Starting phenix.real_space_refine on Tue Jun 24 00:50:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pib_17679/06_2025/8pib_17679.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pib_17679/06_2025/8pib_17679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pib_17679/06_2025/8pib_17679.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pib_17679/06_2025/8pib_17679.map" model { file = "/net/cci-nas-00/data/ceres_data/8pib_17679/06_2025/8pib_17679.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pib_17679/06_2025/8pib_17679.cif" } resolution = 2.6 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= 0.007 sd= 0.057 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 1 6.06 5 P 90 5.49 5 Mg 1 5.21 5 S 110 5.16 5 C 17170 2.51 5 N 4934 2.21 5 O 5542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 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: 27848 Number of models: 1 Model: "" Number of chains: 10 Chain: "P" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1073 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 10423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1321, 10423 Classifications: {'peptide': 1321} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1265} Chain breaks: 1 Chain: "J" Number of atoms: 10249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1318, 10249 Classifications: {'peptide': 1318} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1262} Chain breaks: 3 Chain: "K" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 655 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "G" Number of atoms: 1811 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 233, 1803 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 223} Conformer: "B" Number of residues, atoms: 233, 1803 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 223} bond proxies already assigned to first conformer: 1816 Chain: "H" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1741 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 9, 'TRANS': 216} Chain breaks: 1 Chain: "R" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 260 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 5} Link IDs: {'rna3p': 11} Chain: "B" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 826 Classifications: {'DNA': 40} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 39} Chain: "A" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 808 Classifications: {'DNA': 40} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 39} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17579 SG CYS J 814 58.060 125.179 93.358 1.00 99.44 S ATOM 18144 SG CYS J 888 59.993 122.325 92.265 1.00 96.47 S ATOM 18195 SG CYS J 895 58.920 125.138 89.708 1.00 90.42 S ATOM 18216 SG CYS J 898 61.786 125.619 92.033 1.00 96.47 S Time building chain proxies: 17.25, per 1000 atoms: 0.62 Number of scatterers: 27848 At special positions: 0 Unit cell: (140.608, 169.728, 157.248, 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 1 29.99 S 110 16.00 P 90 15.00 Mg 1 11.99 O 5542 8.00 N 4934 7.00 C 17170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS P 51 " - pdb=" SG CYS P 139 " distance=2.03 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: 6.73 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 898 " Number of angles added : 6 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6132 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 52 sheets defined 40.3% alpha, 17.9% beta 41 base pairs and 66 stacking pairs defined. Time for finding SS restraints: 12.27 Creating SS restraints... Processing helix chain 'P' and resid 13 through 24 Processing helix chain 'P' and resid 65 through 72 removed outlier: 3.538A pdb=" N ILE P 69 " --> pdb=" O HIS P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 99 Processing helix chain 'P' and resid 121 through 132 Processing helix chain 'P' and resid 134 through 153 Processing helix chain 'I' and resid 4 through 10 removed outlier: 3.730A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG I 10 " --> pdb=" O THR I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.528A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.776A pdb=" N ALA I 51 " --> pdb=" O TYR I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 4.138A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 3.949A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 289 through 294 removed outlier: 3.956A pdb=" N ALA I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 289 through 294' 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: 4.119A 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 447 through 449 No H-bonds generated for 'chain 'I' and resid 447 through 449' Processing helix chain 'I' and resid 455 through 480 removed outlier: 3.954A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 481 through 482 No H-bonds generated for 'chain 'I' and resid 481 through 482' Processing helix chain 'I' and resid 483 through 487 removed outlier: 3.850A pdb=" N THR I 486 " --> pdb=" O ASP I 483 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 492 removed outlier: 3.676A pdb=" N ASP I 491 " --> pdb=" O MET I 488 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 551 through 555 Processing helix chain 'I' and resid 662 through 667 Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 removed outlier: 4.109A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 826 Processing helix chain 'I' and resid 858 through 864 removed outlier: 4.206A pdb=" N LYS I 864 " --> pdb=" O ALA I 861 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 983 Processing helix chain 'I' and resid 985 through 990 Processing helix chain 'I' and resid 993 through 1000 removed outlier: 3.718A pdb=" N TRP I 997 " --> pdb=" O PRO I 993 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU I 998 " --> pdb=" O ARG I 994 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1037 removed outlier: 3.515A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.179A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.629A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.904A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1177 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1242 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 1311 Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.725A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 96 through 101 Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.547A pdb=" N SER J 119 " --> pdb=" O TRP J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 removed outlier: 3.737A pdb=" N TYR J 140 " --> pdb=" O GLU J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 192 removed outlier: 3.514A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 207 removed outlier: 3.663A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU J 207 " --> pdb=" O GLU J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 230 removed outlier: 3.580A pdb=" N SER J 230 " --> pdb=" O ALA J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 285 Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 327 through 331 Processing helix chain 'J' and resid 336 through 342 removed outlier: 3.558A pdb=" N LEU J 342 " --> pdb=" O PHE J 338 " (cutoff:3.500A) 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 403 removed outlier: 3.962A pdb=" N ARG J 403 " --> pdb=" O LYS J 399 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 416 removed outlier: 4.060A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 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 removed outlier: 3.902A pdb=" N LEU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 581 through 583 No H-bonds generated for 'chain 'J' and resid 581 through 