Starting phenix.real_space_refine on Mon May 26 05:26:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pib_17679/05_2025/8pib_17679.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pib_17679/05_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_17679/05_2025/8pib_17679.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pib_17679/05_2025/8pib_17679.map" model { file = "/net/cci-nas-00/data/ceres_data/8pib_17679/05_2025/8pib_17679.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pib_17679/05_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-5687/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: 16.04, per 1000 atoms: 0.58 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: 6.64 Conformation dependent library (CDL) restraints added in 3.6 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: 11.77 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: 14.24 Time building geometry restraints manager: 7.76 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: 2.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.130 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 77.110 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.100 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:10.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.970 ------------------------------------------------------------------------------- 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 : 3.322 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: 1.3497 time to fit residues: 523.8189 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 : 2.987 ------------------------------------------------------------------------------- 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 = 55)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.068054 restraints weight = 76125.276| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.84 r_work: 0.3025 rms_B_bonded: 3.36 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 7.06603 ( 6) SS BOND : bond 0.00003 ( 1) SS BOND : angle 2.41461 ( 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 : 3.119 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: 0.8573 (mp10) cc_final: 0.8269 (mp10) REVERT: P 15 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7768 (tp-100) REVERT: P 100 LYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6872 (tppt) REVERT: P 150 ILE cc_start: 0.6630 (mm) cc_final: 0.6310 (tp) REVERT: I 201 ARG cc_start: 0.8549 (mtm-85) cc_final: 0.8317 (mtm-85) REVERT: I 694 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8142 (mtp85) REVERT: I 1329 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7565 (mt-10) REVERT: J 136 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8040 (pm20) REVERT: J 166 LEU cc_start: 0.9268 (mm) cc_final: 0.8936 (pp) REVERT: J 206 ASN cc_start: 0.9161 (m110) cc_final: 0.8754 (m110) REVERT: J 404 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7557 (tm-30) REVERT: J 714 GLU cc_start: 0.8744 (tp30) cc_final: 0.8295 (tp30) REVERT: J 990 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8545 (mpt-90) REVERT: J 1084 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7427 (pp30) REVERT: K 56 GLU cc_start: 0.8551 (pm20) cc_final: 0.8245 (pm20) REVERT: H 65 LEU cc_start: 0.9200 (pp) cc_final: 0.8918 (pt) REVERT: H 68 TYR cc_start: 0.8624 (p90) cc_final: 0.8220 (p90) outliers start: 112 outliers final: 46 residues processed: 370 average time/residue: 1.5073 time to fit residues: 646.1798 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 : 3.234 ------------------------------------------------------------------------------- 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: 5.9990 chunk 94 optimal weight: 0.9990 chunk 208 optimal weight: 9.9990 chunk 185 optimal weight: 0.9990 chunk 332 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 307 optimal weight: 3.9990 chunk 233 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.097495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.066849 restraints weight = 76466.179| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.79 r_work: 0.2995 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 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 = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 28468 Z= 0.173 Angle : 0.553 11.129 38862 Z= 0.286 Chirality : 0.042 0.343 4442 Planarity : 0.004 0.143 4762 Dihedral : 16.816 179.756 4730 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.86 % Favored : 97.08 % Rotamer: Outliers : 4.11 % Allowed : 23.72 % Favored : 72.18 % 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: 0.78 (0.15), residues: 3293 helix: 1.84 (0.15), residues: 1196 sheet: 0.41 (0.24), residues: 488 loop : -0.43 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 4 HIS 0.003 0.001 HIS G 66 PHE 0.014 0.001 PHE P 78 TYR 0.015 0.001 TYR J 631 ARG 0.007 0.000 ARG J 322 Details of bonding type rmsd hydrogen bonds : bond 0.03961 ( 1250) hydrogen bonds : angle 4.26337 ( 3450) metal