Starting phenix.real_space_refine on Tue Jun 24 04:07:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uwh_26832/06_2025/7uwh_26832.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uwh_26832/06_2025/7uwh_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7uwh_26832/06_2025/7uwh_26832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uwh_26832/06_2025/7uwh_26832.map" model { file = "/net/cci-nas-00/data/ceres_data/7uwh_26832/06_2025/7uwh_26832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uwh_26832/06_2025/7uwh_26832.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27927 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 650 Classifications: {'DNA': 32} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 31} Chain breaks: 1 Chain: "B" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 776 Classifications: {'DNA': 37, 'RNA': 1} Modifications used: {'rna3p_pur': 1} Link IDs: {'rna3p': 37} Chain: "C" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1439 Classifications: {'peptide': 190} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 177} Chain: "G" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "H" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1772 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 219} Chain: "I" Number of atoms: 10407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1319, 10407 Classifications: {'peptide': 1319} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1263} Chain breaks: 1 Chain: "J" Number of atoms: 10272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1318, 10272 Classifications: {'peptide': 1318} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1264} Chain breaks: 4 Chain: "K" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain: "R" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 221 Classifications: {'RNA': 10} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17261 SG CYS J 70 104.775 67.238 24.091 1.00 50.10 S ATOM 17275 SG CYS J 72 103.785 67.333 20.717 1.00 40.99 S ATOM 17383 SG CYS J 85 106.993 68.686 21.222 1.00 42.62 S ATOM 17407 SG CYS J 88 103.786 70.466 22.977 1.00 39.36 S ATOM 23095 SG CYS J 814 109.407 80.418 89.464 1.00 20.28 S ATOM 23660 SG CYS J 888 106.955 80.172 86.587 1.00 14.12 S ATOM 23711 SG CYS J 895 107.844 77.071 88.554 1.00 10.63 S ATOM 23732 SG CYS J 898 105.658 79.677 90.131 1.00 10.55 S Time building chain proxies: 14.73, per 1000 atoms: 0.53 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: 6.31 Conformation dependent library (CDL) restraints added in 3.3 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: 9.21 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: 12.33 Time building geometry restraints manager: 7.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4876 1.32 - 1.45: 7082 1.45 - 1.57: 16207 1.57 - 1.69: 156 1.69 - 1.81: 193 Bond restraints: 28514 Sorted by residual: bond pdb=" CA ARG C 143 " pdb=" C ARG C 143 " ideal model delta sigma weight residual 1.524 1.470 0.054 1.26e-02 6.30e+03 1.83e+01 bond pdb=" CA ILE I 292 " pdb=" CB ILE I 292 " ideal model delta sigma weight residual 1.540 1.594 -0.054 1.39e-02 5.18e+03 1.53e+01 bond pdb=" O3' DA A 26 " pdb=" P DC A 27 " ideal model delta sigma weight residual 1.607 1.665 -0.058 1.50e-02 4.44e+03 1.50e+01 bond pdb=" N TYR C 165 " pdb=" CA TYR C 165 " ideal model delta sigma weight residual 1.455 1.414 0.041 1.17e-02 7.31e+03 1.25e+01 bond pdb=" N GLN J 94 " pdb=" CA GLN J 94 " ideal model delta sigma weight residual 1.456 1.415 0.041 1.25e-02 6.40e+03 1.08e+01 ... (remaining 28509 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 38036 2.19 - 4.38: 737 4.38 - 6.57: 75 6.57 - 8.76: 9 8.76 - 10.95: 2 Bond angle restraints: 38859 Sorted by residual: angle pdb=" N GLY C 21 " pdb=" CA GLY C 21 " pdb=" C GLY C 21 " ideal model delta sigma weight residual 112.34 123.29 -10.95 2.04e+00 2.40e-01 2.88e+01 angle pdb=" N TRP J1193 " pdb=" CA TRP J1193 " pdb=" C TRP J1193 " ideal model delta sigma weight residual 111.28 116.95 -5.67 1.09e+00 8.42e-01 2.70e+01 angle pdb=" N ASN J 153 " pdb=" CA ASN J 153 " pdb=" C ASN J 153 " ideal model delta sigma weight residual 111.28 116.80 -5.52 1.09e+00 8.42e-01 2.57e+01 angle pdb=" N GLN J 157 " pdb=" CA GLN J 157 " pdb=" C GLN J 157 " ideal model delta sigma weight residual 110.80 121.44 -10.64 2.13e+00 2.20e-01 2.50e+01 angle pdb=" N VAL I1186 " pdb=" CA VAL I1186 " pdb=" C VAL I1186 " ideal model delta sigma weight residual 111.89 119.04 -7.15 1.44e+00 4.82e-01 2.46e+01 ... (remaining 38854 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 15566 18.07 - 36.14: 1171 36.14 - 54.21: 436 54.21 - 72.28: 140 72.28 - 90.35: 38 Dihedral angle restraints: 17351 sinusoidal: 7699 harmonic: 9652 Sorted by residual: dihedral pdb=" CA PHE J1325 " pdb=" C PHE J1325 " pdb=" N GLN J1326 " pdb=" CA GLN J1326 " ideal model delta harmonic sigma weight residual 180.00 157.52 22.48 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA GLY J 852 " pdb=" C GLY J 852 " pdb=" N THR J 853 " pdb=" CA THR J 853 " ideal model delta harmonic sigma weight residual -180.00 -159.21 -20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA SER I1295 " pdb=" C SER I1295 " pdb=" N ASP I1296 " pdb=" CA ASP I1296 " ideal model delta harmonic sigma weight residual -180.00 -159.44 -20.56 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 17348 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 4008 0.078 - 0.157: 406 0.157 - 0.235: 19 0.235 - 0.313: 2 0.313 - 0.392: 6 Chirality restraints: 4441 Sorted by residual: chirality pdb=" CB ILE I 292 " pdb=" CA ILE I 292 " pdb=" CG1 ILE I 292 " pdb=" CG2 ILE I 292 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CA ILE J1248 " pdb=" N ILE J1248 " pdb=" C ILE J1248 " pdb=" CB ILE J1248 " both_signs ideal model delta sigma weight residual False 2.43 2.78 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA ASP J 516 " pdb=" N ASP J 516 " pdb=" C ASP J 516 " pdb=" CB ASP J 516 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 