Starting phenix.real_space_refine on Sat Aug 8 13:09:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pim_17686/08_2026/8pim_17686.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pim_17686/08_2026/8pim_17686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pim_17686/08_2026/8pim_17686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pim_17686/08_2026/8pim_17686.map" model { file = "/net/cci-nas-00/data/ceres_data/8pim_17686/08_2026/8pim_17686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pim_17686/08_2026/8pim_17686.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 85 5.49 5 Mg 1 5.21 5 S 113 5.16 5 C 17428 2.51 5 N 4995 2.21 5 O 5608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28232 Number of models: 1 Model: "" Number of chains: 10 Chain: "P" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1294 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 150} Chain: "I" Number of atoms: 10439 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1321, 10423 Classifications: {'peptide': 1321} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1265} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 1321, 10423 Classifications: {'peptide': 1321} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1265} Chain breaks: 1 bond proxies already assigned to first conformer: 10571 Chain: "J" Number of atoms: 10449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1343, 10449 Classifications: {'peptide': 1343} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1287} Chain breaks: 2 Chain: "K" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 663 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "R" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 355 Classifications: {'RNA': 17} Modifications used: {'5*END': 1, 'rna2p_pyr': 3, 'rna3p_pur': 7, 'rna3p_pyr': 7} Link IDs: {'rna2p': 3, 'rna3p': 13} Chain: "A" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 712 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "B" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 722 Classifications: {'DNA': 35} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 34} 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: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1784 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12191 SG CYS J 70 24.919 69.392 83.484 1.00172.69 S ATOM 12205 SG CYS J 72 23.943 65.689 83.174 1.00168.77 S ATOM 12313 SG CYS J 85 22.241 67.928 85.711 1.00156.88 S ATOM 12337 SG CYS J 88 25.911 66.947 86.170 1.00150.50 S ATOM 18025 SG CYS J 814 58.348 126.000 92.238 1.00128.61 S ATOM 18590 SG CYS J 888 59.553 122.578 91.528 1.00141.08 S ATOM 18641 SG CYS J 895 58.952 125.130 88.643 1.00134.28 S ATOM 18662 SG CYS J 898 61.953 125.439 90.906 1.00132.75 S Time building chain proxies: 7.45, per 1000 atoms: 0.26 Number of scatterers: 28232 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 2 29.99 S 113 16.00 P 85 15.00 Mg 1 11.99 O 5608 8.00 N 4995 7.00 C 17428 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " Number of angles added : 12 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6244 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 47 sheets defined 38.8% alpha, 18.1% beta 35 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain 'P' and resid 13 through 24 Processing helix chain 'P' and resid 65 through 71 removed outlier: 3.550A pdb=" N ILE P 69 " --> pdb=" O HIS P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 98 Processing helix chain 'P' and resid 105 through 109 Processing helix chain 'P' and resid 120 through 124 removed outlier: 3.865A pdb=" N PHE P 123 " --> pdb=" O GLU P 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 10 removed outlier: 3.931A pdb=" N ARG I 10 " --> pdb=" O THR I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 28 No H-bonds generated for 'chain 'I' and resid 26 through 28' Processing helix chain 'I' and resid 29 through 40 removed outlier: 3.726A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE I 35 " --> pdb=" O GLN I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.794A 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 Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 3.602A 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 295 removed outlier: 4.167A pdb=" N ALA I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS I 295 " --> pdb=" O TYR I 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 289 through 295' Processing helix chain 'I' and resid 318 through 329 Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.916A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 482 Processing helix chain 'I' and resid 488 through 493 removed outlier: 3.879A pdb=" N ILE I 493 " --> pdb=" O PRO I 489 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 509 removed outlier: 3.842A pdb=" N SER I 509 " --> pdb=" O PHE I 505 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 551 through 555 Processing helix chain 'I' and resid 608 through 614 removed outlier: 3.706A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 614' Processing helix chain 'I' and resid 624 through 628 removed outlier: 3.788A pdb=" N HIS I 628 " --> pdb=" O GLU I 625 " (cutoff:3.500A) 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: 4.148A 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 825 Processing helix chain 'I' and resid 942 through 984 removed outlier: 3.940A pdb=" N GLU I 963 " --> pdb=" O ASP I 959 " (cutoff:3.500A) Processing helix chain 'I' and resid 985 through 992 Processing helix chain 'I' and resid 994 through 998 removed outlier: 3.999A pdb=" N LEU I 998 " --> pdb=" O ASP I 995 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1101 through 1107 removed outlier: 4.202A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.546A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 4.059A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1176 removed outlier: 3.557A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.532A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1243 Processing helix chain 'I' and resid 1271 through 1282 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 1333 removed outlier: 3.761A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.500A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.647A 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: 3.567A pdb=" N ILE J 135 " --> pdb=" O PRO J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 191 Processing helix chain 'J' and resid 193 through 208 removed outlier: 3.853A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 285 Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 