coordination : bond 0.00929 ( 4) metal coordination : angle 7.71015 ( 6) SS BOND : bond 0.00002 ( 1) SS BOND : angle 2.23605 ( 2) covalent geometry : bond 0.00400 (28463) covalent geometry : angle 0.54475 (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 386 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 270 time to evaluate : 2.965 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: 0.8094 (tmm160) cc_final: 0.7757 (tmm160) REVERT: P 13 GLN cc_start: 0.8587 (mp10) cc_final: 0.8186 (mp10) REVERT: P 15 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7768 (tp-100) REVERT: P 26 VAL cc_start: 0.8681 (t) cc_final: 0.8479 (p) REVERT: P 150 ILE cc_start: 0.6607 (mm) cc_final: 0.6292 (tp) REVERT: I 83 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8717 (mm-40) REVERT: I 121 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8433 (tt0) REVERT: I 241 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6432 (tm) REVERT: I 530 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8654 (pt) REVERT: I 694 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8192 (mtp85) REVERT: I 1329 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7562 (mt-10) REVERT: J 136 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8002 (pm20) REVERT: J 166 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8909 (pp) REVERT: J 206 ASN cc_start: 0.9166 (m110) cc_final: 0.8754 (m110) REVERT: J 354 VAL cc_start: 0.9238 (OUTLIER) cc_final: 0.8940 (t) REVERT: J 398 LYS cc_start: 0.8738 (mttp) cc_final: 0.8523 (mtmm) REVERT: J 404 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7576 (tm-30) REVERT: K 56 GLU cc_start: 0.8619 (pm20) cc_final: 0.8208 (pm20) REVERT: H 65 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8931 (pt) outliers start: 116 outliers final: 52 residues processed: 354 average time/residue: 1.4272 time to fit residues: 587.6935 Evaluate side-chains 323 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 259 time to evaluate : 2.940 ------------------------------------------------------------------------------- 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 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 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 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 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 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 889 ASP 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 1243 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 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: 1.9990 chunk 218 optimal weight: 0.5980 chunk 209 optimal weight: 10.0000 chunk 309 optimal weight: 0.3980 chunk 114 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 248 optimal weight: 0.0770 chunk 113 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 337 optimal weight: 7.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.098946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.068407 restraints weight = 80400.286| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.91 r_work: 0.3030 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 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 = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1199 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= 0.113 Angle : 0.531 10.149 38862 Z= 0.273 Chirality : 0.041 0.324 4442 Planarity : 0.004 0.144 4762 Dihedral : 16.756 179.839 4722 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.83 % Favored : 97.11 % Rotamer: Outliers : 3.54 % Allowed : 24.50 % 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: 1.85 (0.15), residues: 1208 sheet: 0.49 (0.24), residues: 488 loop : -0.39 (0.15), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 997 HIS 0.004 0.000 HIS G 160 PHE 0.012 0.001 PHE P 78 TYR 0.012 0.001 TYR J 631 ARG 0.010 0.000 ARG I 275 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 1250) hydrogen bonds : angle 4.10330 ( 3450) metal coordination : bond 0.00465 ( 4) metal coordination : angle 7.12884 ( 6) SS BOND : bond 0.00096 ( 1) SS BOND : angle 3.30553 ( 2) covalent geometry : bond 0.00257 (28463) covalent geometry : angle 0.52309 (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 381 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 281 time to evaluate : 2.880 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: 0.7855 (tmm160) cc_final: 0.7619 (tmm160) REVERT: P 13 GLN cc_start: 0.8616 (mp10) cc_final: 0.8229 (mp10) REVERT: P 15 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7789 (tp-100) REVERT: P 58 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7186 (tt0) REVERT: P 132 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8000 (pm20) REVERT: P 138 ARG cc_start: 0.8693 (mtm110) cc_final: 0.8265 (mtm110) REVERT: P 150 ILE cc_start: 0.6607 (mm) cc_final: 0.6280 (tp) REVERT: I 83 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8711 (mm-40) REVERT: I 121 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: I 