4438 not shown) Planarity restraints: 4806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN J 94 " 0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C GLN J 94 " -0.073 2.00e-02 2.50e+03 pdb=" O GLN J 94 " 0.028 2.00e-02 2.50e+03 pdb=" N THR J 95 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA I 313 " -0.020 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C ALA I 313 " 0.070 2.00e-02 2.50e+03 pdb=" O ALA I 313 " -0.027 2.00e-02 2.50e+03 pdb=" N ASN I 314 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO I1185 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.08e+00 pdb=" C PRO I1185 " 0.052 2.00e-02 2.50e+03 pdb=" O PRO I1185 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL I1186 " -0.017 2.00e-02 2.50e+03 ... (remaining 4803 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 589 2.67 - 3.23: 26109 3.23 - 3.79: 43529 3.79 - 4.34: 59732 4.34 - 4.90: 98019 Nonbonded interactions: 227978 Sorted by model distance: nonbonded pdb=" O3' A R 20 " pdb="MG MG J1503 " model vdw 2.114 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1503 " model vdw 2.133 2.170 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1503 " model vdw 2.173 2.170 nonbonded pdb=" OE1 GLU I 562 " pdb=" OG SER I 662 " model vdw 2.217 3.040 nonbonded pdb=" OG SER G 49 " pdb=" OE2 GLU I1083 " model vdw 2.217 3.040 ... (remaining 227973 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and resid 7 through 232) selection = (chain 'H' and resid 7 through 232) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.040 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: 0.030 Extract box with map and model: 0.940 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 70.810 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.110 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.624 28522 Z= 0.269 Angle : 0.720 18.232 38871 Z= 0.447 Chirality : 0.047 0.392 4441 Planarity : 0.004 0.056 4806 Dihedral : 15.818 90.351 11139 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.51 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.003 0.000 TRP J 580 HIS 0.004 0.000 HIS J 651 PHE 0.022 0.001 PHE C 154 TYR 0.013 0.001 TYR C 165 ARG 0.009 0.000 ARG J 47 Details of bonding type rmsd hydrogen bonds : bond 0.16869 ( 1103) hydrogen bonds : angle 6.51528 ( 3092) metal coordination : bond 0.30241 ( 8) metal coordination : angle 10.45164 ( 12) covalent geometry : bond 0.00349 (28514) covalent geometry : angle 0.69620 (38859) *********************** 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 : 3.263 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: 0.5088 time to fit residues: 401.0455 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 : 3.710 ------------------------------------------------------------------------------- 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 286 optimal weight: 1.9990 chunk 256 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 265 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 161 optimal weight: 0.9990 chunk 197 optimal weight: 0.6980 chunk 307 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 HIS H 186 ASN I 314 ASN I 834 GLN I1257 GLN I1264 GLN J 209 ASN J 274 ASN ** J 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 594 GLN J 651 HIS J 777 HIS J 921 GLN J 951 GLN J1244 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.144723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.094074 restraints weight = 48043.946| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.45 r_work: 0.3082 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 28522 Z= 0.164 Angle : 0.595 11.526 38871 Z= 0.310 Chirality : 0.043 0.262 4441 Planarity : 0.004 0.058 4806 Dihedral : 14.390 87.092 4600 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.37 % Allowed : 9.58 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3340 helix: 1.21 (0.15), residues: 1208 sheet: -0.63 (0.26), residues: 402 loop : -1.74 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 68 HIS 0.006 0.001 HIS I1023 PHE 0.019 0.001 PHE C 159 TYR 0.025 0.001 TYR H 177 ARG 0.006 0.000 ARG I 974 Details of bonding type rmsd hydrogen bonds : bond 0.04268 ( 1103) hydrogen bonds : angle 4.80159 ( 3092) metal coordination : bond 0.00994 ( 8) metal coordination : angle 2.50623 ( 12) covalent geometry : bond 0.00377 (28514) covalent geometry : angle 0.59310 (38859) *********************** 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 438 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 399 time to evaluate : 2.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 ARG cc_start: 0.9192 (tpm170) cc_final: 0.8989 (mmm160) REVERT: C 57 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8930 (mt) REVERT: C 108 ASP cc_start: 0.8116 (t0) cc_final: 0.7569 (t0) REVERT: C 124 LYS cc_start: 0.9006 (tptp) cc_final: 0.8610 (tptp) REVERT: C 140 LYS cc_start: 0.9396 (tptp) cc_final: 0.9052 (tptp) REVERT: C 147 MET cc_start: 0.9071 (tpp) cc_final: 0.8725 (tpt) REVERT: C 182 HIS cc_start: 0.8232 (m90) cc_final: 0.7860 (m90) REVERT: H 75 GLN cc_start: 0.8362 (tm-30) cc_final: 0.7633 (tm-30) REVERT: H 80 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8124 (mt-10) REVERT: I 239 MET cc_start: 0.8514 (ppp) cc_final: 0.7629 (tmm) REVERT: I 1024 GLU cc_start: 0.8264 (pt0) cc_final: 0.8000 (pt0) REVERT: I 1304 MET cc_start: 0.9229 (tpt) cc_final: 0.8985 (tpt) REVERT: J 128 LEU cc_start: 0.9424 (mt) cc_final: 0.9124 (mt) REVERT: J 802 ASP cc_start: 0.8356 (m-30) cc_final: 0.7929 (m-30) REVERT: J 901 ARG cc_start: 0.9318 (OUTLIER) cc_final: 0.8999 (ptm160) REVERT: J 1167 LYS cc_start: 0.8991 (tppt) cc_final: 0.8766 (tppt) REVERT: J 1195 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8272 (tm-30) REVERT: J 1199 PHE cc_start: 0.8991 (m-80) cc_final: 0.8478 (m-80) REVERT: J 1212 ASP cc_start: 0.8461 (m-30) cc_final: 0.8089 (m-30) REVERT: J 1330 ARG cc_start: 0.8740 (ttp80) cc_final: 0.8482 (ttp80) REVERT: K 43 ASN cc_start: 0.8820 (t0) cc_final: 0.8556 (t0) REVERT: K 55 GLU cc_start: 0.8474 (pt0) cc_final: 0.8203 (pt0) REVERT: K 73 GLN cc_start: 0.8695 (pp30) cc_final: 0.8486 (pp30) outliers start: 39 outliers final: 20 residues processed: 423 average time/residue: 0.4646 time to fit residues: 297.5300 Evaluate side-chains 376 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 354 time to evaluate : 3.