336 through 342 removed outlier: 3.610A 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 404 Processing helix chain 'J' and resid 405 through 416 removed outlier: 3.780A pdb=" N ILE J 416 " --> pdb=" O LEU J 412 " (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 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.778A 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 588 through 592 removed outlier: 4.025A 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: 3.642A pdb=" N VAL J 618 " --> pdb=" O LEU J 614 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE J 619 " --> pdb=" O LYS J 615 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 4.076A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.696A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.646A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.795A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 928 No H-bonds generated for 'chain 'J' and resid 926 through 928' Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.696A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.318A 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: 3.806A 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 Processing helix chain 'J' and resid 1360 through 1375 removed outlier: 3.744A pdb=" N ALA J1364 " --> pdb=" O GLY J1360 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP J1368 " --> pdb=" O ALA J1364 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 17 through 34 removed outlier: 3.540A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.771A pdb=" N GLU K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 84 Processing helix chain 'G' and resid 32 through 48 removed outlier: 3.577A pdb=" N GLY G 36 " --> pdb=" O GLU G 32 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N HIS G 37 " --> pdb=" O ARG G 33 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY G 40 " --> pdb=" O GLY G 36 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN G 41 " --> pdb=" O HIS G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.598A 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 159 Processing helix chain 'G' and resid 212 through 234 removed outlier: 4.257A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.611A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (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 Processing helix chain 'H' and resid 160 through 166 removed outlier: 5.990A pdb=" N GLU H 163 " --> pdb=" O HIS H 160 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP H 164 " --> pdb=" O SER H 161 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG H 166 " --> pdb=" O GLU H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 229 Processing sheet with id=AA1, first strand: chain 'P' and resid 27 through 29 removed outlier: 3.651A pdb=" N ASN P 27 " --> pdb=" O GLU P 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 33 through 37 Processing sheet with id=AA3, first strand: chain 'P' and resid 149 through 155 removed outlier: 3.595A pdb=" N SER P 139 " --> pdb=" O VAL P 154 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG P 138 " --> pdb=" O ASP P 134 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU P 132 " --> pdb=" O MET P 140 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU P 142 " --> pdb=" O PHE P 130 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE P 130 " --> pdb=" O LEU P 142 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ASN P 144 " --> pdb=" O ALA P 128 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ALA P 128 " --> pdb=" O ASN P 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.548A 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: 6.026A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (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: 6.262A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N SER I 574 " --> pdb=" O CYS I 559 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 154 through 160 removed outlier: 3.716A pdb=" N LEU I 171 " --> pdb=" O ASP I 160 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AB1, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AB2, first strand: chain 'I' and resid 301 through 303 removed outlier: 6.606A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.415A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AB5, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.570A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.128A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AB8, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AB9, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.461A pdb=" N VAL I 818 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE I1079 " --> pdb=" O VAL I 818 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 830 through 841 removed outlier: 8.265A pdb=" N LEU I1047 " --> pdb=" O THR I 935 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR I 935 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE I1049 " --> pdb=" O VAL I 933 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL I 933 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS I1051 " --> pdb=" O VAL I 931 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL I 931 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR I1053 " --> pdb=" O ILE I 929 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 849 through 850 removed outlier: 3.839A pdb=" N GLU I 849 " --> pdb=" O VAL I 887 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL I 887 " --> pdb=" O GLU I 849 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.855A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AC5, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AC6, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.759A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 103 through 112 removed outlier: 9.929A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.686A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 159 through 160 removed outlier: 6.754A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD1, first strand: chain 'J' and resid 706 through 709 Processing sheet with id=AD2, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AD3, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AD4, first strand: chain 'J' and resid 826 through 827 removed outlier: 3.731A pdb=" N GLU J 827 " --> pdb=" O ASP J 830 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 842 through 843 removed outlier: 3.866A pdb=" N ARG J 842 " --> pdb=" O LEU J 864 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 957 through 961 removed outlier: 4.453A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 