583' Processing helix chain 'J' and resid 588 through 592 removed outlier: 4.062A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.501A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 647 through 671 removed outlier: 3.863A pdb=" N HIS J 651 " --> pdb=" O PRO J 647 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.633A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 729 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.597A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 884 through 888 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 930 Processing helix chain 'J' and resid 1068 through 1073 removed outlier: 3.583A pdb=" N ASP J1073 " --> pdb=" O ALA J1069 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.865A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.259A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1296 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.564A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 removed outlier: 3.535A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1361 through 1375 removed outlier: 4.352A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 17 through 32 Processing helix chain 'K' and resid 45 through 55 removed outlier: 3.795A pdb=" N GLU K 55 " --> pdb=" O LEU K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 84 Processing helix chain 'G' and resid 34 through 48 Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.611A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) 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 154 through 160 Processing helix chain 'G' and resid 212 through 234 removed outlier: 4.353A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.546A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 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 154 through 159 removed outlier: 3.588A pdb=" N ARG H 158 " --> pdb=" O PRO H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 228 removed outlier: 3.635A pdb=" N ILE H 217 " --> pdb=" O PRO H 213 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG H 218 " --> pdb=" O GLU H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 235 removed outlier: 4.487A pdb=" N LEU H 234 " --> pdb=" O ALA H 230 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 27 through 29 removed outlier: 3.597A pdb=" N ASN P 27 " --> pdb=" O GLU P 58 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS P 77 " --> pdb=" O TYR P 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 32 through 33 removed outlier: 3.920A pdb=" N ILE P 33 " --> pdb=" O GLU P 48 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU P 48 " --> pdb=" O ILE P 33 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'P' and resid 80 through 81 Processing sheet with id=AA4, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.654A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.533A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA I 94 " --> pdb=" O GLY I 125 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLY I 125 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU I 96 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TYR I 123 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL I 98 " --> pdb=" O GLU I 121 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLU I 121 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU I 100 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU I 119 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU I 102 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE I 117 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE I 104 " --> pdb=" O LYS I 115 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 136 through 138 Processing sheet with id=AA7, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.180A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 154 through 160 removed outlier: 3.788A pdb=" N ASP I 160 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU I 171 " --> pdb=" O ASP I 160 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 226 through 229 removed outlier: 4.678A pdb=" N GLU I 226 " --> pdb=" O PHE I 337 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 239 through 240 removed outlier: 4.061A pdb=" N MET I 239 " --> pdb=" O ILE I 285 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE I 285 " --> pdb=" O MET I 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'I' and resid 250 through 251 removed outlier: 3.916A pdb=" N ALA I 251 " --> pdb=" O ARG I 267 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG I 267 " --> pdb=" O ALA I 251 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'I' and resid 255 through 257 removed outlier: 7.006A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 301 through 303 removed outlier: 6.793A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.738A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AB7, first strand: chain 'I' and resid 633 through 637 Processing sheet with id=AB8, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.501A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.064A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC2, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC3, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.360A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.823A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 849 through 850 removed outlier: 3.638A pdb=" N GLU I 849 " --> pdb=" O VAL I 887 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.856A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 7.651A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU J 449 " --> pdb=" O VAL J 354 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N THR J 356 " --> pdb=" O LEU J 449 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AC9, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.727A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.687A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 10.095A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.801A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 159 through 160 removed outlier: 6.885A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD4, first strand: chain 'J' and resid 706 through 708 Processing sheet with id=AD5, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AD6, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AD7, first strand: chain 'J' and resid 825 through 826 removed outlier: 7.077A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.844A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.305A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 991 through 996 removed outlier: 3.670A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 1024 through 1028 removed outlier: 4.482A pdb=" N ALA J1122 " --> pdb=" O VAL J1027 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 1034 through 1038 Processing sheet with id=AE4, first strand: chain 'J' and resid 1046 through 1050 removed outlier: 3.792A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 1186 through 1190 removed outlier: 4.348A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.570A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.714A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU G 198 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.527A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AF1, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.756A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AF3, first strand: chain 'H' and resid 15 through 20 removed outlier: 6.589A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N THR H 196 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL H 192 " --> pdb=" O THR H 196 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU H 206 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 97 through 105 removed outlier: 3.654A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AF6, first strand: chain 'H' and resid 110 through 111 removed outlier: 7.570A pdb=" N VAL H 110 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 152 through 153 1145 hydrogen bonds defined for protein. 