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 980 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 239 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 185 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 106 optimal weight: 8.9990 chunk 221 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 chunk 20 optimal weight: 7.9990 chunk 127 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 chunk 107 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 HIS H 132 HIS I 766 ASN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 ASN J 651 HIS J 951 GLN J 954 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.145297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.095032 restraints weight = 48257.384| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.43 r_work: 0.3131 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28522 Z= 0.125 Angle : 0.542 9.254 38871 Z= 0.281 Chirality : 0.041 0.246 4441 Planarity : 0.004 0.058 4806 Dihedral : 14.107 85.749 4591 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.37 % Allowed : 11.61 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3340 helix: 1.38 (0.15), residues: 1208 sheet: -0.60 (0.26), residues: 409 loop : -1.72 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP J1020 HIS 0.006 0.001 HIS G 117 PHE 0.018 0.001 PHE C 154 TYR 0.024 0.001 TYR H 177 ARG 0.011 0.000 ARG I 694 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 1103) hydrogen bonds : angle 4.51818 ( 3092) metal coordination : bond 0.00545 ( 8) metal coordination : angle 1.80920 ( 12) covalent geometry : bond 0.00284 (28514) covalent geometry : angle 0.54075 (38859) *********************** 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 422 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 383 time to evaluate : 3.790 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: C 57 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8985 (mt) REVERT: C 62 LYS cc_start: 0.9348 (tppp) cc_final: 0.9081 (tppt) REVERT: C 88 MET cc_start: 0.8685 (tpp) cc_final: 0.7802 (tpp) REVERT: C 108 ASP cc_start: 0.8041 (t0) cc_final: 0.7474 (t0) REVERT: C 124 LYS cc_start: 0.8935 (tptp) cc_final: 0.8707 (tptp) REVERT: C 140 LYS cc_start: 0.9467 (tptp) cc_final: 0.9220 (tptp) REVERT: C 159 PHE cc_start: 0.8281 (m-10) cc_final: 0.8061 (m-10) REVERT: C 182 HIS cc_start: 0.8273 (m90) cc_final: 0.7955 (m90) REVERT: H 75 GLN cc_start: 0.8351 (tm-30) cc_final: 0.7627 (tm-30) REVERT: H 80 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8225 (mt-10) REVERT: H 186 ASN cc_start: 0.8328 (t0) cc_final: 0.7934 (t0) REVERT: H 188 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8472 (mm-30) REVERT: I 239 MET cc_start: 0.8643 (ppp) cc_final: 0.8132 (tmm) REVERT: I 351 LEU cc_start: 0.9146 (mt) cc_final: 0.8931 (mt) REVERT: I 545 PHE cc_start: 0.8136 (t80) cc_final: 0.7916 (t80) REVERT: I 685 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8488 (mtt) REVERT: I 696 ASP cc_start: 0.7447 (t0) cc_final: 0.7201 (t0) REVERT: J 128 LEU cc_start: 0.9426 (mt) cc_final: 0.9150 (mt) REVERT: J 222 LYS cc_start: 0.9129 (mmmt) cc_final: 0.8929 (tppt) REVERT: J 506 VAL cc_start: 0.9256 (t) cc_final: 0.9000 (t) REVERT: J 802 ASP cc_start: 0.8335 (m-30) cc_final: 0.7852 (m-30) REVERT: J 1167 LYS cc_start: 0.9033 (tppt) cc_final: 0.8743 (tppt) REVERT: J 1199 PHE cc_start: 0.8981 (m-80) cc_final: 0.8555 (m-80) REVERT: K 43 ASN cc_start: 0.8862 (t0) cc_final: 0.8531 (t0) REVERT: K 55 GLU cc_start: 0.8478 (pt0) cc_final: 0.8185 (pt0) REVERT: K 74 GLU cc_start: 0.9374 (tm-30) cc_final: 0.9099 (pp20) outliers start: 39 outliers final: 22 residues processed: 408 average time/residue: 0.4865 time to fit residues: 306.8489 Evaluate side-chains 375 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 351 time to evaluate : 5.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain I residue 164 THR 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 685 MET Chi-restraints excluded: chain I residue 692 THR Chi-restraints excluded: chain I residue 876 GLU Chi-restraints excluded: chain I residue 1016 GLU 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 J residue 92 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1175 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 173 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 118 optimal weight: 0.0980 chunk 327 optimal weight: 2.9990 chunk 299 optimal weight: 0.0050 chunk 285 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 798 GLN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 594 GLN J 951 GLN J1244 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.144708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.094163 restraints weight = 48426.958| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.43 r_work: 0.3070 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28522 Z= 0.131 Angle : 0.533 9.094 38871 Z= 0.277 Chirality : 0.041 0.228 4441 Planarity : 0.004 0.057 4806 Dihedral : 13.917 84.698 4583 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.44 % Allowed : 13.12 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 3340 helix: 1.47 (0.15), residues: 1208 sheet: -0.46 (0.27), residues: 405 loop : -1.65 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 68 HIS 0.007 0.001 HIS J 545 PHE 0.014 0.001 PHE I1025 TYR 0.018 0.001 TYR H 177 ARG 0.007 0.000 ARG J1330 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 1103) hydrogen bonds : angle 4.38061 ( 3092) metal coordination : bond 0.00717 ( 8) metal coordination : angle 1.87313 ( 12) covalent geometry : bond 0.00299 (28514) covalent geometry : angle 0.53254 (38859) *********************** 