.9173 (t0) REVERT: C 154 PHE cc_start: 0.9237 (m-80) cc_final: 0.8939 (m-10) REVERT: C 182 HIS cc_start: 0.8671 (m90) cc_final: 0.8139 (m90) REVERT: G 200 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8283 (ttpt) REVERT: H 10 LYS cc_start: 0.8969 (mtpt) cc_final: 0.8527 (mtmm) REVERT: H 41 ASN cc_start: 0.9030 (t0) cc_final: 0.8710 (t0) REVERT: H 188 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8705 (mm-30) REVERT: I 208 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8883 (mp) REVERT: I 239 MET cc_start: 0.8611 (ppp) cc_final: 0.8390 (tmm) REVERT: I 330 HIS cc_start: 0.8293 (m-70) cc_final: 0.7906 (m-70) REVERT: I 488 MET cc_start: 0.8932 (mmm) cc_final: 0.8678 (mmp) REVERT: I 696 ASP cc_start: 0.7979 (t0) cc_final: 0.7724 (t0) REVERT: I 949 GLU cc_start: 0.9180 (tt0) cc_final: 0.8954 (tt0) REVERT: I 1233 LEU cc_start: 0.9562 (OUTLIER) cc_final: 0.9104 (mt) REVERT: I 1322 SER cc_start: 0.8971 (m) cc_final: 0.8698 (m) REVERT: J 213 LYS cc_start: 0.9100 (tppt) cc_final: 0.8877 (tppt) REVERT: J 304 ASP cc_start: 0.8375 (m-30) cc_final: 0.8155 (m-30) REVERT: J 740 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8433 (mp) REVERT: J 802 ASP cc_start: 0.8560 (m-30) cc_final: 0.8072 (m-30) REVERT: J 811 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8189 (mt-10) REVERT: J 873 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8098 (mt-10) REVERT: J 1167 LYS cc_start: 0.9101 (tppt) cc_final: 0.8792 (tppt) REVERT: J 1199 PHE cc_start: 0.8963 (m-80) cc_final: 0.8662 (m-80) REVERT: J 1244 GLN cc_start: 0.8569 (mm-40) cc_final: 0.8335 (mm-40) REVERT: K 43 ASN cc_start: 0.9168 (t0) cc_final: 0.8834 (t0) REVERT: K 55 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8281 (pt0) REVERT: K 69 ARG cc_start: 0.8920 (ttm110) cc_final: 0.8457 (tpp-160) REVERT: K 72 GLN cc_start: 0.9426 (tp-100) cc_final: 0.9202 (mm-40) outliers start: 53 outliers final: 38 residues processed: 393 average time/residue: 0.1999 time to fit residues: 121.8863 Evaluate side-chains 384 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 340 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 VAL 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 160 HIS Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 183 ILE 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 208 ILE Chi-restraints excluded: chain I residue 209 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 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 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 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 743 MET 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 1173 ARG Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 55 GLU 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: 0.8980 chunk 138 optimal weight: 0.9980 chunk 247 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 222 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 314 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.140461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.088674 restraints weight = 48135.797| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.42 r_work: 0.2981 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 28522 Z= 0.174 Angle : 0.599 10.861 38865 Z= 0.311 Chirality : 0.043 0.219 4441 Planarity : 0.004 0.058 4806 Dihedral : 13.592 136.797 4532 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.12 % Favored : 94.85 % Rotamer: Outliers : 1.82 % Allowed : 15.68 % Favored : 82.50 % 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: -0.53 (0.15), residues: 3340 helix: 1.31 (0.15), residues: 1202 sheet: -0.54 (0.26), residues: 430 loop : -1.58 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG I 272 TYR 0.019 0.001 TYR H 177 PHE 0.013 0.001 PHE G 231 TRP 0.010 0.001 TRP C 68 HIS 0.006 0.001 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (28514) covalent geometry : angle 0.59876 / 0.31 (38853) hydrogen bonds : bond 0.03924 / 4.28 ( 1103) hydrogen bonds : angle 4.43053 / 4.81 ( 3092) metal coordination : bond 0.00705 / 0.69 ( 8) metal coordination : angle 0.92314 / 1.64 ( 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 399 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 347 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 MET cc_start: 0.9016 (tpp) cc_final: 0.8477 (tpp) REVERT: C 104 TYR cc_start: 0.6460 (m-80) cc_final: 0.6090 (m-80) REVERT: C 108 ASP cc_start: 0.8020 (t0) cc_final: 0.7454 (t0) REVERT: C 124 LYS cc_start: 0.9076 (tptp) cc_final: 0.8825 (tptp) REVERT: C 147 MET cc_start: 0.8808 (tpp) cc_final: 0.8491 (tpt) REVERT: C 151 ASP cc_start: 0.9505 (t0) cc_final: 0.9230 (t0) REVERT: C 154 PHE cc_start: 0.9307 (m-80) cc_final: 0.9020 (m-10) REVERT: C 182 HIS cc_start: 0.8685 (m90) cc_final: 0.8133 (m90) REVERT: G 200 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8308 (ttpt) REVERT: H 10 LYS cc_start: 0.9010 (mtpt) cc_final: 0.8587 (mtmm) REVERT: H 41 ASN cc_start: 0.9053 (t0) cc_final: 0.8739 (t0) REVERT: H 188 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8666 (mp0) REVERT: I 208 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8876 (mp) REVERT: I 315 MET cc_start: 0.8828 (ttp) cc_final: 0.8103 (mtm) REVERT: I 330 HIS cc_start: 0.8336 (m-70) cc_final: 0.7936 (m-70) REVERT: I 365 GLU cc_start: 0.8855 (tp30) cc_final: 0.8618 (tp30) REVERT: I 696 ASP cc_start: 0.7921 (t0) cc_final: 0.7692 (t0) REVERT: I 949 GLU cc_start: 0.9184 (tt0) cc_final: 0.8957 (tt0) REVERT: I 1210 ILE cc_start: 0.9202 (tt) cc_final: 0.8896 (pt) REVERT: I 1233 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9150 (mt) REVERT: I 1322 SER cc_start: 0.8971 (m) cc_final: 0.8691 (m) REVERT: J 213 LYS cc_start: 0.9136 (tppt) cc_final: 0.8922 (tppt) REVERT: J 304 ASP cc_start: 0.8368 (m-30) cc_final: 0.8154 (m-30) REVERT: J 802 ASP cc_start: 0.8520 (m-30) cc_final: 0.8027 (m-30) REVERT: J 811 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8207 (mt-10) REVERT: J 873 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8120 (mt-10) REVERT: J 1167 LYS cc_start: 0.9110 (tppt) cc_final: 0.8862 (tppt) REVERT: J 1199 PHE cc_start: 0.8996 (m-80) cc_final: 0.8695 (m-80) REVERT: K 74 GLU cc_start: 0.9346 (tm-30) cc_final: 0.8864 (pp20) outliers start: 52 outliers final: 41 residues processed: 385 average time/residue: 0.2031 time to fit residues: 121.8860 Evaluate side-chains 385 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 340 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 190 VAL 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 160 HIS Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 93 GLN 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 208 ILE Chi-restraints excluded: chain I residue 209 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 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 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 120 LEU Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 416 ILE 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 1173 ARG 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: 0.7980 chunk 154 optimal weight: 8.9990 chunk 224 optimal weight: 8.9990 chunk 259 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 301 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.140815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.089378 restraints weight = 48010.485| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.42 r_work: 0.2993 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28522 Z= 0.156 Angle : 0.605 11.531 38865 Z= 0.312 Chirality : 0.043 0.214 4441 Planarity : 0.004 0.061 4806 Dihedral : 13.557 136.173 4532 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.94 % Favored : 95.03 % Rotamer: Outliers : 1.68 % Allowed : 15.82 % Favored : 82.50 % 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: -0.50 (0.15), residues: 3340 helix: 1.31 (0.15), residues: 1202 sheet: -0.52 (0.26), residues: 431 loop : -1.54 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 69 TYR 0.017 0.001 TYR H 177 PHE 0.011 0.001 PHE I 230 TRP 0.037 0.001 TRP J1020 HIS 0.004 0.001 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (28514) covalent geometry : angle 0.60520 / 0.31 (38853) hydrogen bonds : bond 0.03832 / 4.18 ( 1103) hydrogen bonds : angle 4.39125 / 4.78 ( 3092) metal coordination : bond 0.00590 / 0.58 ( 8) metal coordination : angle 0.91834 / 1.60 ( 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 397 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 349 time to evaluate : 1.078 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: C 88 MET cc_start: 0.8875 (tpp) cc_final: 0.8468 (tpp) REVERT: C 104 TYR cc_start: 0.6362 (m-80) cc_final: 0.6015 (m-80) REVERT: C 108 ASP cc_start: 0.8041 (t0) cc_final: 0.7407 (t0) REVERT: C 124 LYS cc_start: 0.9066 (tptp) cc_final: 0.8812 (tptp) REVERT: C 151 ASP cc_start: 0.9458 (t0) cc_final: 0.9258 (t0) REVERT: C 159 PHE cc_start: 0.8581 (m-10) cc_final: 0.8063 (m-10) REVERT: C 182 HIS cc_start: 0.8647 (m90) cc_final: 0.8097 (m90) REVERT: G 95 LYS cc_start: 0.9125 (mtmm) cc_final: 0.8892 (mttp) REVERT: G 200 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8305 (ttpt) REVERT: H 10 LYS cc_start: 0.8994 (mtpt) cc_final: 0.8598 (mtmm) REVERT: H 41 ASN cc_start: 0.9018 (t0) cc_final: 0.8715 (t0) REVERT: I 208 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8873 (mp) REVERT: I 315 MET cc_start: 0.8742 (ttp) cc_final: 0.8067 (mtm) REVERT: I 330 HIS cc_start: 0.8327 (m-70) cc_final: 0.7997 (m-70) REVERT: I 365 GLU cc_start: 0.8787 (tp30) cc_final: 0.8557 (tp30) REVERT: I 696 ASP cc_start: 0.7869 (t0) cc_final: 0.7613 (t0) REVERT: I 949 GLU cc_start: 0.9147 (tt0) cc_final: 0.8926 (tt0) REVERT: I 1034 ARG cc_start: 0.8469 (mmp80) cc_final: 0.8231 (mmp80) REVERT: I 1210 ILE cc_start: 0.9168 (tt) cc_final: 0.8905 (pt) REVERT: I 1233 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9144 (mt) REVERT: I 1322 SER cc_start: 0.8966 (m) cc_final: 0.8688 (m) REVERT: J 213 LYS cc_start: 0.9139 (tppt) cc_final: 0.8921 (tppt) REVERT: J 304 ASP cc_start: 0.8347 (m-30) cc_final: 0.8132 (m-30) REVERT: J 802 ASP cc_start: 0.8513 (m-30) cc_final: 0.8022 (m-30) REVERT: J 873 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8126 (mt-10) REVERT: J 1167 LYS cc_start: 0.9113 (tppt) cc_final: 0.8851 (tppt) REVERT: J 1199 PHE cc_start: 0.8976 (m-80) cc_final: 0.8676 (m-80) REVERT: J 1244 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8187 (mm-40) REVERT: J 1345 ARG cc_start: 0.8344 (mtp-110) cc_final: 0.8088 (ttm-80) REVERT: K 69 ARG cc_start: 0.8921 (ttm110) cc_final: 0.8472 (tpp-160) REVERT: K 74 GLU cc_start: 0.9337 (tm-30) cc_final: 0.8899 (pp20) outliers start: 48 outliers final: 40 residues processed: 384 average time/residue: 0.2080 time to fit residues: 123.8491 Evaluate side-chains 386 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 342 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 190 VAL 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 160 HIS Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 93 GLN 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 208 ILE Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 439 LYS 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 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 120 LEU Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 416 ILE 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 1173 ARG 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: 3.9990 chunk 110 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 chunk 263 optimal weight: 0.0570 chunk 148 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 319 optimal weight: 0.6980 chunk 18 optimal weight: 0.0370 chunk 140 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 266 optimal weight: 0.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 GLN ** J 954 ASN ** 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 = 0.3981 r_free = 0.3981 target = 0.141166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.089727 restraints weight = 48038.101| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.42 r_work: 0.3002 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28522 Z= 0.146 Angle : 0.609 13.729 38865 Z= 0.313 Chirality : 0.043 0.211 4441 Planarity : 0.004 0.057 4806 Dihedral : 13.520 135.311 4532 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.79 % Favored : 95.18 % Rotamer: Outliers : 1.65 % Allowed : 16.06 % Favored : 82.29 % 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: -0.43 (0.15), residues: 3340 helix: 1.37 (0.15), residues: 1195 sheet: -0.45 (0.26), residues: 426 loop : -1.50 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG I 275 TYR 0.017 0.001 TYR H 177 PHE 0.027 0.001 PHE I 230 TRP 0.030 0.001 TRP J1020 HIS 0.005 0.001 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (28514) covalent geometry : angle 0.60846 / 0.31 (38853) hydrogen bonds : bond 0.03750 / 4.08 ( 1103) hydrogen bonds : angle 4.37614 / 4.79 ( 3092) metal coordination : bond 0.00533 / 0.53 ( 8) metal coordination : angle 0.88410 / 1.55 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9779.60 seconds wall clock time: 167 minutes 12.99 seconds (10032.99 seconds total)