965 through 967 removed outlier: 3.962A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 1024 through 1025 Processing sheet with id=AD9, first strand: chain 'J' and resid 1098 through 1100 Processing sheet with id=AE1, first strand: chain 'J' and resid 1186 through 1191 removed outlier: 4.548A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LYS J1172 " --> pdb=" O GLU J1168 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N GLU J1168 " --> pdb=" O LYS J1172 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ARG J1174 " --> pdb=" O GLY J1166 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL J1204 " --> pdb=" O GLY J1161 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.661A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 12 through 17 removed outlier: 4.924A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.652A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AE6, first strand: chain 'G' and resid 108 through 111 Processing sheet with id=AE7, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AE8, first strand: chain 'H' and resid 13 through 18 removed outlier: 6.470A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU H 206 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 97 through 104 removed outlier: 3.826A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 5.837A 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: 6.678A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AF2, first strand: chain 'H' and resid 108 through 111 removed outlier: 7.311A pdb=" N GLY H 108 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N HIS H 132 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL H 110 " --> pdb=" O ILE H 130 " (cutoff:3.500A) 1156 hydrogen bonds defined for protein. 3245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 174 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 7.14 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.95: 1 0.95 - 1.26: 4724 1.26 - 1.58: 23755 1.58 - 1.89: 366 1.89 - 2.21: 1 Bond restraints: 28847 Sorted by residual: bond pdb=" CG PRO P 133 " pdb=" CD PRO P 133 " ideal model delta sigma weight residual 1.503 0.635 0.868 3.40e-02 8.65e+02 6.51e+02 bond pdb=" CB PRO P 133 " pdb=" CG PRO P 133 " ideal model delta sigma weight residual 1.492 2.205 -0.713 5.00e-02 4.00e+02 2.04e+02 bond pdb=" CA PRO P 133 " pdb=" CB PRO P 133 " ideal model delta sigma weight residual 1.533 1.468 0.065 1.42e-02 4.96e+03 2.10e+01 bond pdb=" C3' DG B 5 " pdb=" C2' DG B 5 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C3' DC A 39 " pdb=" C2' DC A 39 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 28842 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.42: 39344 10.42 - 20.84: 7 20.84 - 31.26: 1 31.26 - 41.68: 0 41.68 - 52.10: 2 Bond angle restraints: 39354 Sorted by residual: angle pdb=" N PRO P 133 " pdb=" CD PRO P 133 " pdb=" CG PRO P 133 " ideal model delta sigma weight residual 103.20 51.10 52.10 1.50e+00 4.44e-01 1.21e+03 angle pdb=" CA PRO P 133 " pdb=" CB PRO P 133 " pdb=" CG PRO P 133 " ideal model delta sigma weight residual 104.50 61.32 43.18 1.90e+00 2.77e-01 5.17e+02 angle pdb=" CB PRO P 133 " pdb=" CG PRO P 133 " pdb=" CD PRO P 133 " ideal model delta sigma weight residual 106.10 75.34 30.76 3.20e+00 9.77e-02 9.24e+01 angle pdb=" CA PRO P 133 " pdb=" N PRO P 133 " pdb=" CD PRO P 133 " ideal model delta sigma weight residual 112.00 99.09 12.91 1.40e+00 5.10e-01 8.50e+01 angle pdb=" CA PRO P 110 " pdb=" N PRO P 110 " pdb=" CD PRO P 110 " ideal model delta sigma weight residual 112.00 99.68 12.32 1.40e+00 5.10e-01 7.74e+01 ... (remaining 39349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 16588 35.54 - 71.08: 937 71.08 - 106.62: 46 106.62 - 142.16: 3 142.16 - 177.70: 3 Dihedral angle restraints: 17577 sinusoidal: 7872 harmonic: 9705 Sorted by residual: dihedral pdb=" O4' C R 2 " pdb=" C1' C R 2 " pdb=" N1 C R 2 " pdb=" C2 C R 2 " ideal model delta sinusoidal sigma weight residual -128.00 49.70 -177.70 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA PRO P 133 " pdb=" CB PRO P 133 " pdb=" CG PRO P 133 " pdb=" CD PRO P 133 " ideal model delta sinusoidal sigma weight residual 38.00 155.60 -117.60 1 2.00e+01 2.50e-03 3.51e+01 dihedral pdb=" CA ASN I 314 " pdb=" C ASN I 314 " pdb=" N MET I 315 " pdb=" CA MET I 315 " ideal model delta harmonic sigma weight residual 180.00 155.05 24.95 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 17574 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3966 0.066 - 0.133: 517 0.133 - 0.199: 13 0.199 - 0.265: 1 0.265 - 0.332: 1 Chirality restraints: 4498 Sorted by residual: chirality pdb=" CB ILE P 118 " pdb=" CA ILE P 118 " pdb=" CG1 ILE P 118 " pdb=" CG2 ILE P 118 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA PRO P 110 " pdb=" N PRO P 110 " pdb=" C PRO P 110 " pdb=" CB PRO P 110 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB ILE J1190 " pdb=" CA ILE J1190 " pdb=" CG1 ILE J1190 " pdb=" CG2 ILE J1190 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.13e-01 ... (remaining 4495 not shown) Planarity restraints: 4849 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR P 109 " 0.080 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO P 110 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO P 110 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO P 110 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU P 132 " -0.068 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO P 133 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO P 133 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO P 133 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU P 132 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.61e+00 pdb=" CD GLU P 132 " 0.041 2.00e-02 2.50e+03 pdb=" OE1 GLU P 132 " -0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU P 132 " -0.014 2.00e-02 2.50e+03 ... (remaining 4846 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 356 2.63 - 3.20: 24494 3.20 - 3.77: 45812 3.77 - 4.33: 60399 4.33 - 4.90: 99415 Nonbonded interactions: 230476 Sorted by model distance: nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1503 " model vdw 2.064 2.170 nonbonded pdb=" OD2 ASP J 462 " pdb="MG MG J1503 " model vdw 2.068 2.170 nonbonded pdb=" OP2 U R 17 " pdb="MG MG J1503 " model vdw 2.072 2.170 nonbonded pdb=" OD2 ASP J 460 " pdb="MG MG J1503 " model vdw 2.074 2.170 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1503 " model vdw 2.078 2.170 ... (remaining 230471 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 218 or resid 220 through 233)) selection = (chain 'H' and (resid 3 through 218 