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: 41 poor density : 372 time to evaluate : 4.750 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 62 LYS cc_start: 0.9387 (tppp) cc_final: 0.9127 (tptt) REVERT: C 88 MET cc_start: 0.8471 (tpp) cc_final: 0.7541 (tpp) REVERT: C 108 ASP cc_start: 0.8080 (t0) cc_final: 0.7542 (t0) REVERT: C 124 LYS cc_start: 0.8994 (tptp) cc_final: 0.8763 (tptp) REVERT: C 140 LYS cc_start: 0.9457 (tptp) cc_final: 0.9251 (tptp) REVERT: C 159 PHE cc_start: 0.8452 (m-10) cc_final: 0.8222 (m-10) REVERT: C 182 HIS cc_start: 0.8341 (m90) cc_final: 0.7873 (m90) REVERT: H 75 GLN cc_start: 0.8336 (tm-30) cc_final: 0.7570 (tm-30) REVERT: H 80 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8340 (mt-10) REVERT: I 239 MET cc_start: 0.8688 (ppp) cc_final: 0.8210 (tmm) REVERT: I 330 HIS cc_start: 0.7634 (m-70) cc_final: 0.7101 (m90) REVERT: I 351 LEU cc_start: 0.9148 (mt) cc_final: 0.8904 (mt) REVERT: I 685 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8494 (mtt) REVERT: I 696 ASP cc_start: 0.7470 (t0) cc_final: 0.7249 (t0) REVERT: I 949 GLU cc_start: 0.9142 (tt0) cc_final: 0.8835 (tt0) REVERT: I 1273 MET cc_start: 0.9279 (mmm) cc_final: 0.8799 (mtt) REVERT: I 1322 SER cc_start: 0.8936 (m) cc_final: 0.8656 (m) REVERT: J 161 THR cc_start: 0.9399 (OUTLIER) cc_final: 0.8977 (p) REVERT: J 506 VAL cc_start: 0.9256 (t) cc_final: 0.8985 (t) REVERT: J 515 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.6876 (mmm-85) REVERT: J 802 ASP cc_start: 0.8494 (m-30) cc_final: 0.8038 (m-30) REVERT: J 1167 LYS cc_start: 0.9037 (tppt) cc_final: 0.8752 (tppt) REVERT: J 1199 PHE cc_start: 0.9009 (m-80) cc_final: 0.8593 (m-80) REVERT: J 1344 LEU cc_start: 0.7702 (mt) cc_final: 0.7360 (mt) REVERT: K 42 GLU cc_start: 0.8418 (mp0) cc_final: 0.8169 (mp0) REVERT: K 43 ASN cc_start: 0.8976 (t0) cc_final: 0.8646 (t0) REVERT: K 55 GLU cc_start: 0.8567 (pt0) cc_final: 0.8280 (pt0) REVERT: K 68 GLU cc_start: 0.9187 (tt0) cc_final: 0.8962 (mt-10) REVERT: K 69 ARG cc_start: 0.8935 (ttm110) cc_final: 0.8467 (tpp-160) outliers start: 41 outliers final: 27 residues processed: 401 average time/residue: 0.5954 time to fit residues: 373.1451 Evaluate side-chains 374 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 344 time to evaluate : 4.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 615 VAL 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 1016 GLU Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 515 ARG Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1175 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 171 optimal weight: 5.9990 chunk 285 optimal weight: 1.9990 chunk 223 optimal weight: 0.9980 chunk 281 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 186 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 HIS G 160 HIS I 952 GLN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J 424 ASN J 594 GLN ** J 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1218 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.140795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.088785 restraints weight = 47884.141| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.42 r_work: 0.2935 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2543 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= 0.227 Angle : 0.592 11.298 38871 Z= 0.307 Chirality : 0.043 0.224 4441 Planarity : 0.004 0.056 4806 Dihedral : 13.915 83.946 4583 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.10 % Allowed : 13.75 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.15), residues: 3340 helix: 1.43 (0.15), residues: 1199 sheet: -0.63 (0.25), residues: 449 loop : -1.68 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP J1020 HIS 0.009 0.001 HIS J 545 PHE 0.025 0.001 PHE I 545 TYR 0.020 0.001 TYR J 631 ARG 0.006 0.001 ARG J 47 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 1103) hydrogen bonds : angle 4.45863 ( 3092) metal coordination : bond 0.00982 ( 8) metal coordination : angle 1.17027 ( 12) covalent geometry : bond 0.00527 (28514) covalent geometry : angle 0.59133 (38859) *********************** 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 408 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 348 time to evaluate : 3.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 MET cc_start: 0.8717 (tpp) cc_final: 0.8483 (tpp) REVERT: C 104 TYR cc_start: 0.6573 (m-80) cc_final: 0.6223 (m-80) REVERT: C 108 ASP cc_start: 0.8123 (t0) cc_final: 0.7644 (t0) REVERT: C 124 LYS cc_start: 0.9043 (tptp) cc_final: 0.8826 (tptp) REVERT: C 140 LYS cc_start: 0.9453 (tptp) cc_final: 0.9236 (tptp) REVERT: C 151 ASP cc_start: 0.9485 (t0) cc_final: 0.9268 (t0) REVERT: C 154 PHE cc_start: 0.9171 (m-10) cc_final: 0.8823 (m-10) REVERT: C 159 PHE cc_start: 0.8550 (m-10) cc_final: 0.8193 (m-10) REVERT: C 182 HIS cc_start: 0.8497 (m90) cc_final: 0.7997 (m90) REVERT: H 75 GLN cc_start: 0.8444 (tm-30) cc_final: 0.7644 (tm-30) REVERT: H 188 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8626 (mm-30) REVERT: I 202 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8684 (ptt90) REVERT: I 239 MET cc_start: 0.8678 (ppp) cc_final: 0.8272 (tmm) REVERT: I 330 HIS cc_start: 0.8058 (m-70) cc_final: 0.7755 (m170) REVERT: I 351 LEU cc_start: 0.9205 (mt) cc_final: 0.8914 (mt) REVERT: I 1273 MET cc_start: 0.9330 (mmm) cc_final: 0.9006 (mtt) REVERT: I 1322 SER cc_start: 0.8958 (m) cc_final: 0.8687 (m) REVERT: J 213 LYS cc_start: 0.9113 (tppt) cc_final: 0.8890 (tppt) REVERT: J 697 MET cc_start: 0.9220 (tmm) cc_final: 0.8884 (tmm) REVERT: J 740 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8406 (mp) REVERT: J 802 ASP cc_start: 0.8632 (m-30) cc_final: 0.8264 (m-30) REVERT: J 811 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8235 (mt-10) REVERT: J 873 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: J 1167 LYS cc_start: 0.9071 (tppt) cc_final: 0.8755 (tppt) REVERT: J 1199 PHE cc_start: 0.8934 (m-80) cc_final: 0.8567 (m-80) REVERT: K 43 ASN cc_start: 0.9082 (t0) cc_final: 0.8708 (t0) REVERT: K 55 GLU cc_start: 0.8624 (pt0) cc_final: 0.8324 (pt0) REVERT: K 68 GLU cc_start: 0.9156 (tt0) cc_final: 0.8945 (mt-10) REVERT: K 71 GLU cc_start: 0.9128 (tm-30) cc_final: 0.8881 (tm-30) outliers start: 60 outliers final: 37 residues processed: 391 average time/residue: 0.4786 time to fit residues: 292.3302 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 : 3.