3236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 107 hydrogen bonds 214 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 66 stacking parallelities Total time for adding SS restraints: 15.03 Time building geometry restraints manager: 7.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9171 1.34 - 1.46: 5166 1.46 - 1.58: 13754 1.58 - 1.70: 180 1.70 - 1.82: 192 Bond restraints: 28463 Sorted by residual: bond pdb=" CB PRO P 133 " pdb=" CG PRO P 133 " ideal model delta sigma weight residual 1.492 1.611 -0.119 5.00e-02 4.00e+02 5.65e+00 bond pdb=" C3' DA A 2 " pdb=" O3' DA A 2 " ideal model delta sigma weight residual 1.422 1.471 -0.049 3.00e-02 1.11e+03 2.65e+00 bond pdb=" CB GLN K 62 " pdb=" CG GLN K 62 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.33e+00 bond pdb=" CA GLU P 132 " pdb=" C GLU P 132 " ideal model delta sigma weight residual 1.524 1.541 -0.017 1.26e-02 6.30e+03 1.83e+00 bond pdb=" CB LYS J 395 " pdb=" CG LYS J 395 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.75e+00 ... (remaining 28458 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 38646 3.15 - 6.30: 173 6.30 - 9.45: 26 9.45 - 12.60: 5 12.60 - 15.74: 4 Bond angle restraints: 38854 Sorted by residual: angle pdb=" CA PRO P 133 " pdb=" N PRO P 133 " pdb=" CD PRO P 133 " ideal model delta sigma weight residual 112.00 102.89 9.11 1.40e+00 5.10e-01 4.23e+01 angle pdb=" CB MET I 488 " pdb=" CG MET I 488 " pdb=" SD MET I 488 " ideal model delta sigma weight residual 112.70 128.44 -15.74 3.00e+00 1.11e-01 2.75e+01 angle pdb=" N PRO P 133 " pdb=" CA PRO P 133 " pdb=" C PRO P 133 " ideal model delta sigma weight residual 112.47 121.37 -8.90 2.06e+00 2.36e-01 1.87e+01 angle pdb=" CB MET J1095 " pdb=" CG MET J1095 " pdb=" SD MET J1095 " ideal model delta sigma weight residual 112.70 125.66 -12.96 3.00e+00 1.11e-01 1.87e+01 angle pdb=" CB MET I 1 " pdb=" CG MET I 1 " pdb=" SD MET I 1 " ideal model delta sigma weight residual 112.70 124.77 -12.07 3.00e+00 1.11e-01 1.62e+01 ... (remaining 38849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 16323 35.59 - 71.18: 934 71.18 - 106.77: 37 106.77 - 142.36: 0 142.36 - 177.95: 4 Dihedral angle restraints: 17298 sinusoidal: 7773 harmonic: 9525 Sorted by residual: dihedral pdb=" O4' U R 6 " pdb=" C1' U R 6 " pdb=" N1 U R 6 " pdb=" C2 U R 6 " ideal model delta sinusoidal sigma weight residual 200.00 42.49 157.51 1 1.50e+01 4.44e-03 8.21e+01 dihedral pdb=" CA VAL H 192 " pdb=" C VAL H 192 " pdb=" N GLU H 193 " pdb=" CA GLU H 193 " ideal model delta harmonic sigma weight residual -180.00 -153.05 -26.95 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CB CYS P 51 " pdb=" SG CYS P 51 " pdb=" SG CYS P 139 " pdb=" CB CYS P 139 " ideal model delta sinusoidal sigma weight residual 93.00 57.75 35.25 1 1.00e+01 1.00e-02 1.76e+01 ... (remaining 17295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4043 0.073 - 0.147: 392 0.147 - 0.220: 5 0.220 - 0.293: 1 0.293 - 0.367: 1 Chirality restraints: 4442 Sorted by residual: chirality pdb=" CG LEU P 143 " pdb=" CB LEU P 143 " pdb=" CD1 LEU P 143 " pdb=" CD2 LEU P 143 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA PRO P 133 " pdb=" N PRO P 133 " pdb=" C PRO P 133 " pdb=" CB PRO P 133 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA GLU P 132 " pdb=" N GLU P 132 " pdb=" C GLU P 132 " pdb=" CB GLU P 132 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 4439 not shown) Planarity restraints: 4762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU P 132 " -0.097 5.00e-02 4.00e+02 1.43e-01 3.27e+01 pdb=" N PRO P 133 " 0.247 5.00e-02 4.00e+02 pdb=" CA PRO P 133 " -0.076 5.00e-02 4.00e+02 pdb=" CD PRO P 133 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 10 " 0.049 5.00e-02 4.00e+02 7.41e-02 8.78e+00 pdb=" N PRO H 11 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO H 11 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 11 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU K 11 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" CD GLU K 11 " -0.034 2.00e-02 2.50e+03 pdb=" OE1 GLU K 11 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU K 11 " 0.012 2.00e-02 2.50e+03 ... (remaining 4759 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 235 2.57 - 3.15: 21386 3.15 - 3.73: 45732 3.73 - 4.32: 61290 4.32 - 4.90: 102050 Nonbonded interactions: 230693 Sorted by model distance: nonbonded pdb=" OP1 U R 17 " pdb="MG MG J1502 " model vdw 1.982 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1502 " model vdw 2.052 2.170 nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1502 " model vdw 2.053 2.170 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1502 " model vdw 2.069 2.170 nonbonded pdb=" O3' G R 16 " pdb="MG MG J1502 " model vdw 2.102 2.170 ... (remaining 230688 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 3 through 159 or resid 167 through 218 or resid 220 throug \ h 235)) selection = (chain 'H' and (resid 3 through 218 or resid 220 through 235)) } 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=0.46 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: 3.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.190 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 81.050 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.130 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:12.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.119 28468 Z= 0.115 Angle : 0.581 15.745 38862 Z= 0.292 Chirality : 0.041 0.367 4442 Planarity : 0.004 0.143 4762 Dihedral : 19.352 177.947 11163 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.64 % Favored : 97.30 % Rotamer: Outliers : 2.65 % Allowed : 25.35 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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: 0.93 (0.15), residues: 3293 helix: 1.98 (0.16), residues: 1166 sheet: 0.52 (0.24), residues: 491 loop : -0.33 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J1193 HIS 0.002 0.000 HIS J1366 PHE 0.011 0.001 PHE P 130 TYR 0.020 0.001 TYR G 185 ARG 0.012 0.000 ARG K 67 Details of bonding type rmsd hydrogen bonds : bond 0.13194 ( 1250) hydrogen bonds : angle 5.14411 ( 3450) metal coordination : bond 0.00422 ( 4) metal coordination : angle 5.53219 ( 6) SS BOND : bond 0.00099 ( 1) SS BOND : angle 2.19386 ( 2) covalent geometry : bond 0.00265 (28463) covalent geometry : angle 0.57668 (38854) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 263 time to evaluate : 3.