241 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6435 (tm) REVERT: I 374 GLU cc_start: 0.8850 (mp0) cc_final: 0.8602 (mp0) REVERT: I 530 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8632 (pt) REVERT: I 694 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8212 (mtp85) REVERT: I 951 MET cc_start: 0.8735 (mmm) cc_final: 0.8471 (mmt) REVERT: I 1327 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8480 (mp) REVERT: J 136 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7986 (pm20) REVERT: J 166 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8908 (pp) REVERT: J 300 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8086 (tp40) REVERT: J 404 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7614 (tm-30) REVERT: J 1084 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7472 (pp30) REVERT: K 3 ARG cc_start: 0.8573 (ttm-80) cc_final: 0.8185 (ttm-80) REVERT: K 55 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7295 (mt-10) REVERT: K 56 GLU cc_start: 0.8619 (pm20) cc_final: 0.8061 (pm20) REVERT: K 79 GLU cc_start: 0.3059 (OUTLIER) cc_final: 0.2782 (tt0) REVERT: G 93 GLN cc_start: 0.8491 (mp10) cc_final: 0.8009 (mp10) REVERT: G 145 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8808 (tttp) outliers start: 100 outliers final: 42 residues processed: 360 average time/residue: 1.4859 time to fit residues: 619.4688 Evaluate side-chains 321 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 262 time to evaluate : 3.020 ------------------------------------------------------------------------------- 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 132 GLU 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 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 453 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 1327 LEU 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 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 825 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 982 LEU 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 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: 0.9980 chunk 188 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 337 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 87 optimal weight: 0.0570 overall best weight: 2.0104 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.096393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.065782 restraints weight = 69452.839| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.69 r_work: 0.2975 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 28468 Z= 0.215 Angle : 0.593 12.755 38862 Z= 0.304 Chirality : 0.043 0.324 4442 Planarity : 0.004 0.140 4762 Dihedral : 16.803 179.501 4718 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.16 % Favored : 96.78 % Rotamer: Outliers : 3.86 % Allowed : 24.53 % Favored : 71.61 % 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: 0.67 (0.15), residues: 3293 helix: 1.75 (0.15), residues: 1197 sheet: 0.14 (0.23), residues: 507 loop : -0.43 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 4 HIS 0.004 0.001 HIS J1252 PHE 0.038 0.002 PHE P 126 TYR 0.017 0.001 TYR J 631 ARG 0.011 0.000 ARG J 322 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 1250) hydrogen bonds : angle 4.22981 ( 3450) metal coordination : bond 0.01234 ( 4) metal coordination : angle 8.47590 ( 6) SS BOND : bond 0.00029 ( 1) SS BOND : angle 2.55449 ( 2) covalent geometry : bond 0.00501 (28463) covalent geometry : angle 0.58385 (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 378 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 269 time to evaluate : 3.208 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: 0.8103 (tmm160) cc_final: 0.7816 (tmm160) REVERT: P 13 GLN cc_start: 0.8722 (mp10) cc_final: 0.8241 (mp10) REVERT: P 15 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7822 (tp-100) REVERT: P 132 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8077 (pm20) REVERT: P 138 ARG cc_start: 0.8864 (mtm110) cc_final: 0.8433 (mtm110) REVERT: I 83 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8688 (mm-40) REVERT: I 121 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8409 (tt0) REVERT: I 241 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6425 (tm) REVERT: I 530 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8677 (pt) REVERT: I 694 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8159 (mtp85) REVERT: I 951 MET cc_start: 0.8726 (mmm) cc_final: 0.8467 (mmt) REVERT: I 1329 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7579 (mt-10) REVERT: J 136 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7961 (pm20) REVERT: J 166 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8913 (pp) REVERT: J 206 ASN cc_start: 0.9164 (m110) cc_final: 0.8771 (m110) REVERT: J 398 LYS cc_start: 0.8857 (mtmm) cc_final: 0.8576 (mttp) REVERT: K 18 ASP cc_start: 0.8546 (m-30) cc_final: 0.8298 (m-30) REVERT: K 79 GLU cc_start: 0.3075 (OUTLIER) cc_final: 0.2808 (tt0) outliers start: 109 outliers final: 