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 202 ARG Chi-restraints excluded: chain I residue 209 ILE 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 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 1016 GLU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain 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 159 ILE Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 873 GLU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1353 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 67 optimal weight: 0.9990 chunk 275 optimal weight: 0.9980 chunk 248 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 286 optimal weight: 0.8980 chunk 298 optimal weight: 30.0000 chunk 29 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 135 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS ** I 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN ** J 954 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 = 0.3998 r_free = 0.3998 target = 0.142353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.090990 restraints weight = 48112.736| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.43 r_work: 0.3024 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28522 Z= 0.139 Angle : 0.545 9.959 38871 Z= 0.284 Chirality : 0.041 0.206 4441 Planarity : 0.004 0.058 4806 Dihedral : 13.852 83.473 4583 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.93 % Allowed : 14.21 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 3340 helix: 1.42 (0.15), residues: 1207 sheet: -0.49 (0.26), residues: 426 loop : -1.58 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 68 HIS 0.006 0.001 HIS J 545 PHE 0.022 0.001 PHE I 545 TYR 0.015 0.001 TYR J 631 ARG 0.007 0.000 ARG K 69 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 1103) hydrogen bonds : angle 4.33930 ( 3092) metal coordination : bond 0.00517 ( 8) metal coordination : angle 0.91235 ( 12) covalent geometry : bond 0.00319 (28514) covalent geometry : angle 0.54497 (38859) *********************** 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 418 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 363 time to evaluate : 3.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 TYR cc_start: 0.6570 (m-80) cc_final: 0.6249 (m-80) REVERT: C 108 ASP cc_start: 0.8105 (t0) cc_final: 0.7548 (t0) REVERT: C 124 LYS cc_start: 0.9058 (tptp) cc_final: 0.8836 (tptp) REVERT: C 151 ASP cc_start: 0.9445 (t0) cc_final: 0.9235 (t0) REVERT: C 154 PHE cc_start: 0.9172 (m-10) cc_final: 0.8943 (m-10) REVERT: C 159 PHE cc_start: 0.8486 (m-10) cc_final: 0.7964 (m-10) REVERT: C 182 HIS cc_start: 0.8497 (m90) cc_final: 0.7959 (m90) REVERT: H 188 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8490 (mp0) REVERT: I 202 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8676 (ptt90) REVERT: I 239 MET cc_start: 0.8712 (ppp) cc_final: 0.8165 (ppp) REVERT: I 330 HIS cc_start: 0.8087 (m-70) cc_final: 0.7848 (m170) REVERT: I 949 GLU cc_start: 0.9152 (tt0) cc_final: 0.8841 (tt0) REVERT: I 1034 ARG cc_start: 0.8561 (mmp80) cc_final: 0.8231 (mmp80) REVERT: I 1151 LEU cc_start: 0.7290 (tp) cc_final: 0.7017 (tp) REVERT: I 1273 MET cc_start: 0.9277 (mmm) cc_final: 0.8910 (mtt) REVERT: I 1322 SER cc_start: 0.8951 (m) cc_final: 0.8675 (m) REVERT: J 304 ASP cc_start: 0.8327 (m-30) cc_final: 0.8118 (m-30) REVERT: J 506 VAL cc_start: 0.9255 (t) cc_final: 0.8948 (t) REVERT: J 697 MET cc_start: 0.9181 (tmm) cc_final: 0.8782 (tmm) REVERT: J 802 ASP cc_start: 0.8595 (m-30) cc_final: 0.8247 (m-30) REVERT: J 811 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8191 (mt-10) REVERT: J 873 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8066 (mt-10) REVERT: J 1167 LYS cc_start: 0.9096 (tppt) cc_final: 0.8763 (tppt) REVERT: J 1199 PHE cc_start: 0.8948 (m-80) cc_final: 0.8616 (m-80) REVERT: K 43 ASN cc_start: 0.9054 (t0) cc_final: 0.8746 (t0) REVERT: K 68 GLU cc_start: 0.9160 (tt0) cc_final: 0.8959 (mt-10) outliers start: 55 outliers final: 37 residues processed: 399 average time/residue: 0.4366 time to fit residues: 268.4313 Evaluate side-chains 381 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 342 time to evaluate : 2.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 160 HIS 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 202 ARG Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 615 VAL 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 1016 GLU 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 I residue 1253 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 873 GLU Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1353 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 236 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 chunk 187 optimal weight: 0.5980 chunk 238 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 chunk 156 optimal weight: 6.9990 chunk 262 optimal weight: 5.9990 chunk 226 optimal weight: 6.9990 chunk 319 optimal weight: 0.7980 chunk 148 optimal weight: 0.7980 chunk 267 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN I 834 GLN I 952 GLN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4002 r_free = 0.4002 target = 0.142681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.091467 restraints weight = 48120.809| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.43 r_work: 0.3077 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28522 Z= 0.132 Angle : 0.548 11.331 38871 Z= 0.283 Chirality : 0.041 0.194 4441 Planarity : 0.004 0.057 4806 Dihedral : 13.812 85.398 4583 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.03 % Favored : 94.94 % Rotamer: Outliers : 1.89 % Allowed : 14.77 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 3340 helix: 1.43 (0.15), residues: 1214 sheet: -0.37 (0.26), residues: 414 loop : -1.54 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 68 HIS 0.006 0.001 HIS J 545 PHE 0.009 0.001 PHE G 231 TYR 0.014 0.001 TYR J 631 ARG 0.008 0.000 ARG K 69 Details of bonding type rmsd hydrogen bonds : bond 0.03530 ( 1103) hydrogen bonds : angle 4.28412 ( 3092) metal coordination : bond 0.00484 ( 8) metal coordination : angle 0.73563 ( 12) covalent geometry : bond 0.00302 (28514) covalent geometry : angle 0.54794 (38859) *********************** 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 412 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 358 time to evaluate : 2.