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 18 GLN cc_start: 0.8861 (tt0) cc_final: 0.8614 (tp40) REVERT: P 22 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8302 (mm-30) REVERT: P 33 ILE cc_start: 0.7072 (tp) cc_final: 0.6801 (pp) REVERT: P 150 ILE cc_start: 0.6695 (mm) cc_final: 0.6373 (tp) REVERT: J 714 GLU cc_start: 0.8753 (tp30) cc_final: 0.8299 (tp30) REVERT: G 93 GLN cc_start: 0.7971 (mp10) cc_final: 0.7439 (mp10) REVERT: H 25 LYS cc_start: 0.8856 (mtpp) cc_final: 0.8543 (tttp) REVERT: H 65 LEU cc_start: 0.9145 (pp) cc_final: 0.8828 (pt) outliers start: 75 outliers final: 67 residues processed: 330 average time/residue: 1.3559 time to fit residues: 525.7350 Evaluate side-chains 316 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 249 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 CYS Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 995 ASP Chi-restraints excluded: chain I residue 1155 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 666 GLU Chi-restraints excluded: chain J residue 670 SER Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1088 VAL Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 168 ILE Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 285 optimal weight: 0.1980 chunk 256 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 172 optimal weight: 8.9990 chunk 136 optimal weight: 0.1980 chunk 264 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 197 optimal weight: 7.9990 chunk 306 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 95 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 424 ASN J 792 ASN J 875 ASN ** J 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN H 186 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.098802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.068046 restraints weight = 76125.074| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.84 r_work: 0.3025 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 28468 Z= 0.155 Angle : 0.549 9.858 38862 Z= 0.284 Chirality : 0.042 0.329 4442 Planarity : 0.004 0.148 4762 Dihedral : 16.856 179.210 4788 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.86 % Favored : 97.08 % Rotamer: Outliers : 3.96 % Allowed : 22.90 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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: 0.87 (0.15), residues: 3293 helix: 1.89 (0.15), residues: 1205 sheet: 0.42 (0.24), residues: 496 loop : -0.37 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 409 HIS 0.002 0.001 HIS G 66 PHE 0.015 0.001 PHE P 78 TYR 0.013 0.001 TYR J 631 ARG 0.007 0.000 ARG P 138 Details of bonding type rmsd hydrogen bonds : bond 0.03953 ( 1250) hydrogen bonds : angle 4.36653 ( 3450) metal coordination : bond 0.00654 ( 4) metal coordination : angle 7.06605 ( 6) SS BOND : bond 0.00003 ( 1) SS BOND : angle 2.41462 ( 2) covalent geometry : bond 0.00357 (28463) covalent geometry : angle 0.54147 (38854) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 282 time to evaluate : 3.287 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: P 13 GLN cc_start: 0.8593 (mp10) cc_final: 0.8291 (mp10) REVERT: P 15 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7763 (tp-100) REVERT: P 100 LYS cc_start: 0.7148 (OUTLIER) cc_final: 0.6886 (tppt) REVERT: P 150 ILE cc_start: 0.6633 (mm) cc_final: 0.6316 (tp) REVERT: I 201 ARG cc_start: 0.8546 (mtm-85) cc_final: 0.8312 (mtm-85) REVERT: I 694 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8143 (mtp85) REVERT: I 1329 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7562 (mt-10) REVERT: J 136 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8041 (pm20) REVERT: J 166 LEU cc_start: 0.9269 (mm) cc_final: 0.8938 (pp) REVERT: J 206 ASN cc_start: 0.9150 (m110) cc_final: 0.8746 (m110) REVERT: J 404 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7554 (tm-30) REVERT: J 714 GLU cc_start: 0.8747 (tp30) cc_final: 0.8291 (tp30) REVERT: J 990 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8546 (mpt-90) REVERT: J 1084 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7451 (pp30) REVERT: K 56 GLU cc_start: 0.8553 (pm20) cc_final: 0.8246 (pm20) REVERT: H 65 LEU cc_start: 0.9200 (pp) cc_final: 0.8919 (pt) REVERT: H 68 TYR cc_start: 0.8616 (p90) cc_final: 0.8214 (p90) outliers start: 112 outliers final: 46 residues processed: 370 average time/residue: 1.5162 time to fit residues: 649.0736 Evaluate side-chains 308 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 254 time to evaluate : 3.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 100 LYS Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 694 ARG Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 404 GLU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 889 ASP Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 990 ARG Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1084 GLN Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 123 optimal weight: 3.9990 chunk 10 optimal weight: 20.0000 chunk 239 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 208 optimal weight: 9.9990 chunk 185 optimal weight: 0.9980 chunk 332 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 307 optimal weight: 0.6980 chunk 233 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 95 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 962 ASN J1195 GLN K 43 ASN G 186 ASN H 186 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.098794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.068222 restraints weight = 76431.199| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.83 r_work: 0.3028 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 28468 Z= 0.132 Angle : 0.533 10.000 38862 Z= 0.275 Chirality : 0.041 0.338 4442 Planarity : 0.004 0.143 4762 Dihedral : 16.765 179.396 4730 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.70 % Favored : 97.24 % Rotamer: Outliers : 3.82 % Allowed : 23.89 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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: 0.83 (0.15), residues: 3293 helix: 1.84 (0.15), residues: 1209 sheet: 0.42 (0.23), residues: 499 loop : -0.38 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 4 HIS 0.003 0.001 HIS H 66 PHE 0.013 0.001 PHE P 78 TYR 0.013 0.001 TYR J 631 ARG 0.008 0.000 ARG J 322 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 1250) hydrogen bonds : angle 4.19900 ( 3450) metal coordination : bond 0.00618 ( 4) metal coordination : angle 7.00491 ( 6) SS BOND : bond 0.00060 ( 1) SS BOND : angle 2.19766 ( 2) covalent geometry : bond 0.00302 (28463) covalent geometry : angle 0.52590 (38854) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 274 time to evaluate : 3.005 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: P 11 ARG cc_start: 0.7981 (tmm160) cc_final: 0.7652 (tmm160) REVERT: P 13 GLN cc_start: 0.8569 (mp10) cc_final: 0.8181 (mp10) REVERT: P 15 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7748 (tp-100) REVERT: P 123 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7957 (t80) REVERT: P 150 ILE cc_start: 0.6603 (mm) cc_final: 0.6287 (tp) REVERT: I 83 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8727 (mm-40) REVERT: I 241 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6447 (tm) REVERT: I 694 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8167 (mtp85) REVERT: I 1329 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7544 (mt-10) REVERT: J 136 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8006 (pm20) REVERT: J 166 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8927 (pp) REVERT: J 206 ASN cc_start: 0.9160 (m110) cc_final: 0.8751 (m110) REVERT: J 300 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8185 (tt0) REVERT: J 404 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7612 (tm-30) REVERT: J 990 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8562 (mpt-90) REVERT: J 1084 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7426 (pp30) REVERT: K 56 GLU cc_start: 0.8592 (pm20) cc_final: 0.8200 (pm20) REVERT: H 65 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8930 (pt) outliers start: 108 outliers final: 51 residues processed: 353 average time/residue: 1.8216 time to fit residues: 753.0065 Evaluate side-chains 322 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 258 time to evaluate : 3.