53 residues processed: 346 average time/residue: 1.5207 time to fit residues: 610.8752 Evaluate side-chains 323 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 259 time to evaluate : 3.294 ------------------------------------------------------------------------------- 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 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 325 LEU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 439 LYS Chi-restraints excluded: chain I residue 453 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 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 94 GLN 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 393 THR 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 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 125 LYS 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: 0.6980 chunk 138 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 212 optimal weight: 0.9980 chunk 331 optimal weight: 3.9990 chunk 166 optimal weight: 0.0770 chunk 111 optimal weight: 7.9990 chunk 317 optimal weight: 0.9990 chunk 199 optimal weight: 0.7980 chunk 202 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.098196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.067869 restraints weight = 70486.798| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.71 r_work: 0.3023 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- 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 = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 28468 Z= 0.118 Angle : 0.561 13.291 38862 Z= 0.286 Chirality : 0.041 0.311 4442 Planarity : 0.004 0.137 4762 Dihedral : 16.752 179.550 4717 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.70 % Favored : 97.24 % Rotamer: Outliers : 3.19 % Allowed : 25.52 % Favored : 71.29 % 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: 0.78 (0.15), residues: 3293 helix: 1.87 (0.15), residues: 1194 sheet: 0.26 (0.23), residues: 505 loop : -0.41 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 4 HIS 0.003 0.001 HIS I 447 PHE 0.037 0.001 PHE P 126 TYR 0.013 0.001 TYR I 123 ARG 0.013 0.000 ARG I 275 Details of bonding type rmsd hydrogen bonds : bond 0.03433 ( 1250) hydrogen bonds : angle 4.10006 ( 3450) metal coordination : bond 0.00528 ( 4) metal coordination : angle 7.68557 ( 6) SS BOND : bond 0.00151 ( 1) SS BOND : angle 3.60683 ( 2) covalent geometry : bond 0.00274 (28463) covalent geometry : angle 0.55234 (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 364 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 274 time to evaluate : 3.224 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 13 GLN cc_start: 0.8711 (mp10) cc_final: 0.8244 (mp10) REVERT: P 15 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7762 (tp-100) REVERT: P 123 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7683 (t80) REVERT: P 132 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8044 (pm20) REVERT: I 83 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8684 (mm-40) REVERT: I 121 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8215 (tt0) REVERT: I 241 LEU cc_start: 0.6819 (OUTLIER) cc_final: 0.6424 (tm) REVERT: I 275 ARG cc_start: 0.9390 (mmm160) cc_final: 0.9004 (tpm-80) REVERT: I 530 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8637 (pt) REVERT: I 694 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8210 (mtp85) REVERT: I 951 MET cc_start: 0.8755 (mmm) cc_final: 0.8526 (mmt) REVERT: I 1327 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8528 (mp) REVERT: J 136 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7932 (pm20) REVERT: J 166 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8900 (pp) REVERT: J 206 ASN cc_start: 0.9124 (m110) cc_final: 0.8720 (m110) REVERT: J 300 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8176 (tt0) REVERT: J 992 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8333 (mmmm) REVERT: K 56 GLU cc_start: 0.8815 (pm20) cc_final: 0.8253 (pm20) REVERT: K 79 GLU cc_start: 0.3186 (OUTLIER) cc_final: 0.2944 (tt0) REVERT: H 65 LEU cc_start: 0.9064 (pp) cc_final: 0.8846 (pt) outliers start: 90 outliers final: 45 residues processed: 344 average time/residue: 1.4577 time to fit residues: 582.8902 Evaluate side-chains 322 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 263 time to evaluate : 3.109 ------------------------------------------------------------------------------- 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 325 LEU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 453 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 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 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 160 LEU Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 300 GLN 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 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 1309 ILE 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 156 SER Chi-restraints excluded: chain H residue 187 