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 MET cc_start: 0.9108 (mmt) cc_final: 0.8777 (tpp) REVERT: C 104 TYR cc_start: 0.6556 (m-80) cc_final: 0.6169 (m-80) REVERT: C 108 ASP cc_start: 0.8102 (t0) cc_final: 0.7465 (t0) REVERT: C 117 MET cc_start: 0.3268 (tmm) cc_final: 0.3061 (tmm) REVERT: C 151 ASP cc_start: 0.9400 (t0) cc_final: 0.9181 (t0) REVERT: C 154 PHE cc_start: 0.9167 (m-10) cc_final: 0.8795 (m-10) REVERT: C 159 PHE cc_start: 0.8532 (m-10) cc_final: 0.8117 (m-10) REVERT: C 182 HIS cc_start: 0.8472 (m90) cc_final: 0.7925 (m90) REVERT: H 188 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8498 (mp0) REVERT: I 239 MET cc_start: 0.8764 (ppp) cc_final: 0.8213 (ppp) REVERT: I 330 HIS cc_start: 0.7971 (m-70) cc_final: 0.7742 (m170) REVERT: I 351 LEU cc_start: 0.9209 (mt) cc_final: 0.8897 (mt) REVERT: I 365 GLU cc_start: 0.8771 (tp30) cc_final: 0.8492 (tp30) REVERT: I 685 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8497 (mtt) REVERT: I 1273 MET cc_start: 0.9268 (mmm) cc_final: 0.8873 (mtt) REVERT: I 1322 SER cc_start: 0.8948 (m) cc_final: 0.8665 (m) REVERT: J 213 LYS cc_start: 0.9080 (tppt) cc_final: 0.8864 (tppt) REVERT: J 304 ASP cc_start: 0.8299 (m-30) cc_final: 0.8080 (m-30) REVERT: J 506 VAL cc_start: 0.9217 (t) cc_final: 0.8886 (t) REVERT: J 515 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.6941 (mmm-85) REVERT: J 697 MET cc_start: 0.9163 (tmm) cc_final: 0.8854 (tmm) REVERT: J 802 ASP cc_start: 0.8519 (m-30) cc_final: 0.8173 (m-30) REVERT: J 811 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8185 (mt-10) REVERT: J 873 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.8040 (mt-10) REVERT: J 1167 LYS cc_start: 0.9112 (tppt) cc_final: 0.8779 (tppt) REVERT: J 1199 PHE cc_start: 0.8944 (m-80) cc_final: 0.8638 (m-80) REVERT: K 43 ASN cc_start: 0.9081 (t0) cc_final: 0.8794 (t0) REVERT: K 55 GLU cc_start: 0.8403 (pt0) cc_final: 0.8190 (pt0) REVERT: K 69 ARG cc_start: 0.8860 (ttm110) cc_final: 0.8431 (tpp-160) outliers start: 54 outliers final: 36 residues processed: 391 average time/residue: 0.4500 time to fit residues: 271.4434 Evaluate side-chains 379 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 340 time to evaluate : 3.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 160 HIS 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 82 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 615 VAL 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 1016 GLU 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 1253 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 515 ARG Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 873 GLU Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1353 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 102 optimal weight: 8.9990 chunk 187 optimal weight: 0.0470 chunk 168 optimal weight: 6.9990 chunk 95 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 136 optimal weight: 0.7980 chunk 160 optimal weight: 0.9980 chunk 311 optimal weight: 8.9990 chunk 186 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 HIS ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 954 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 = 0.3992 r_free = 0.3992 target = 0.142041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.090635 restraints weight = 48216.222| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.43 r_work: 0.3019 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28522 Z= 0.156 Angle : 0.567 10.971 38871 Z= 0.291 Chirality : 0.041 0.196 4441 Planarity : 0.004 0.057 4806 Dihedral : 13.816 86.959 4583 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.88 % Favored : 95.09 % Rotamer: Outliers : 1.82 % Allowed : 15.40 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 3340 helix: 1.44 (0.15), residues: 1210 sheet: -0.35 (0.26), residues: 431 loop : -1.51 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 68 HIS 0.007 0.001 HIS J 545 PHE 0.013 0.001 PHE G 231 TYR 0.022 0.001 TYR H 177 ARG 0.014 0.000 ARG I 275 Details of bonding type rmsd hydrogen bonds : bond 0.03628 ( 1103) hydrogen bonds : angle 4.28972 ( 3092) metal coordination : bond 0.00598 ( 8) metal coordination : angle 0.82312 ( 12) covalent geometry : bond 0.00363 (28514) covalent geometry : angle 0.56679 (38859) *********************** 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 393 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 341 time to evaluate : 2.