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 CYS Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 694 ARG Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1340 GLU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 300 GLN Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 404 GLU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 666 GLU Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 990 ARG Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1084 GLN Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 20 optimal weight: 2.9990 chunk 218 optimal weight: 0.9990 chunk 209 optimal weight: 10.0000 chunk 309 optimal weight: 7.9990 chunk 114 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 248 optimal weight: 0.0980 chunk 113 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 337 optimal weight: 7.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 77 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1114 GLN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN H 186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.098886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.068317 restraints weight = 80359.263| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.87 r_work: 0.3027 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 28468 Z= 0.124 Angle : 0.530 10.163 38862 Z= 0.273 Chirality : 0.041 0.330 4442 Planarity : 0.004 0.143 4762 Dihedral : 16.735 179.827 4723 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.73 % Favored : 97.21 % Rotamer: Outliers : 3.75 % Allowed : 24.28 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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: 0.85 (0.15), residues: 3293 helix: 1.87 (0.15), residues: 1202 sheet: 0.43 (0.23), residues: 502 loop : -0.38 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 409 HIS 0.003 0.001 HIS G 160 PHE 0.015 0.001 PHE J1034 TYR 0.014 0.001 TYR I 123 ARG 0.012 0.000 ARG I 275 Details of bonding type rmsd hydrogen bonds : bond 0.03455 ( 1250) hydrogen bonds : angle 4.10454 ( 3450) metal coordination : bond 0.00588 ( 4) metal coordination : angle 7.02295 ( 6) SS BOND : bond 0.00044 ( 1) SS BOND : angle 2.39852 ( 2) covalent geometry : bond 0.00284 (28463) covalent geometry : angle 0.52261 (38854) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 274 time to evaluate : 3.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 11 ARG cc_start: 0.7878 (tmm160) cc_final: 0.7602 (tmm160) REVERT: P 13 GLN cc_start: 0.8584 (mp10) cc_final: 0.8188 (mp10) REVERT: P 15 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7783 (tp-100) REVERT: P 26 VAL cc_start: 0.8627 (t) cc_final: 0.8418 (p) REVERT: P 58 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7149 (tt0) REVERT: P 150 ILE cc_start: 0.6581 (mm) cc_final: 0.6273 (tp) REVERT: I 83 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8712 (mm-40) REVERT: I 121 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8383 (tt0) REVERT: I 241 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6421 (tm) REVERT: I 275 ARG cc_start: 0.9396 (mmm160) cc_final: 0.9011 (tpm-80) REVERT: I 694 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8195 (mtp85) REVERT: I 951 MET cc_start: 0.8724 (mmm) cc_final: 0.8469 (mmt) REVERT: I 1329 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7564 (mt-10) REVERT: J 136 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7983 (pm20) REVERT: J 166 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8910 (pp) REVERT: J 300 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: J 404 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7621 (tm-30) REVERT: J 990 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8542 (mpt-90) REVERT: J 1084 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7412 (pp30) REVERT: K 3 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7994 (ttm-80) REVERT: K 55 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7221 (mt-10) REVERT: K 56 GLU cc_start: 0.8629 (pm20) cc_final: 0.8093 (pm20) REVERT: K 79 GLU cc_start: 0.3081 (OUTLIER) cc_final: 0.2769 (tt0) REVERT: G 145 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8771 (tttp) outliers start: 106 outliers final: 46 residues processed: 352 average time/residue: 1.4825 time to fit residues: 604.4930 Evaluate side-chains 321 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 258 time to evaluate : 3.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 27 ASN Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 694 ARG Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1340 GLU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 300 GLN Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 404 GLU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 666 GLU Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 990 ARG Chi-restraints excluded: chain J residue 1084 GLN Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 187 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 171 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 337 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 41 optimal weight: 30.0000 chunk 79 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 95 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN G 186 ASN H 186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.096875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.066193 restraints weight = 69496.537| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.71 r_work: 0.2986 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 28468 Z= 0.196 Angle : 0.578 12.026 38862 Z= 0.297 Chirality : 0.043 0.309 4442 Planarity : 0.004 0.143 4762 Dihedral : 16.773 177.297 4720 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.01 % Favored : 96.93 % Rotamer: Outliers : 4.18 % Allowed : 24.14 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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 (0.15), residues: 3293 helix: 1.79 (0.15), residues: 1197 sheet: 0.26 (0.23), residues: 499 loop : -0.43 (0.15), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 4 HIS 0.004 0.001 HIS I 273 PHE 0.039 0.001 PHE P 126 TYR 0.016 0.001 TYR J 631 ARG 0.011 0.000 ARG J 322 Details of bonding type rmsd hydrogen bonds : bond 0.04020 ( 1250) hydrogen bonds : angle 4.21431 ( 3450) metal coordination : bond 0.01094 ( 4) metal coordination : angle 8.09618 ( 6) SS BOND : bond 0.00044 ( 1) SS BOND : angle 3.24008 ( 2) covalent geometry : bond 0.00457 (28463) covalent geometry : angle 0.56831 (38854) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 268 time to evaluate : 3.085 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: P 2 GLN cc_start: 0.5408 (tm-30) cc_final: 0.4913 (tm-30) REVERT: P 11 ARG cc_start: 0.8053 (tmm160) cc_final: 0.7751 (tmm160) REVERT: P 13 GLN cc_start: 0.8694 (mp10) cc_final: 0.8221 (mp10) REVERT: P 15 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7806 (tp-100) REVERT: P 58 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7069 (tt0) REVERT: P 123 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7649 (t80) REVERT: I 83 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8680 (mm-40) REVERT: I 121 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8415 (tt0) REVERT: I 241 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6363 (tm) REVERT: I 654 ASP cc_start: 0.8447 (m-30) cc_final: 0.8242 (m-30) REVERT: I 694 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8186 (mtp85) REVERT: I 951 MET cc_start: 0.8724 (mmm) cc_final: 0.8473 (mmt) REVERT: I 1329 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7562 (mt-10) REVERT: J 136 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7964 (pm20) REVERT: J 166 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8916 (pp) REVERT: J 206 ASN cc_start: 0.9166 (m110) cc_final: 0.8770 (m110) REVERT: J 354 VAL cc_start: 0.9254 (OUTLIER) cc_final: 0.8957 (t) REVERT: J 404 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7634 (tm-30) REVERT: K 18 ASP cc_start: 0.8525 (m-30) cc_final: 0.8288 (m-30) REVERT: K 56 GLU cc_start: 0.8620 (pm20) cc_final: 0.8063 (pm20) REVERT: K 79 GLU cc_start: 0.2969 (OUTLIER) cc_final: 0.2712 (tt0) outliers start: 118 outliers final: 54 residues processed: 353 average time/residue: 1.5545 time to fit residues: 634.4382 Evaluate side-chains 326 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 259 time to evaluate : 3.