or resid 220 through 233)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 34.320 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 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 : 0.007 0.868 28855 Z= 0.259 Angle : 0.691 52.096 39366 Z= 0.413 Chirality : 0.042 0.332 4498 Planarity : 0.004 0.112 4849 Dihedral : 19.415 177.702 11333 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.47 % Favored : 97.50 % Rotamer: Outliers : 2.60 % Allowed : 28.33 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.15), residues: 3359 helix: 2.30 (0.16), residues: 1159 sheet: 0.71 (0.24), residues: 505 loop : -0.20 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 69 TYR 0.017 0.001 TYR H 185 PHE 0.005 0.001 PHE J1100 TRP 0.004 0.000 TRP J 868 HIS 0.004 0.000 HIS H 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00722 / 0.26 (28847) covalent geometry : angle 0.68956 / 0.41 (39354) hydrogen bonds : bond 0.12939 / 8.45 ( 1243) hydrogen bonds : angle 5.21014 / 3.64 ( 3419) metal coordination : bond 0.00386 / 0.23 ( 8) metal coordination : angle 2.31243 / 1.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 414 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 37 LYS cc_start: 0.6199 (mmpt) cc_final: 0.5874 (mmtt) REVERT: P 109 THR cc_start: 0.8077 (m) cc_final: 0.7612 (p) REVERT: I 142 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8592 (mt-10) REVERT: I 189 ASP cc_start: 0.8955 (t0) cc_final: 0.8722 (t0) REVERT: I 426 ILE cc_start: 0.9236 (mt) cc_final: 0.9019 (pt) REVERT: I 461 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8474 (tm-30) REVERT: I 488 MET cc_start: 0.8860 (mmp) cc_final: 0.8458 (mmt) REVERT: I 541 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8492 (mp0) REVERT: I 562 GLU cc_start: 0.8594 (tt0) cc_final: 0.8391 (tt0) REVERT: I 574 SER cc_start: 0.8989 (t) cc_final: 0.8764 (t) REVERT: I 704 MET cc_start: 0.9071 (mmm) cc_final: 0.8777 (tpp) REVERT: I 835 GLU cc_start: 0.8185 (tt0) cc_final: 0.7973 (tt0) REVERT: I 849 GLU cc_start: 0.8829 (pm20) cc_final: 0.8579 (pm20) REVERT: I 1178 LYS cc_start: 0.9507 (mppt) cc_final: 0.9233 (mmmt) REVERT: I 1188 ASP cc_start: 0.7924 (t0) cc_final: 0.7538 (t0) REVERT: I 1297 ASP cc_start: 0.7059 (t0) cc_final: 0.6494 (t0) REVERT: I 1321 GLU cc_start: 0.8720 (tp30) cc_final: 0.8343 (tp30) REVERT: J 340 GLN cc_start: 0.8956 (tp40) cc_final: 0.8666 (tp40) REVERT: J 783 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9144 (mm) REVERT: J 792 ASN cc_start: 0.8786 (m-40) cc_final: 0.8450 (t0) REVERT: J 825 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.7803 (p) REVERT: J 837 ASP cc_start: 0.8995 (t0) cc_final: 0.8684 (t0) REVERT: J 839 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8660 (p) REVERT: J 1023 HIS cc_start: 0.9135 (m-70) cc_final: 0.8918 (m90) REVERT: J 1250 ASP cc_start: 0.9214 (OUTLIER) cc_final: 0.8921 (m-30) REVERT: J 1350 ASN cc_start: 0.8583 (m-40) cc_final: 0.8063 (m-40) REVERT: J 1373 ARG cc_start: 0.8947 (ttm170) cc_final: 0.8734 (mpt180) REVERT: K 7 GLN cc_start: 0.8895 (tp40) cc_final: 0.8530 (tp40) REVERT: K 15 ASN cc_start: 0.8248 (t0) cc_final: 0.8042 (t0) REVERT: K 69 ARG cc_start: 0.8611 (mmm-85) cc_final: 0.8309 (mmm160) REVERT: G 58 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8172 (mt-10) REVERT: G 80 GLU cc_start: 0.8554 (tt0) cc_final: 0.8252 (tm-30) REVERT: G 158 ARG cc_start: 0.8270 (ttm-80) cc_final: 0.7960 (ptp-110) REVERT: G 194 GLN cc_start: 0.8517 (pm20) cc_final: 0.8306 (mp10) REVERT: H 68 TYR cc_start: 0.8387 (m-10) cc_final: 0.8186 (m-10) REVERT: H 177 TYR cc_start: 0.8618 (m-80) cc_final: 0.8050 (m-80) REVERT: H 205 MET cc_start: 0.7871 (mtp) cc_final: 0.7552 (ttt) outliers start: 72 outliers final: 36 residues processed: 475 average time/residue: 0.2041 time to fit residues: 150.8404 Evaluate side-chains 291 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 251 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 134 ASP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 519 ASN Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 1012 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 564 VAL Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 753 SER Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1164 SER Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1172 LYS Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain H residue 232 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 4.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 13 GLN I 387 ASN I 811 ASN I 965 GLN I1013 GLN I1111 GLN I1116 HIS I1324 ASN J 294 ASN J1098 GLN K 29 GLN ** G 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 GLN H 227 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.076536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.052564 restraints weight = 158077.080| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 4.59 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 28855 Z= 0.260 Angle : 0.643 11.613 39366 Z= 0.338 Chirality : 0.044 0.258 4498 Planarity : 0.005 0.073 4849 Dihedral : 16.316 179.429 4778 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.80 % Favored : 97.17 % Rotamer: Outliers : 4.38 % Allowed : 24.86 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.15), residues: 3359 helix: 2.09 (0.15), residues: 1169 sheet: 0.57 (0.23), residues: 514 loop : -0.27 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 944 TYR 0.050 0.002 TYR P 111 PHE 0.023 0.002 PHE P 126 TRP 0.019 0.002 TRP I 183 HIS 0.006 0.001 HIS I1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.26 (28847) covalent geometry : angle 0.64124 / 0.34 (39354) hydrogen bonds : bond 0.04375 / 2.90 ( 1243) hydrogen bonds : angle 4.58332 / 3.19 ( 3419) metal coordination : bond 0.01157 / 0.61 ( 8) metal coordination : angle 2.45989 / 1.21 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 247 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 11 ARG cc_start: 0.7640 (ttt-90) cc_final: 0.7265 (ttt-90) REVERT: P 32 MET cc_start: 0.9237 (mmm) cc_final: 0.8953 (mmm) REVERT: P 95 GLN cc_start: 0.9083 (mm-40) cc_final: 0.8881 (mm-40) REVERT: P 140 MET cc_start: 0.9409 (mtm) cc_final: 0.8490 (mtm) REVERT: I 81 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.7987 (p0) REVERT: I 142 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8474 (mt-10) REVERT: I 183 TRP cc_start: 0.8437 (m-10) cc_final: 0.7762 (m-10) REVERT: I 189 ASP cc_start: 0.9035 (t0) cc_final: 0.8808 (t0) REVERT: I 426 ILE cc_start: 0.9185 (mt) cc_final: 0.8981 (pt) REVERT: I 461 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8518 (tm-30) REVERT: I 503 LYS cc_start: 0.9176 (mmtm) cc_final: 0.8927 (mmtt) REVERT: I 541 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8509 (mp0) REVERT: I 562 GLU cc_start: 0.8673 (tt0) cc_final: 0.8422 (tm-30) REVERT: I 593 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8452 (ttmm) REVERT: I 654 ASP cc_start: 0.7903 (t0) cc_final: 0.7652 (t70) REVERT: I 704 MET cc_start: 0.8800 (mmm) cc_final: 0.8486 (tpp) REVERT: I 849 GLU cc_start: 0.8893 (pm20) cc_final: 0.8602 (pm20) REVERT: I 1107 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8630 (mtp) REVERT: I 1203 ASP cc_start: 0.7646 (m-30) cc_final: 0.7268 (t0) REVERT: I 1297 ASP cc_start: 0.7507 (t0) cc_final: 0.7030 (t0) REVERT: I 1321 GLU cc_start: 0.8596 (tp30) cc_final: 0.8210 (tp30) REVERT: J 180 MET cc_start: 0.7685 (ptp) cc_final: 0.7237 (mtm) REVERT: J 563 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8383 (mm) REVERT: J 792 ASN cc_start: 0.8835 (m-40) cc_final: 0.8454 (t0) REVERT: J 837 ASP cc_start: 0.9052 (t0) cc_final: 0.8762 (t0) REVERT: J 913 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8344 (mm-30) REVERT: J 1054 THR cc_start: 0.5699 (OUTLIER) cc_final: 0.5480 (t) REVERT: J 1189 MET cc_start: 0.8923 (tpp) cc_final: 0.8575 (tpp) REVERT: J 1250 ASP cc_start: 0.9094 (m-30) cc_final: 0.8879 (m-30) REVERT: J 1253 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9138 (mm) REVERT: J 1254 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7995 (mt-10) REVERT: J 1370 MET cc_start: 0.9259 (tpp) cc_final: 0.8633 (tpp) REVERT: K 7 GLN cc_start: 0.8813 (tp40) cc_final: 0.8444 (tp40) REVERT: K 8 ASP cc_start: 0.8524 (p0) cc_final: 0.7980 (p0) REVERT: K 15 ASN cc_start: 0.8442 (t0) cc_final: 0.8114 (t0) REVERT: K 43 ASN cc_start: 0.9439 (t0) cc_final: 0.9199 (t0) REVERT: K 44 ASP cc_start: 0.8659 (m-30) cc_final: 0.8378 (m-30) REVERT: K 69 ARG cc_start: 0.8854 (mmm-85) cc_final: 0.7935 (mmm160) REVERT: K 72 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8488 (tm-30) REVERT: K 73 GLN cc_start: 0.8518 (mp10) cc_final: 0.7893 (mt0) REVERT: G 25 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8528 (mtmm) REVERT: G 58 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7900 (mt-10) REVERT: G 80 GLU cc_start: 0.8450 (tt0) cc_final: 0.8125 (tm-30) REVERT: G 181 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7708 (pm20) REVERT: H 20 SER cc_start: 0.8752 (OUTLIER) cc_final: 0.8429 (m) REVERT: H 142 MET cc_start: 0.8363 (ptp) cc_final: 0.7197 (pmm) outliers start: 124 outliers final: 61 residues processed: 353 average time/residue: 0.1689 time to fit residues: 98.2754 Evaluate side-chains 293 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 222 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain P residue 130 PHE Chi-restraints excluded: chain P residue 133 PRO Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 318 SER Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 593 LYS Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 790 ASP Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 838 CYS Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 1012 GLU Chi-restraints excluded: chain I residue 1107 MET Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1286 THR Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 733 SER Chi-restraints excluded: chain J residue 753 SER Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 910 ASN Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1172 LYS Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1365 TYR Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain H residue 232 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 257 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 273 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 298 optimal weight: 3.9990 chunk 243 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 357 ASN I 659 GLN I 811 ASN J 94 GLN J 979 ASN J1279 GLN ** G 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 HIS ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.075764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.052146 restraints weight = 155879.526| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 4.43 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 28855 Z= 0.206 Angle : 0.582 12.710 39366 Z= 0.306 Chirality : 0.043 0.270 4498 Planarity : 0.004 0.083 4849 Dihedral : 16.360 179.706 4759 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.59 % Favored : 97.35 % Rotamer: Outliers : 4.13 % Allowed : 24.31 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.15), residues: 3359 helix: 2.07 (0.15), residues: 1176 sheet: 0.46 (0.23), residues: 515 loop : -0.31 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 478 TYR 0.031 0.002 TYR P 111 PHE 0.015 0.001 PHE I1323 TRP 0.009 0.001 TRP I 183 HIS 0.004 0.001 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 (28847) covalent geometry : angle 0.58100 / 0.31 (39354) hydrogen bonds : bond 0.04021 / 2.69 ( 1243) hydrogen bonds : angle 4.42657 / 3.09 ( 3419) metal coordination : bond 0.00896 / 0.43 ( 8) metal coordination : angle 1.91945 / 1.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 234 time to evaluate : 1.034 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: 0.7660 (ttt-90) cc_final: 0.7338 (ttt-90) REVERT: P 32 MET cc_start: 0.9247 (mmm) cc_final: 0.8955 (mmm) REVERT: P 76 SER cc_start: 0.8952 (t) cc_final: 0.8347 (m) REVERT: P 95 GLN cc_start: 0.9141 (mm-40) cc_final: 0.8837 (mm-40) REVERT: P 127 GLN cc_start: 0.8530 (mp10) cc_final: 0.8282 (mm-40) REVERT: P 140 MET cc_start: 0.9398 (mtm) cc_final: 0.8558 (mtm) REVERT: I 142 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8342 (mt-10) REVERT: I 183 TRP cc_start: 0.8499 (m-10) cc_final: 0.7751 (m-10) REVERT: I 189 ASP cc_start: 0.9032 (t0) cc_final: 0.8815 (t0) REVERT: I 541 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8511 (mp0) REVERT: I 593 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.8576 (ttmm) REVERT: I 654 ASP cc_start: 0.7846 (t0) cc_final: 0.7644 (t0) REVERT: I 704 MET cc_start: 0.8817 (mmm) cc_final: 0.8498 (tpp) REVERT: I 849 GLU cc_start: 0.8910 (pm20) cc_final: 0.8624 (pm20) REVERT: I 1107 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8662 (mtp) REVERT: I 1203 ASP cc_start: 0.7654 (m-30) cc_final: 0.7274 (t0) REVERT: I 1297 ASP cc_start: 0.7689 (t0) cc_final: 0.7247 (t0) REVERT: I 1321 GLU cc_start: 0.8696 (tp30) cc_final: 0.8213 (tp30) REVERT: J 177 ASP cc_start: 0.8393 (t0) cc_final: 0.8122 (p0) REVERT: J 192 MET cc_start: 0.8886 (ptm) cc_final: 0.8648 (ptp) REVERT: J 298 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7876 (ttm) REVERT: J 743 MET cc_start: 