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7787 (pt) REVERT: C 88 MET cc_start: 0.9231 (mmt) cc_final: 0.8672 (tpp) REVERT: C 104 TYR cc_start: 0.6588 (m-80) cc_final: 0.6220 (m-80) REVERT: C 108 ASP cc_start: 0.8210 (t0) cc_final: 0.7672 (t0) REVERT: C 151 ASP cc_start: 0.9522 (t0) cc_final: 0.9289 (t0) REVERT: C 154 PHE cc_start: 0.9318 (m-80) cc_final: 0.8947 (m-10) REVERT: C 159 PHE cc_start: 0.8721 (m-10) cc_final: 0.8374 (m-10) REVERT: C 182 HIS cc_start: 0.8625 (m90) cc_final: 0.8060 (m90) REVERT: H 188 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8563 (mp0) REVERT: I 239 MET cc_start: 0.8754 (ppp) cc_final: 0.8275 (ppp) REVERT: I 330 HIS cc_start: 0.8108 (m-70) cc_final: 0.7832 (m170) REVERT: I 365 GLU cc_start: 0.8772 (tp30) cc_final: 0.8543 (tp30) REVERT: I 685 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8582 (mtt) REVERT: I 949 GLU cc_start: 0.9222 (tt0) cc_final: 0.8988 (tt0) REVERT: I 1273 MET cc_start: 0.9311 (mmm) cc_final: 0.8944 (mtt) REVERT: I 1322 SER cc_start: 0.8963 (m) cc_final: 0.8682 (m) REVERT: J 213 LYS cc_start: 0.9127 (tppt) cc_final: 0.8907 (tppt) REVERT: J 304 ASP cc_start: 0.8344 (m-30) cc_final: 0.8123 (m-30) REVERT: J 506 VAL cc_start: 0.9271 (t) cc_final: 0.8946 (t) REVERT: J 515 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.6947 (mmm-85) REVERT: J 697 MET cc_start: 0.9213 (tmm) cc_final: 0.8943 (tmm) REVERT: J 802 ASP cc_start: 0.8578 (m-30) cc_final: 0.8230 (m-30) REVERT: J 811 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8175 (mt-10) REVERT: J 873 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.8021 (mt-10) REVERT: J 1167 LYS cc_start: 0.9124 (tppt) cc_final: 0.8780 (tppt) REVERT: J 1199 PHE cc_start: 0.9024 (m-80) cc_final: 0.8696 (m-80) REVERT: K 43 ASN cc_start: 0.9121 (t0) cc_final: 0.8815 (t0) REVERT: K 74 GLU cc_start: 0.9394 (tm-30) cc_final: 0.8889 (pp20) outliers start: 52 outliers final: 41 residues processed: 377 average time/residue: 0.4327 time to fit residues: 253.4486 Evaluate side-chains 379 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 334 time to evaluate : 2.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 160 HIS 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 82 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 615 VAL 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 1016 GLU 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 I residue 1253 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 515 ARG Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 873 GLU Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 75 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 262 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 224 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 chunk 91 optimal weight: 0.0370 chunk 4 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 308 optimal weight: 0.3980 chunk 264 optimal weight: 1.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 314 ASN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 979 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.143418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.092441 restraints weight = 48079.892| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.43 r_work: 0.3053 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28522 Z= 0.118 Angle : 0.567 10.975 38871 Z= 0.290 Chirality : 0.041 0.185 4441 Planarity : 0.004 0.063 4806 Dihedral : 13.763 88.938 4583 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.46 % Favored : 95.51 % Rotamer: Outliers : 1.54 % Allowed : 15.68 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 3340 helix: 1.48 (0.15), residues: 1212 sheet: -0.23 (0.27), residues: 412 loop : -1.45 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 68 HIS 0.005 0.001 HIS C 162 PHE 0.010 0.001 PHE J 892 TYR 0.020 0.001 TYR H 177 ARG 0.013 0.000 ARG I 275 Details of bonding type rmsd hydrogen bonds : bond 0.03374 ( 1103) hydrogen bonds : angle 4.23460 ( 3092) metal coordination : bond 0.00347 ( 8) metal coordination : angle 0.81039 ( 12) covalent geometry : bond 0.00268 (28514) covalent geometry : angle 0.56694 (38859) *********************** 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 400 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 356 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 MET cc_start: 0.9081 (mmt) cc_final: 0.8699 (tpp) REVERT: C 104 TYR cc_start: 0.6650 (m-80) cc_final: 0.6264 (m-80) REVERT: C 108 ASP cc_start: 0.8190 (t0) cc_final: 0.7634 (t0) REVERT: C 147 MET cc_start: 0.8886 (tpp) cc_final: 0.8585 (tpp) REVERT: C 151 ASP cc_start: 0.9467 (t0) cc_final: 0.9221 (t0) REVERT: C 154 PHE cc_start: 0.9179 (m-80) cc_final: 0.8778 (m-10) REVERT: C 159 PHE cc_start: 0.8701 (m-10) cc_final: 0.8364 (m-10) REVERT: C 173 LYS cc_start: 0.9483 (mmmm) cc_final: 0.9202 (ttmt) REVERT: C 182 HIS cc_start: 0.8551 (m90) cc_final: 0.7976 (m90) REVERT: I 239 MET cc_start: 0.8730 (ppp) cc_final: 0.8241 (ppp) REVERT: I 365 GLU cc_start: 0.8692 (tp30) cc_final: 0.8475 (tp30) REVERT: I 685 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8510 (mtt) REVERT: I 1034 ARG cc_start: 0.8481 (mmp80) cc_final: 0.8259 (mmp80) REVERT: I 1273 MET cc_start: 0.9257 (mmm) cc_final: 0.8873 (mtt) REVERT: I 1322 SER cc_start: 0.8952 (m) cc_final: 0.8645 (m) REVERT: J 213 LYS cc_start: 0.9118 (tppt) cc_final: 0.8914 (tppt) REVERT: J 304 ASP cc_start: 0.8290 (m-30) cc_final: 0.8067 (m-30) REVERT: J 506 VAL cc_start: 0.9136 (t) cc_final: 0.8802 (t) REVERT: J 515 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.6925 (mmm-85) REVERT: J 697 MET cc_start: 0.9193 (tmm) cc_final: 0.8927 (tmm) REVERT: J 802 ASP cc_start: 0.8554 (m-30) cc_final: 0.8232 (m-30) REVERT: J 811 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8152 (mt-10) REVERT: J 873 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8045 (mt-10) REVERT: J 1151 LYS cc_start: 0.8853 (mmmt) cc_final: 0.8591 (tptm) REVERT: J 1167 LYS cc_start: 0.9129 (tppt) cc_final: 0.8797 (tppt) REVERT: J 1194 ARG cc_start: 0.8670 (ptm160) cc_final: 0.8455 (mtp-110) REVERT: J 1199 PHE cc_start: 0.8951 (m-80) cc_final: 0.8653 (m-80) REVERT: K 43 ASN cc_start: 0.9129 (t0) cc_final: 0.8833 (t0) REVERT: K 74 GLU cc_start: 0.9395 (tm-30) cc_final: 0.8904 (pp20) outliers start: 44 outliers final: 33 residues processed: 385 average time/residue: 0.4299 time to fit residues: 256.3819 Evaluate side-chains 376 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 340 time to evaluate : 3.