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 142 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 156 optimal weight: 0.4980 chunk 168 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 273 optimal weight: 4.9990 chunk 220 optimal weight: 3.9990 chunk 69 optimal weight: 0.0010 overall best weight: 0.8588 ------------------------------------------------------------------------------- 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 J 962 ASN K 43 ASN ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3758 r_free = 0.3758 target = 0.098049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.067822 restraints weight = 68608.851| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.66 r_work: 0.3021 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 28468 Z= 0.131 Angle : 0.567 14.130 38862 Z= 0.288 Chirality : 0.041 0.302 4442 Planarity : 0.004 0.134 4762 Dihedral : 16.704 179.738 4713 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.95 % Favored : 96.99 % Rotamer: Outliers : 2.90 % Allowed : 26.02 % Favored : 71.08 % 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: 1.86 (0.15), residues: 1195 sheet: 0.24 (0.23), residues: 514 loop : -0.38 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 409 HIS 0.003 0.001 HIS H 66 PHE 0.033 0.001 PHE P 126 TYR 0.016 0.001 TYR I 123 ARG 0.012 0.000 ARG J 322 Details of bonding type rmsd hydrogen bonds : bond 0.03498 ( 1250) hydrogen bonds : angle 4.07706 ( 3450) metal coordination : bond 0.00659 ( 4) metal coordination : angle 7.53863 ( 6) SS BOND : bond 0.00041 ( 1) SS BOND : angle 3.39701 ( 2) covalent geometry : bond 0.00305 (28463) covalent geometry : angle 0.55876 (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 350 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 268 time to evaluate : 2.934 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: 0.5143 (tm-30) cc_final: 0.4909 (tm-30) REVERT: P 11 ARG cc_start: 0.7932 (tmm160) cc_final: 0.7459 (tmm160) REVERT: P 13 GLN cc_start: 0.8737 (mp10) cc_final: 0.8190 (mp10) REVERT: P 15 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7782 (tp-100) REVERT: P 58 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7129 (tt0) REVERT: P 132 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8049 (pm20) REVERT: I 83 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8688 (mm-40) REVERT: I 121 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8320 (tt0) REVERT: I 241 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6431 (tm) REVERT: I 530 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8636 (pt) REVERT: I 694 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8184 (mtp85) REVERT: I 849 GLU cc_start: 0.8221 (pm20) cc_final: 0.8015 (pt0) REVERT: I 951 MET cc_start: 0.8756 (mmm) cc_final: 0.8512 (mmt) REVERT: I 1327 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8548 (mp) REVERT: J 136 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7878 (pm20) REVERT: J 166 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8889 (pp) REVERT: J 206 ASN cc_start: 0.9141 (m110) cc_final: 0.8738 (m110) REVERT: J 354 VAL cc_start: 0.9226 (OUTLIER) cc_final: 0.8925 (t) REVERT: J 762 ASN cc_start: 0.7645 (OUTLIER) cc_final: 0.7415 (m110) REVERT: J 992 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8335 (mmmm) REVERT: K 56 GLU cc_start: 0.8816 (pm20) cc_final: 0.8254 (pm20) REVERT: K 79 GLU cc_start: 0.3271 (OUTLIER) cc_final: 0.3014 (tt0) REVERT: G 93 GLN cc_start: 0.8246 (mp10) cc_final: 0.7689 (mp10) outliers start: 82 outliers final: 42 residues processed: 327 average time/residue: 1.5093 time to fit residues: 571.8026 Evaluate side-chains 315 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 258 time to evaluate : 2.966 ------------------------------------------------------------------------------- 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 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 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 333 ILE Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 453 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 1327 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 94 GLN 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 666 GLU Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 706 VAL 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 1344 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 146 VAL Chi-restraints excluded: chain H residue 187 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 156 optimal weight: 3.9990 chunk 227 optimal weight: 0.0050 chunk 34 optimal weight: 5.9990 chunk 218 optimal weight: 3.9990 chunk 268 optimal weight: 1.9990 chunk 297 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 196 optimal weight: 3.9990 chunk 304 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 235 optimal weight: 10.0000 overall best weight: 1.1798 ------------------------------------------------------------------------------- 