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 CYS Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 27 ASN Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 439 LYS Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 694 ARG Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1340 GLU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 404 GLU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 666 GLU Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 196 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 287 optimal weight: 0.5980 chunk 138 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 212 optimal weight: 0.5980 chunk 331 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 317 optimal weight: 4.9990 chunk 199 optimal weight: 0.8980 chunk 202 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN K 43 ASN H 186 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.098004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.067579 restraints weight = 70551.285| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.70 r_work: 0.3017 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 28468 Z= 0.129 Angle : 0.564 12.762 38862 Z= 0.288 Chirality : 0.041 0.318 4442 Planarity : 0.004 0.140 4762 Dihedral : 16.735 177.563 4718 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 3.33 % Allowed : 25.13 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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: 0.81 (0.15), residues: 3293 helix: 1.86 (0.15), residues: 1196 sheet: 0.25 (0.23), residues: 510 loop : -0.36 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 4 HIS 0.003 0.000 HIS J1366 PHE 0.036 0.001 PHE P 126 TYR 0.013 0.001 TYR J 631 ARG 0.013 0.000 ARG I 275 Details of bonding type rmsd hydrogen bonds : bond 0.03528 ( 1250) hydrogen bonds : angle 4.11683 ( 3450) metal coordination : bond 0.00643 ( 4) metal coordination : angle 7.63913 ( 6) SS BOND : bond 0.00786 ( 1) SS BOND : angle 3.11687 ( 2) covalent geometry : bond 0.00299 (28463) covalent geometry : angle 0.55574 (38854) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 274 time to evaluate : 3.106 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: P 11 ARG cc_start: 0.8041 (tmm160) cc_final: 0.7808 (tmm160) REVERT: P 13 GLN cc_start: 0.8669 (mp10) cc_final: 0.8201 (mp10) REVERT: P 15 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7793 (tp-100) REVERT: P 123 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7651 (t80) REVERT: P 132 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7929 (pm20) REVERT: P 142 LEU cc_start: 0.8909 (tm) cc_final: 0.8682 (tm) REVERT: I 83 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8673 (mm-40) REVERT: I 121 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: I 241 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6375 (tm) REVERT: I 694 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8176 (mtp85) REVERT: I 951 MET cc_start: 0.8746 (mmm) cc_final: 0.8491 (mmt) REVERT: I 1327 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8517 (mp) REVERT: I 1329 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7539 (mt-10) REVERT: J 136 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7925 (pm20) REVERT: J 166 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8898 (pp) REVERT: J 206 ASN cc_start: 0.9158 (m110) cc_final: 0.8749 (m110) REVERT: J 354 VAL cc_start: 0.9235 (OUTLIER) cc_final: 0.8931 (t) REVERT: J 404 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7596 (tm-30) REVERT: J 1084 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7558 (pp30) REVERT: K 3 ARG cc_start: 0.8551 (ttm-80) cc_final: 0.8317 (ttm-80) REVERT: K 79 GLU cc_start: 0.3190 (OUTLIER) cc_final: 0.2940 (tt0) REVERT: G 58 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8527 (mt-10) REVERT: G 93 GLN cc_start: 0.8412 (mp10) cc_final: 0.7918 (mp10) outliers start: 94 outliers final: 47 residues processed: 343 average time/residue: 1.5157 time to fit residues: 600.8801 Evaluate side-chains 320 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 257 time to evaluate : 3.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 CYS Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain P residue 132 GLU Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 694 ARG Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 404 GLU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 666 GLU Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1084 GLN Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 196 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 142 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 chunk 168 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 chunk 273 optimal weight: 0.7980 chunk 220 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 95 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 792 ASN ** J 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN G 186 ASN H 186 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.097318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.067013 restraints weight = 68787.182| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.66 r_work: 0.3005 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 28468 Z= 0.158 Angle : 0.591 14.201 38862 Z= 0.300 Chirality : 0.042 0.310 4442 Planarity : 0.004 0.138 4762 Dihedral : 16.708 177.253 4713 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.95 % Favored : 96.99 % Rotamer: Outliers : 3.01 % Allowed : 25.84 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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: 0.79 (0.15), residues: 3293 helix: 1.88 (0.15), residues: 1189 sheet: 0.18 (0.23), residues: 520 loop : -0.37 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 4 HIS 0.003 0.001 HIS J1366 PHE 0.034 0.001 PHE P 126 TYR 0.017 0.001 TYR I 123 ARG 0.012 0.000 ARG J 322 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 1250) hydrogen bonds : angle 4.12744 ( 3450) metal coordination : bond 0.00861 ( 4) metal coordination : angle 7.80428 ( 6) SS BOND : bond 0.00364 ( 1) SS BOND : angle 6.59456 ( 2) covalent geometry : bond 0.00368 (28463) covalent geometry : angle 0.58066 (38854) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 269 time to evaluate : 3.218 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: P 2 GLN cc_start: 0.5274 (tm-30) cc_final: 0.5010 (tm-30) REVERT: P 11 ARG cc_start: 0.8030 (tmm160) cc_final: 0.7789 (tmm160) REVERT: P 13 GLN cc_start: 0.8703 (mp10) cc_final: 0.8222 (mp10) REVERT: P 15 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7798 (tp-100) REVERT: P 51 CYS cc_start: 0.5007 (t) cc_final: 0.4720 (t) REVERT: P 58 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7159 (tt0) REVERT: P 123 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7682 (t80) REVERT: P 132 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7849 (pm20) REVERT: P 138 ARG cc_start: 0.8957 (mtm110) cc_final: 0.8732 (mtm110) REVERT: P 139 CYS cc_start: 0.7923 (t) cc_final: 0.7567 (t) REVERT: P 142 LEU cc_start: 0.8942 (tm) cc_final: 0.8724 (tm) REVERT: I 83 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8676 (mm-40) REVERT: I 121 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8334 (tt0) REVERT: I 241 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6408 (tm) REVERT: I 275 ARG cc_start: 0.9326 (mmm160) cc_final: 0.8910 (tpm-80) REVERT: I 654 ASP cc_start: 0.8409 (m-30) cc_final: 0.8203 (m-30) REVERT: I 694 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8178 (mtp85) REVERT: I 951 MET cc_start: 0.8751 (mmm) cc_final: 0.8507 (mmt) REVERT: I 1327 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8525 (mp) REVERT: I 1329 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7536 (mt-10) REVERT: J 136 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7908 (pm20) REVERT: J 166 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8896 (pp) REVERT: J 206 ASN cc_start: 0.9151 (m110) cc_final: 0.8747 (m110) REVERT: J 354 VAL cc_start: 0.9238 (OUTLIER) cc_final: 0.8935 (t) REVERT: J 404 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7700 (tm-30) REVERT: J 762 ASN cc_start: 0.7765 (OUTLIER) cc_final: 0.7563 (m110) REVERT: J 992 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8380 (mmmm) REVERT: J 1084 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7638 (pp30) REVERT: K 18 ASP cc_start: 0.8513 (m-30) cc_final: 0.8279 (m-30) REVERT: K 56 GLU cc_start: 0.8898 (pm20) cc_final: 0.8338 (pm20) REVERT: K 79 GLU cc_start: 0.3201 (OUTLIER) cc_final: 0.2943 (tt0) outliers start: 85 outliers final: 48 residues processed: 333 average time/residue: 1.5693 time to fit residues: 604.9298 Evaluate side-chains 325 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 259 time to evaluate : 3.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain P residue 132 GLU Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 439 LYS Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 694 ARG Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 404 GLU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 666 GLU Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 992 LYS Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1084 GLN Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 196 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 156 optimal weight: 7.9990 chunk 227 optimal weight: 0.0570 chunk 34 optimal weight: 5.9990 chunk 218 optimal weight: 3.9990 chunk 268 optimal weight: 1.9990 chunk 297 optimal weight: 0.0970 chunk 104 optimal weight: 0.8980 chunk 196 optimal weight: 4.9990 chunk 304 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 235 optimal weight: 9.9990 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 77 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 962 ASN K 31 GLN K 43 ASN H 186 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.098094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.067784 restraints weight = 71195.798| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.72 r_work: 0.3021 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 28468 Z= 0.127 Angle : 0.577 14.878 38862 Z= 0.292 Chirality : 0.041 0.299 4442 Planarity : 0.004 0.136 4762 Dihedral : 16.681 176.969 4713 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.86 % Favored : 97.08 % Rotamer: Outliers : 2.90 % Allowed : 26.30 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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: 0.83 (0.15), residues: 3293 helix: 1.90 (0.15), residues: 1196 sheet: 0.23 (0.23), residues: 520 loop : -0.34 (0.16), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 4 HIS 0.003 0.000 HIS I 447 PHE 0.030 0.001 PHE P 126 TYR 0.016 0.001 TYR I 123 ARG 0.014 0.000 ARG J 322 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 1250) hydrogen bonds : angle 4.07001 ( 3450) metal coordination : bond 0.00607 ( 4) metal coordination : angle 7.46432 ( 6) SS BOND : bond 0.00212 ( 1) SS BOND : angle 6.10676 ( 2) covalent geometry : bond 0.00296 (28463) covalent geometry : angle 0.56797 (38854) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 274 time to evaluate : 3.553 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: P 2 GLN cc_start: 0.5464 (tm-30) cc_final: 0.5253 (tm-30) REVERT: P 13 GLN cc_start: 0.8684 (mp10) cc_final: 0.8232 (mp10) REVERT: P 15 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7799 (tp-100) REVERT: P 58 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7224 (tt0) REVERT: P 123 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7667 (t80) REVERT: P 132 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7788 (pm20) REVERT: I 40 GLU cc_start: 0.7950 (pt0) cc_final: 0.7693 (pm20) REVERT: I 83 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8681 (mm-40) REVERT: I 121 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8306 (tt0) REVERT: I 241 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6386 (tm) REVERT: I 694 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8192 (mtp85) REVERT: I 951 MET cc_start: 0.8746 (mmm) cc_final: 0.8516 (mmt) REVERT: J 136 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7924 (pm20) REVERT: J 166 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8883 (pp) REVERT: J 206 ASN cc_start: 0.9131 (m110) cc_final: 0.8728 (m110) REVERT: J 354 VAL cc_start: 0.9220 (OUTLIER) cc_final: 0.8917 (t) REVERT: J 404 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7651 (tm-30) REVERT: J 762 ASN cc_start: 0.7567 (OUTLIER) cc_final: 0.7360 (m110) REVERT: J 992 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8378 (mmmm) REVERT: J 1084 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7757 (pp30) REVERT: J 1101 LEU cc_start: 0.8717 (mp) cc_final: 0.8367 (mp) REVERT: K 56 GLU cc_start: 0.8885 (pm20) cc_final: 0.8380 (pm20) REVERT: K 79 GLU cc_start: 0.3319 (OUTLIER) cc_final: 0.3108 (tt0) outliers start: 82 outliers final: 46 residues processed: 337 average time/residue: 2.4810 time to fit residues: 990.9778 Evaluate side-chains 326 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 264 time to evaluate : 3.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain P residue 132 GLU Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 694 ARG Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 404 GLU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 666 GLU Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 992 LYS Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1084 GLN Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 196 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 290 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 36 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 237 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 285 optimal weight: 5.9990 chunk 4 optimal weight: 30.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 792 ASN K 31 GLN K 43 ASN G 186 ASN H 93 GLN H 186 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.096938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.066737 restraints weight = 65495.427| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.59 r_work: 0.2999 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 28468 Z= 0.173 Angle : 0.607 15.378 38862 Z= 0.307 Chirality : 0.042 0.292 4442 Planarity : 0.004 0.134 4762 Dihedral : 16.700 176.607 4710 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.10 % Favored : 96.84 % Rotamer: Outliers : 2.62 % Allowed : 26.58 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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: 0.80 (0.15), residues: 3293 helix: 1.87 (0.15), residues: 1199 sheet: 0.21 (0.24), residues: 507 loop : -0.37 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 4 HIS 0.003 0.001 HIS J1366 PHE 0.029 0.001 PHE P 126 TYR 0.017 0.001 TYR I 123 ARG 0.013 0.000 ARG J 322 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 1250) hydrogen bonds : angle 4.12984 ( 3450) metal coordination : bond 0.00973 ( 4) metal coordination : angle 7.94321 ( 6) SS BOND : bond 0.00372 ( 1) SS BOND : angle 2.95857 ( 2) covalent geometry : bond 0.00405 (28463) covalent geometry : angle 0.59854 (38854) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 269 time to evaluate : 2.957 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: P 11 ARG cc_start: 0.8058 (tmm160) cc_final: 0.7674 (tmm160) REVERT: P 13 GLN cc_start: 0.8821 (mp10) cc_final: 0.8274 (mp10) REVERT: P 15 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7894 (tp-100) REVERT: P 58 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7402 (tt0) REVERT: P 123 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7688 (t80) REVERT: P 132 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7873 (pm20) REVERT: I 40 GLU cc_start: 0.8264 (pt0) cc_final: 0.7891 (pm20) REVERT: I 83 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8814 (mm-40) REVERT: I 121 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8519 (tt0) REVERT: I 275 ARG cc_start: 0.9354 (mmm160) cc_final: 0.8997 (tpm-80) REVERT: I 694 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8346 (mtp85) REVERT: I 951 MET cc_start: 0.8962 (mmm) cc_final: 0.8724 (mmt) REVERT: J 136 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8057 (pm20) REVERT: J 166 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8881 (pp) REVERT: J 354 VAL cc_start: 0.9298 (OUTLIER) cc_final: 0.9011 (t) REVERT: J 404 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7851 (tm-30) REVERT: J 762 ASN cc_start: 0.7994 (OUTLIER) cc_final: 0.7786 (m110) REVERT: J 992 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8396 (mmmm) REVERT: K 18 ASP cc_start: 0.8743 (m-30) cc_final: 0.8498 (m-30) REVERT: K 56 GLU cc_start: 0.8963 (pm20) cc_final: 0.8523 (pm20) outliers start: 74 outliers final: 45 residues processed: 325 average time/residue: 1.5653 time to fit residues: 588.4648 Evaluate side-chains 319 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 261 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain P residue 132 GLU Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 694 ARG Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 404 GLU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 666 GLU Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 992 LYS Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 187 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 209 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 168 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 336 optimal weight: 5.9990 chunk 284 optimal weight: 2.9990 chunk 330 optimal weight: 10.0000 chunk 138 optimal weight: 0.7980 chunk 194 optimal weight: 0.5980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN H 93 GLN H 186 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.097120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.066585 restraints weight = 76266.059| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.79 r_work: 0.2990 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 28468 Z= 0.158 Angle : 0.611 16.216 38862 Z= 0.308 Chirality : 0.042 0.282 4442 Planarity : 0.004 0.131 4762 Dihedral : 16.690 176.388 4707 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.04 % Favored : 96.90 % Rotamer: Outliers : 2.30 % Allowed : 27.01 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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: 0.80 (0.15), residues: 3293 helix: 1.87 (0.15), residues: 1200 sheet: 0.20 (0.23), residues: 508 loop : -0.37 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 4 HIS 0.003 0.001 HIS J1366 PHE 0.028 0.001 PHE P 126 TYR 0.017 0.001 TYR I 123 ARG 0.015 0.000 ARG J 322 Details of bonding type rmsd hydrogen bonds : bond 0.03693 ( 1250) hydrogen bonds : angle 4.13169 ( 3450) metal coordination : bond 0.00854 ( 4) metal coordination : angle 7.97096 ( 6) SS BOND : bond 0.00323 ( 1) SS BOND : angle 3.30544 ( 2) covalent geometry : bond 0.00370 (28463) covalent geometry : angle 0.60210 (38854) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 264 time to evaluate : 3.203 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: P 11 ARG cc_start: 0.8042 (tmm160) cc_final: 0.7694 (tmm160) REVERT: P 13 GLN cc_start: 0.8739 (mp10) cc_final: 0.8250 (mp10) REVERT: P 15 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7794 (tp-100) REVERT: P 58 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6858 (tt0) REVERT: P 123 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7662 (t80) REVERT: P 132 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7861 (pm20) REVERT: I 40 GLU cc_start: 0.7975 (pt0) cc_final: 0.7711 (pm20) REVERT: I 83 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8708 (mm-40) REVERT: I 121 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8335 (tt0) REVERT: I 275 ARG cc_start: 0.9330 (mmm160) cc_final: 0.8856 (tpm-80) REVERT: I 951 MET cc_start: 0.8743 (mmm) cc_final: 0.8511 (mmt) REVERT: J 136 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7909 (pm20) REVERT: J 166 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8885 (pp) REVERT: J 354 VAL cc_start: 0.9247 (OUTLIER) cc_final: 0.8943 (t) REVERT: J 992 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8405 (mmmm) REVERT: J 1101 LEU cc_start: 0.8723 (mp) cc_final: 0.8360 (mp) REVERT: K 18 ASP cc_start: 0.8527 (m-30) cc_final: 0.8278 (m-30) REVERT: K 56 GLU cc_start: 0.8881 (pm20) cc_final: 0.8445 (pm20) outliers start: 65 outliers final: 43 residues processed: 310 average time/residue: 1.5638 time to fit residues: 563.4412 Evaluate side-chains 311 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 258 time to evaluate : 2.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain P residue 132 GLU Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1340 GLU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 666 GLU Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 992 LYS Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 187 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 223 optimal weight: 0.5980 chunk 297 optimal weight: 0.6980 chunk 133 optimal weight: 0.8980 chunk 50 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 277 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 285 optimal weight: 0.9990 chunk 204 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 95 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 792 ASN ** J 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN G 186 ASN H 93 GLN H 186 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.098346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.067705 restraints weight = 79477.209| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.89 r_work: 0.3019 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 28468 Z= 0.124 Angle : 0.601 17.282 38862 Z= 0.303 Chirality : 0.041 0.280 4442 Planarity : 0.004 0.131 4762 Dihedral : 16.648 176.481 4705 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.01 % Favored : 96.93 % Rotamer: Outliers : 1.95 % Allowed : 27.43 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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: 0.84 (0.15), residues: 3293 helix: 1.93 (0.15), residues: 1199 sheet: 0.24 (0.24), residues: 506 loop : -0.37 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 4 HIS 0.003 0.000 HIS J1366 PHE 0.028 0.001 PHE P 126 TYR 0.017 0.001 TYR I 123 ARG 0.015 0.000 ARG J 322 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 1250) hydrogen bonds : angle 4.06665 ( 3450) metal coordination : bond 0.00528 ( 4) metal coordination : angle 7.48952 ( 6) SS BOND : bond 0.01095 ( 1) SS BOND : angle 1.77908 ( 2) covalent geometry : bond 0.00291 (28463) covalent geometry : angle 0.59409 (38854) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26186.14 seconds wall clock time: 452 minutes 25.24 seconds (27145.24 seconds total)