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 H residue 13 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 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 1016 GLU 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 1233 LEU Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 515 ARG 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 997 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 75 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 13 optimal weight: 4.9990 chunk 251 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 196 optimal weight: 0.8980 chunk 58 optimal weight: 0.1980 chunk 60 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 121 optimal weight: 0.7980 chunk 264 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN I 314 ASN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 954 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 = 0.4000 r_free = 0.4000 target = 0.142611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.091360 restraints weight = 47941.286| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.42 r_work: 0.2987 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28522 Z= 0.141 Angle : 0.580 14.611 38871 Z= 0.296 Chirality : 0.041 0.190 4441 Planarity : 0.004 0.057 4806 Dihedral : 13.737 89.632 4583 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.82 % Favored : 95.15 % Rotamer: Outliers : 1.61 % Allowed : 15.99 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.15), residues: 3340 helix: 1.50 (0.15), residues: 1209 sheet: -0.25 (0.26), residues: 422 loop : -1.42 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 68 HIS 0.008 0.001 HIS I 330 PHE 0.012 0.001 PHE I 230 TYR 0.020 0.001 TYR H 177 ARG 0.021 0.000 ARG I 275 Details of bonding type rmsd hydrogen bonds : bond 0.03488 ( 1103) hydrogen bonds : angle 4.25529 ( 3092) metal coordination : bond 0.00527 ( 8) metal coordination : angle 0.73618 ( 12) covalent geometry : bond 0.00326 (28514) covalent geometry : angle 0.57989 (38859) ********************** 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 391 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 345 time to evaluate : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 MET cc_start: 0.9173 (mmt) cc_final: 0.8709 (tpp) REVERT: C 104 TYR cc_start: 0.6781 (m-80) cc_final: 0.6355 (m-80) REVERT: C 108 ASP cc_start: 0.8251 (t0) cc_final: 0.7711 (t0) REVERT: C 151 ASP cc_start: 0.9452 (t0) cc_final: 0.9223 (t0) REVERT: C 154 PHE cc_start: 0.9229 (m-80) cc_final: 0.8835 (m-10) REVERT: C 182 HIS cc_start: 0.8588 (m90) cc_final: 0.7988 (m90) REVERT: H 80 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8273 (mt-10) REVERT: I 239 MET cc_start: 0.8614 (ppp) cc_final: 0.8117 (ppp) REVERT: I 365 GLU cc_start: 0.8742 (tp30) cc_final: 0.8532 (tp30) REVERT: I 949 GLU cc_start: 0.9185 (tt0) cc_final: 0.8956 (tt0) REVERT: I 1273 MET cc_start: 0.9307 (mmm) cc_final: 0.8907 (mtt) REVERT: I 1322 SER cc_start: 0.8911 (m) cc_final: 0.8616 (m) REVERT: J 213 LYS cc_start: 0.9133 (tppt) cc_final: 0.8915 (tppt) REVERT: J 304 ASP cc_start: 0.8374 (m-30) cc_final: 0.8169 (m-30) REVERT: J 506 VAL cc_start: 0.9222 (t) cc_final: 0.8895 (t) REVERT: J 515 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.6964 (mmm-85) REVERT: J 697 MET cc_start: 0.9222 (tmm) cc_final: 0.8951 (tmm) REVERT: J 802 ASP cc_start: 0.8611 (m-30) cc_final: 0.8280 (m-30) REVERT: J 811 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8112 (mt-10) REVERT: J 873 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.8043 (mt-10) REVERT: J 1151 LYS cc_start: 0.8912 (mmmt) cc_final: 0.8645 (tptm) REVERT: J 1167 LYS cc_start: 0.9117 (tppt) cc_final: 0.8776 (tppt) REVERT: J 1199 PHE cc_start: 0.8981 (m-80) cc_final: 0.8680 (m-80) REVERT: K 43 ASN cc_start: 0.9161 (t0) cc_final: 0.8891 (t0) outliers start: 46 outliers final: 39 residues processed: 375 average time/residue: 0.4344 time to fit residues: 252.3844 Evaluate side-chains 382 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 341 time to evaluate : 3.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ILE 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 H residue 13 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 186 ASN 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 242 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 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 1016 GLU 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 I residue 1253 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 515 ARG Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 873 GLU Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 75 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 160 optimal weight: 7.9990 chunk 320 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 315 optimal weight: 0.0070 chunk 327 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 239 optimal weight: 0.9990 chunk 206 optimal weight: 0.1980 chunk 166 optimal weight: 2.9990 overall best weight: 0.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN I 314 ASN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.142622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.091427 restraints weight = 48129.549| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.44 r_work: 0.3035 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 28522 Z= 0.174 Angle : 0.698 59.195 38871 Z= 0.385 Chirality : 0.050 1.929 4441 Planarity : 0.004 0.132 4806 Dihedral : 13.737 89.624 4583 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.79 % Favored : 95.18 % Rotamer: Outliers : 1.68 % Allowed : 15.99 % Favored : 82.32 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.15), residues: 3340 helix: 1.51 (0.15), residues: 1209 sheet: -0.26 (0.26), residues: 422 loop : -1.42 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 68 HIS 0.026 0.001 HIS C 162 PHE 0.026 0.001 PHE C 159 TYR 0.018 0.001 TYR C 157 ARG 0.028 0.000 ARG I 275 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 1103) hydrogen bonds : angle 4.25598 ( 3092) metal coordination : bond 0.00485 ( 8) metal coordination : angle 0.73493 ( 12) covalent geometry : bond 0.00370 (28514) covalent geometry : angle 0.69837 (38859) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21311.34 seconds wall clock time: 368 minutes 58.64 seconds (22138.64 seconds total)