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** K 31 GLN K 43 ASN ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN H 186 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.097489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.067074 restraints weight = 71054.356| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.69 r_work: 0.3004 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 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 = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 28468 Z= 0.150 Angle : 0.584 14.878 38862 Z= 0.296 Chirality : 0.042 0.298 4442 Planarity : 0.004 0.131 4762 Dihedral : 16.694 177.622 4710 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.86 % Favored : 97.08 % Rotamer: Outliers : 2.83 % Allowed : 26.30 % Favored : 70.87 % 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: 0.78 (0.15), residues: 3293 helix: 1.87 (0.15), residues: 1194 sheet: 0.25 (0.23), residues: 508 loop : -0.40 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 409 HIS 0.003 0.001 HIS J1366 PHE 0.030 0.001 PHE P 126 TYR 0.017 0.001 TYR I 123 ARG 0.014 0.000 ARG J 322 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 1250) hydrogen bonds : angle 4.08817 ( 3450) metal coordination : bond 0.00823 ( 4) metal coordination : angle 7.75344 ( 6) SS BOND : bond 0.00012 ( 1) SS BOND : angle 3.69514 ( 2) covalent geometry : bond 0.00351 (28463) covalent geometry : angle 0.57589 (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 350 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 270 time to evaluate : 3.186 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: 0.8052 (tmm160) cc_final: 0.7839 (tmm160) REVERT: P 13 GLN cc_start: 0.8707 (mp10) cc_final: 0.8186 (mp10) REVERT: P 15 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7790 (tp-100) REVERT: P 58 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7284 (tt0) REVERT: P 123 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7650 (t80) REVERT: P 132 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7925 (pm20) REVERT: P 138 ARG cc_start: 0.8776 (mtm110) cc_final: 0.8513 (mtm110) REVERT: P 142 LEU cc_start: 0.8937 (tm) cc_final: 0.8726 (tm) REVERT: I 40 GLU cc_start: 0.7970 (pt0) cc_final: 0.7714 (pm20) REVERT: I 83 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8656 (mm-40) REVERT: I 121 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8345 (tt0) REVERT: I 241 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6447 (tm) REVERT: I 275 ARG cc_start: 0.9355 (mmm160) cc_final: 0.8960 (tpm-80) REVERT: I 530 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8637 (pt) REVERT: I 694 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8188 (mtp85) REVERT: I 951 MET cc_start: 0.8751 (mmm) cc_final: 0.8512 (mmt) REVERT: I 1327 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8541 (mp) REVERT: J 136 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7894 (pm20) REVERT: J 166 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8884 (pp) REVERT: J 206 ASN cc_start: 0.9148 (m110) cc_final: 0.8748 (m110) REVERT: J 354 VAL cc_start: 0.9240 (OUTLIER) cc_final: 0.8943 (t) REVERT: J 992 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8382 (mmmm) REVERT: K 18 ASP cc_start: 0.8529 (m-30) cc_final: 0.8282 (m-30) REVERT: K 56 GLU cc_start: 0.8825 (pm20) cc_final: 0.8248 (pm20) REVERT: K 79 GLU cc_start: 0.3331 (OUTLIER) cc_final: 0.3082 (tt0) outliers start: 80 outliers final: 49 residues processed: 330 average time/residue: 1.5173 time to fit residues: 580.9307 Evaluate side-chains 326 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 262 time to evaluate : 3.302 ------------------------------------------------------------------------------- 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 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 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 393 ASP Chi-restraints excluded: chain I residue 453 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 I residue 1293 VAL Chi-restraints excluded: chain I residue 1327 LEU 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 706 VAL 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 1344 LEU Chi-restraints excluded: chain J residue 1351 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 290 optimal weight: 2.9990 chunk 37 optimal weight: 0.0270 chunk 36 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 237 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 191 optimal weight: 3.9990 chunk 285 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- 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 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 792 ASN ** J 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3747 r_free = 0.3747 target = 0.097417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.067194 restraints weight = 65206.328| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.61 r_work: 0.3011 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 