0.8928 (ptm) cc_final: 0.8444 (ptm) REVERT: J 783 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9087 (mm) REVERT: J 792 ASN cc_start: 0.8855 (m-40) cc_final: 0.8455 (t0) REVERT: J 837 ASP cc_start: 0.9041 (t0) cc_final: 0.8765 (t0) REVERT: J 913 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8372 (mm-30) REVERT: J 933 ARG cc_start: 0.5630 (OUTLIER) cc_final: 0.4800 (ptm160) REVERT: J 1054 THR cc_start: 0.5673 (OUTLIER) cc_final: 0.5456 (t) REVERT: J 1175 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7131 (pt) REVERT: J 1250 ASP cc_start: 0.9049 (m-30) cc_final: 0.8815 (m-30) REVERT: J 1253 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.9128 (mm) REVERT: J 1334 GLU cc_start: 0.8829 (tp30) cc_final: 0.8517 (tp30) REVERT: K 1 MET cc_start: 0.6941 (mmm) cc_final: 0.6674 (mmp) REVERT: K 7 GLN cc_start: 0.8714 (tp40) cc_final: 0.8248 (tp40) REVERT: K 8 ASP cc_start: 0.8825 (OUTLIER) cc_final: 0.8598 (p0) REVERT: K 15 ASN cc_start: 0.8429 (t0) cc_final: 0.8066 (t0) REVERT: K 43 ASN cc_start: 0.9400 (t0) cc_final: 0.9036 (t0) REVERT: G 25 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8550 (mtmm) REVERT: G 58 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7847 (mt-10) REVERT: G 80 GLU cc_start: 0.8487 (tt0) cc_final: 0.8155 (tm-30) REVERT: G 181 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7727 (pm20) REVERT: H 142 MET cc_start: 0.8372 (ptp) cc_final: 0.7779 (pmm) outliers start: 117 outliers final: 66 residues processed: 329 average time/residue: 0.1745 time to fit residues: 94.0266 Evaluate side-chains 296 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 218 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 133 PRO Chi-restraints excluded: chain P residue 147 ASN Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 318 SER Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 357 ASN Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 593 LYS Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 790 ASP Chi-restraints excluded: chain I residue 838 CYS Chi-restraints excluded: chain I residue 1012 GLU Chi-restraints excluded: chain I residue 1107 MET Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1286 THR Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 721 SER Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 910 ASN Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 933 ARG Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1023 HIS Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1172 LYS Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1186 TYR Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1365 TYR Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain H residue 232 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 340 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 280 optimal weight: 0.3980 chunk 254 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 218 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 297 optimal weight: 0.0670 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1279 GLN ** G 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 194 GLN ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.076799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.053723 restraints weight = 124791.522| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.94 r_work: 0.2804 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 28855 Z= 0.112 Angle : 0.544 12.926 39366 Z= 0.283 Chirality : 0.042 0.270 4498 Planarity : 0.004 0.087 4849 Dihedral : 16.360 179.952 4750 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.47 % Favored : 97.47 % Rotamer: Outliers : 3.37 % Allowed : 25.28 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.15), residues: 3359 helix: 2.16 (0.15), residues: 1174 sheet: 0.39 (0.23), residues: 520 loop : -0.25 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 107 TYR 0.025 0.001 TYR P 111 PHE 0.016 0.001 PHE J 49 TRP 0.009 0.001 TRP J 115 HIS 0.004 0.001 HIS P 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (28847) covalent geometry : angle 0.54369 / 0.28 (39354) hydrogen bonds : bond 0.03563 / 2.38 ( 1243) hydrogen bonds : angle 4.26047 / 2.97 ( 3419) metal coordination : bond 0.00467 / 0.23 ( 8) metal coordination : angle 1.72305 / 1.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 230 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 32 MET cc_start: 0.9323 (mmm) cc_final: 0.9008 (mmm) REVERT: P 95 GLN cc_start: 0.9190 (mm-40) cc_final: 0.8839 (mm-40) REVERT: P 111 TYR cc_start: 0.7273 (m-80) cc_final: 0.6999 (m-80) REVERT: I 142 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8798 (mt-10) REVERT: I 183 TRP cc_start: 0.8794 (m-10) cc_final: 0.8089 (m-10) REVERT: I 189 ASP cc_start: 0.9038 (t0) cc_final: 0.8789 (t0) REVERT: I 488 MET cc_start: 0.8925 (mmp) cc_final: 0.8607 (mmm) REVERT: I 541 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8564 (mp0) REVERT: I 593 LYS cc_start: 0.9369 (OUTLIER) cc_final: 0.9142 (tptm) REVERT: I 654 ASP cc_start: 0.8318 (t0) cc_final: 0.8084 (t0) REVERT: I 704 MET cc_start: 0.8985 (mmm) cc_final: 0.8663 (tpp) REVERT: I 849 GLU cc_start: 0.9216 (pm20) cc_final: 0.8920 (pm20) REVERT: I 1297 ASP cc_start: 0.7833 (t0) cc_final: 0.7475 (t0) REVERT: J 177 ASP cc_start: 0.8465 (t0) cc_final: 0.8207 (p0) REVERT: J 192 MET cc_start: 0.8937 (ptm) cc_final: 0.8684 (ptp) REVERT: J 298 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8121 (ttm) REVERT: J 304 ASP cc_start: 0.8982 (m-30) cc_final: 0.8621 (t0) REVERT: J 541 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9332 (mp) REVERT: J 783 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9088 (mm) REVERT: J 792 ASN cc_start: 0.8976 (m-40) cc_final: 0.8506 (t0) REVERT: J 837 ASP cc_start: 0.9251 (t0) cc_final: 0.8971 (t0) REVERT: J 844 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8572 (p) REVERT: J 913 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8757 (mm-30) REVERT: J 933 ARG cc_start: 0.5401 (OUTLIER) cc_final: 0.4837 (ptm160) REVERT: J 1054 THR cc_start: 0.5679 (OUTLIER) cc_final: 0.5463 (t) REVERT: J 1175 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7296 (pt) REVERT: J 1250 ASP cc_start: 0.9232 (m-30) cc_final: 0.9031 (m-30) REVERT: J 1253 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.9175 (mm) REVERT: J 1254 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8491 (mt-10) REVERT: J 1334 GLU cc_start: 0.9192 (tp30) cc_final: 0.8986 (tp30) REVERT: K 7 GLN cc_start: 0.8701 (tp40) cc_final: 0.8244 (tp40) REVERT: K 15 ASN cc_start: 0.8427 (t0) cc_final: 0.8082 (t0) REVERT: K 43 ASN cc_start: 0.9477 (t0) cc_final: 0.9009 (t0) REVERT: K 55 GLU cc_start: 0.8471 (mm-30) cc_final: 0.7980 (mm-30) REVERT: G 25 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8749 (mtmm) REVERT: G 58 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8441 (mt-10) REVERT: G 80 GLU cc_start: 0.9035 (tt0) cc_final: 0.8547 (tm-30) REVERT: G 125 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8724 (tppp) REVERT: G 181 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8025 (pm20) REVERT: H 142 MET cc_start: 0.8556 (ptp) cc_final: 0.7972 (pmm) outliers start: 95 outliers final: 54 residues processed: 309 average time/residue: 0.1921 time to fit residues: 96.3643 Evaluate side-chains 281 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 215 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 43 ARG Chi-restraints excluded: chain P residue 133 PRO Chi-restraints excluded: chain P residue 147 ASN Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 318 SER Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 429 MET Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 593 LYS Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 1012 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 564 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 721 SER Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 933 ARG Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1172 LYS Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1186 TYR Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1365 TYR Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 125 LYS Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain H residue 232 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 88 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 180 optimal weight: 0.6980 chunk 222 optimal weight: 0.9980 chunk 212 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 55 optimal weight: 0.0970 chunk 101 optimal weight: 0.0970 chunk 126 optimal weight: 2.9990 overall best weight: 0.9778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1279 GLN ** G 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.076749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.053601 restraints weight = 127157.624| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.99 r_work: 0.2804 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 28855 Z= 0.119 Angle : 0.540 12.969 39366 Z= 0.280 Chirality : 0.041 0.269 4498 Planarity : 0.004 0.086 4849 Dihedral : 16.367 179.815 4748 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.47 % Favored : 97.50 % Rotamer: Outliers : 3.51 % Allowed : 24.76 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.15), residues: 3359 helix: 2.18 (0.15), residues: 1175 sheet: 0.31 (0.23), residues: 510 loop : -0.21 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 69 TYR 0.023 0.001 TYR I 123 PHE 0.015 0.001 PHE I 545 TRP 0.011 0.001 TRP J 115 HIS 0.003 0.001 HIS P 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (28847) covalent geometry : angle 0.53904 / 0.28 (39354) hydrogen bonds : bond 0.03398 / 2.27 ( 1243) hydrogen bonds : angle 4.19590 / 2.94 ( 3419) metal coordination : bond 0.00531 / 0.27 ( 8) metal coordination : angle 1.54357 / 0.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 226 time to evaluate : 1.190 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 32 MET cc_start: 0.9325 (mmm) cc_final: 0.8941 (mmm) REVERT: P 76 SER cc_start: 0.9004 (t) cc_final: 0.8367 (m) REVERT: P 95 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8795 (mm-40) REVERT: P 111 TYR cc_start: 0.7275 (m-80) cc_final: 0.6928 (m-80) REVERT: I 142 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8747 (mt-10) REVERT: I 183 TRP cc_start: 0.8843 (m-10) cc_final: 0.8148 (m-10) REVERT: I 189 ASP cc_start: 0.9038 (t0) cc_final: 0.8787 (t0) REVERT: I 430 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8693 (mtmm) REVERT: I 541 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8561 (mp0) REVERT: I 593 LYS cc_start: 0.9380 (OUTLIER) cc_final: 0.8928 (tptm) REVERT: I 654 ASP cc_start: 0.8349 (t0) cc_final: 0.8086 (t0) REVERT: I 704 MET cc_start: 0.8994 (mmm) cc_final: 0.8672 (tpp) REVERT: I 849 GLU cc_start: 0.9217 (pm20) cc_final: 0.8934 (pm20) REVERT: I 1297 ASP cc_start: 0.7832 (t0) cc_final: 0.7496 (t0) REVERT: J 177 ASP cc_start: 0.8499 (t0) cc_final: 0.8158 (p0) REVERT: J 192 MET cc_start: 0.8956 (ptm) cc_final: 0.8711 (ptp) REVERT: J 229 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8698 (tm-30) REVERT: J 298 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8140 (ttm) REVERT: J 304 ASP cc_start: 0.8968 (m-30) cc_final: 0.8657 (t0) REVERT: J 541 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9332 (mp) REVERT: J 563 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8355 (mm) REVERT: J 783 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9062 (mm) REVERT: J 792 ASN cc_start: 0.8983 (m-40) cc_final: 0.8575 (t0) REVERT: J 825 VAL cc_start: 0.8591 (OUTLIER) cc_final: 0.8323 (p) REVERT: J 837 ASP cc_start: 0.9242 (t0) cc_final: 0.8962 (t0) REVERT: J 913 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8776 (mm-30) REVERT: J 1054 THR cc_start: 0.5704 (OUTLIER) cc_final: 0.5489 (t) REVERT: J 1165 PHE cc_start: 0.6208 (m-10) cc_final: 0.5768 (m-80) REVERT: J 1175 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7443 (pt) REVERT: J 1250 ASP cc_start: 0.9240 (m-30) cc_final: 0.9001 (m-30) REVERT: J 1254 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8464 (mt-10) REVERT: J 1334 GLU cc_start: 0.9216 (tp30) cc_final: 0.8996 (tp30) REVERT: K 7 GLN cc_start: 0.8690 (tp40) cc_final: 0.8224 (tp40) REVERT: K 8 ASP cc_start: 0.8665 (p0) cc_final: 0.7908 (p0) REVERT: K 15 ASN cc_start: 0.8428 (t0) cc_final: 0.8055 (t0) REVERT: K 41 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7906 (tm-30) REVERT: K 43 ASN cc_start: 0.9478 (t0) cc_final: 0.9024 (t0) REVERT: K 55 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8058 (mm-30) REVERT: K 68 GLU cc_start: 0.9525 (tp30) cc_final: 0.9018 (tp30) REVERT: G 25 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8733 (mtmm) REVERT: G 58 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8460 (mt-10) REVERT: G 80 GLU cc_start: 0.9055 (tt0) cc_final: 0.8558 (tm-30) REVERT: G 181 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8012 (pm20) REVERT: H 29 GLU cc_start: 0.8277 (tt0) cc_final: 0.7965 (tm-30) REVERT: H 142 MET cc_start: 0.8607 (ptp) cc_final: 0.8052 (pmm) outliers start: 99 outliers final: 65 residues processed: 313 average time/residue: 0.1842 time to fit residues: 94.3791 Evaluate side-chains 296 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 