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 = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 28468 Z= 0.152 Angle : 0.595 15.297 38862 Z= 0.301 Chirality : 0.042 0.290 4442 Planarity : 0.004 0.129 4762 Dihedral : 16.698 178.138 4710 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 2.69 % Allowed : 26.37 % Favored : 70.94 % 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: 0.78 (0.15), residues: 3293 helix: 1.89 (0.15), residues: 1198 sheet: 0.23 (0.23), residues: 509 loop : -0.42 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 0.013 0.000 ARG J 322 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 1250) hydrogen bonds : angle 4.08634 ( 3450) metal coordination : bond 0.00820 ( 4) metal coordination : angle 7.91288 ( 6) SS BOND : bond 0.00049 ( 1) SS BOND : angle 3.59542 ( 2) covalent geometry : bond 0.00356 (28463) covalent geometry : angle 0.58673 (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 348 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 272 time to evaluate : 3.105 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 2 GLN cc_start: 0.5236 (tm-30) cc_final: 0.4992 (tm-30) REVERT: P 13 GLN cc_start: 0.8696 (mp10) cc_final: 0.8219 (mp10) REVERT: P 15 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7805 (tp-100) REVERT: P 58 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7182 (tt0) REVERT: P 123 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7817 (t80) REVERT: P 132 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7920 (pm20) REVERT: P 142 LEU cc_start: 0.8970 (tm) cc_final: 0.8742 (tm) REVERT: I 40 GLU cc_start: 0.7973 (pt0) cc_final: 0.7722 (pm20) REVERT: I 83 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8685 (mm-40) REVERT: I 121 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8316 (tt0) REVERT: I 530 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8639 (pt) REVERT: I 951 MET cc_start: 0.8737 (mmm) cc_final: 0.8499 (mmt) REVERT: I 1327 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8541 (mp) REVERT: J 136 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7882 (pm20) REVERT: J 166 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8883 (pp) REVERT: J 206 ASN cc_start: 0.9128 (m110) cc_final: 0.8736 (m110) REVERT: J 354 VAL cc_start: 0.9236 (OUTLIER) cc_final: 0.8938 (t) REVERT: J 992 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8412 (mmmm) REVERT: K 11 GLU cc_start: 0.7922 (pp20) cc_final: 0.7580 (mt-10) REVERT: K 18 ASP cc_start: 0.8503 (m-30) cc_final: 0.8252 (m-30) REVERT: K 56 GLU cc_start: 0.8817 (pm20) cc_final: 0.8430 (pm20) outliers start: 76 outliers final: 50 residues processed: 328 average time/residue: 1.5248 time to fit residues: 578.6102 Evaluate side-chains 328 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 266 time to evaluate : 2.862 ------------------------------------------------------------------------------- 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 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 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 277 LEU Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 453 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 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 I residue 1293 VAL Chi-restraints excluded: chain I residue 1327 LEU 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 97 VAL 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 706 VAL 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 1344 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 21 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 209 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 chunk 168 optimal weight: 0.6980 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: 3.9990 chunk 330 optimal weight: 10.0000 chunk 138 optimal weight: 0.0980 chunk 194 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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** K 43 ASN ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN H 186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.097478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.066943 restraints weight = 76132.567| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.81 r_work: 0.2996 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 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 = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 28468 Z= 0.148 Angle : 0.614 15.748 38862 Z= 0.310 Chirality : 0.042 0.282 4442 Planarity : 0.004 0.128 4762 Dihedral : 16.681 177.894 4707 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 2.48 % Allowed : 26.87 % Favored : 70.65 % 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: 0.78 (0.15), residues: 3293 helix: 1.91 (0.15), residues: 1196 sheet: 0.20 (0.23), residues: 504 loop : -0.42 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 4 HIS 0.003 0.001 HIS J1366 PHE 0.016 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 0.03595 ( 1250) hydrogen bonds : angle 4.09965 ( 3450) metal coordination : bond 0.00782 ( 4) metal coordination : angle 7.90594 ( 6) SS BOND : bond 0.00539 ( 1) SS BOND : angle 7.51996 ( 2) covalent geometry : bond 0.00347 (28463) covalent geometry : angle 0.60401 (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 340 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 270 time to evaluate : 3.282 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: 0.7973 (tmm160) cc_final: 0.7692 (tmm160) REVERT: P 13 GLN cc_start: 0.8698 (mp10) cc_final: 0.8195 (mp10) REVERT: P 15 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7750 (tp-100) REVERT: P 51 CYS cc_start: 0.5543 (t) cc_final: 0.5178 (t) REVERT: P 58 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7183 (tt0) REVERT: P 123 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7554 (t80) REVERT: P 138 ARG cc_start: 0.8872 (mtm110) cc_final: 0.8604 (mtm110) REVERT: P 139 CYS cc_start: 0.7927 (t) cc_final: 0.7484 (t) REVERT: P 142 LEU cc_start: 0.9007 (tm) cc_final: 0.8793 (tm) REVERT: I 40 GLU cc_start: 0.8013 (pt0) cc_final: 0.7743 (pm20) REVERT: I 83 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8677 (mm-40) REVERT: I 121 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8279 (tt0) REVERT: I 275 ARG cc_start: 0.9353 (mmm160) cc_final: 0.9000 (tpm-80) REVERT: I 530 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8646 (pt) REVERT: I 951 MET cc_start: 0.8753 (mmm) cc_final: 0.8514 (mmt) REVERT: I 1327 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8548 (mp) REVERT: I 1329 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7556 (mt-10) REVERT: J 136 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7898 (pm20) REVERT: J 166 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8877 (pp) REVERT: J 354 VAL cc_start: 0.9263 (OUTLIER) cc_final: 0.8951 (t) REVERT: J 992 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8407 (mmmm) REVERT: K 3 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8129 (ttm-80) REVERT: K 11 GLU cc_start: 0.7932 (pp20) cc_final: 0.7589 (mt-10) REVERT: K 18 ASP cc_start: 0.8549 (m-30) cc_final: 0.8296 (m-30) REVERT: K 56 GLU cc_start: 0.8809 (pm20) cc_final: 0.8418 (pm20) REVERT: H 137 ASN cc_start: 0.8640 (p0) cc_final: 0.8388 (p0) outliers start: 70 outliers final: 47 residues processed: 323 average time/residue: 1.4913 time to fit residues: 562.9038 Evaluate side-chains 325 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 265 time to evaluate : 3.133 ------------------------------------------------------------------------------- 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 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 319 LEU Chi-restraints excluded: chain I residue 453 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 862 LEU Chi-restraints excluded: chain I residue 935 THR 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 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 97 VAL 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 706 VAL 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 1309 ILE Chi-restraints excluded: chain J residue 1351 VAL 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 223 optimal weight: 0.8980 chunk 297 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 277 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 285 optimal weight: 2.9990 chunk 204 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 792 ASN ** J 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 ASN H 93 GLN H 186 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.097851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.067280 restraints weight = 79184.932| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.85 r_work: 0.3003 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 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 = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1688 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= 0.136 Angle : 0.610 15.465 38862 Z= 0.308 Chirality : 0.042 0.271 4442 Planarity : 0.004 0.129 4762 Dihedral : 16.664 177.909 4705 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.01 % Favored : 96.93 % Rotamer: Outliers : 2.34 % Allowed : 26.97 % 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: 0.81 (0.15), residues: 3293 helix: 1.92 (0.15), residues: 1197 sheet: 0.22 (0.23), residues: 509 loop : -0.40 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP P 4 HIS 0.003 0.001 HIS P 94 PHE 0.014 0.001 PHE P 78 TYR 0.017 0.001 TYR I 123 ARG 0.015 0.000 ARG J 322 Details of bonding type rmsd hydrogen bonds : bond 0.03530 ( 1250) hydrogen bonds : angle 4.08749 ( 3450) metal coordination : bond 0.00669 ( 4) metal coordination : angle 7.74167 ( 6) SS BOND : bond 0.00301 ( 1) SS BOND : angle 7.13616 ( 2) covalent geometry : bond 0.00317 (28463) covalent geometry : angle 0.59997 (38854) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24035.83 seconds wall clock time: 414 minutes 11.05 seconds (24851.05 seconds total)