219 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 43 ARG Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 133 PRO Chi-restraints excluded: chain P residue 147 ASN Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 318 SER Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 429 MET Chi-restraints excluded: chain I residue 430 LYS Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 593 LYS Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 1012 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1286 THR Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 564 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 721 SER Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 910 ASN Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1172 LYS Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1186 TYR Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1365 TYR Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 56 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 322 optimal weight: 4.9990 chunk 326 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 258 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 196 optimal weight: 7.9990 chunk 229 optimal weight: 9.9990 chunk 235 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 435 GLN J1279 GLN K 73 GLN G 23 HIS ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.072668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.049311 restraints weight = 144390.525| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 4.15 r_work: 0.2672 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 28855 Z= 0.315 Angle : 0.704 12.256 39366 Z= 0.364 Chirality : 0.045 0.254 4498 Planarity : 0.005 0.084 4849 Dihedral : 16.513 179.862 4747 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.43 % Favored : 96.51 % Rotamer: Outliers : 4.31 % Allowed : 23.99 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.15), residues: 3359 helix: 1.72 (0.15), residues: 1182 sheet: 0.16 (0.24), residues: 482 loop : -0.38 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG J 137 TYR 0.027 0.002 TYR J 631 PHE 0.030 0.002 PHE I 812 TRP 0.017 0.002 TRP I 183 HIS 0.007 0.001 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00701 / 0.32 (28847) covalent geometry : angle 0.70253 / 0.36 (39354) hydrogen bonds : bond 0.04698 / 3.16 ( 1243) hydrogen bonds : angle 4.59899 / 3.23 ( 3419) metal coordination : bond 0.01715 / 0.91 ( 8) metal coordination : angle 2.57564 / 1.30 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 214 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 32 MET cc_start: 0.9380 (mmm) cc_final: 0.9140 (mmm) REVERT: P 76 SER cc_start: 0.9198 (t) cc_final: 0.8517 (m) REVERT: P 95 GLN cc_start: 0.9238 (mm-40) cc_final: 0.8801 (mm-40) REVERT: P 111 TYR cc_start: 0.7281 (m-80) cc_final: 0.6979 (m-80) REVERT: P 140 MET cc_start: 0.9481 (mtm) cc_final: 0.8710 (mtm) REVERT: I 142 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8947 (mt-10) REVERT: I 183 TRP cc_start: 0.9030 (m-10) cc_final: 0.8304 (m-10) REVERT: I 189 ASP cc_start: 0.9100 (t0) cc_final: 0.8872 (t0) REVERT: I 541 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8664 (mp0) REVERT: I 593 LYS cc_start: 0.9474 (OUTLIER) cc_final: 0.8899 (ttmm) REVERT: I 654 ASP cc_start: 0.8528 (t0) cc_final: 0.8223 (t70) REVERT: I 704 MET cc_start: 0.9146 (mmm) cc_final: 0.8854 (tpp) REVERT: I 849 GLU cc_start: 0.9282 (pm20) cc_final: 0.8933 (pm20) REVERT: I 1164 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.8062 (m-10) REVERT: I 1297 ASP cc_start: 0.8213 (t0) cc_final: 0.7903 (t0) REVERT: I 1312 ASN cc_start: 0.9064 (OUTLIER) cc_final: 0.8528 (p0) REVERT: J 133 ARG cc_start: 0.8935 (mmm-85) cc_final: 0.8544 (tpt170) REVERT: J 177 ASP cc_start: 0.8653 (t0) cc_final: 0.8227 (p0) REVERT: J 229 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8826 (tm-30) REVERT: J 298 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8483 (ttm) REVERT: J 563 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8484 (mm) REVERT: J 783 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9236 (mm) REVERT: J 792 ASN cc_start: 0.9040 (m-40) cc_final: 0.8583 (t0) REVERT: J 830 ASP cc_start: 0.8857 (t0) cc_final: 0.8554 (t0) REVERT: J 913 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8835 (mm-30) REVERT: J 933 ARG cc_start: 0.6308 (mmm-85) cc_final: 0.5155 (ptm160) REVERT: J 1054 THR cc_start: 0.5835 (OUTLIER) cc_final: 0.5622 (t) REVERT: J 1165 PHE cc_start: 0.6558 (m-80) cc_final: 0.6174 (m-80) REVERT: J 1172 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8848 (mmtt) REVERT: J 1175 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7472 (pt) REVERT: K 7 GLN cc_start: 0.8813 (tp40) cc_final: 0.8525 (tp40) REVERT: K 8 ASP cc_start: 0.8684 (p0) cc_final: 0.8477 (p0) REVERT: K 15 ASN cc_start: 0.8693 (t0) cc_final: 0.8305 (t0) REVERT: K 43 ASN cc_start: 0.9482 (t0) cc_final: 0.9013 (t0) REVERT: K 68 GLU cc_start: 0.9477 (tp30) cc_final: 0.9062 (tp30) REVERT: G 58 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8490 (mt-10) REVERT: G 80 GLU cc_start: 0.9175 (tt0) cc_final: 0.8745 (tm-30) REVERT: G 181 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8170 (pm20) REVERT: H 29 GLU cc_start: 0.8470 (tt0) cc_final: 0.8217 (tm-30) REVERT: H 117 HIS cc_start: 0.8533 (t-90) cc_final: 0.8271 (t-90) REVERT: H 142 MET cc_start: 0.8747 (ptp) cc_final: 0.8188 (pmm) outliers start: 122 outliers final: 79 residues processed: 319 average time/residue: 0.1756 time to fit residues: 91.2019 Evaluate side-chains 288 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 198 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 43 ARG Chi-restraints excluded: chain P residue 47 SER Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 133 PRO Chi-restraints excluded: chain P residue 147 ASN Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 318 SER Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 510 GLN Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 593 LYS Chi-restraints excluded: chain I residue 790 ASP Chi-restraints excluded: chain I residue 838 CYS Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 1012 GLU Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1164 PHE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1286 THR Chi-restraints excluded: chain I residue 1312 ASN Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 564 VAL Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 721 SER Chi-restraints excluded: chain J residue 733 SER Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 910 ASN Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1023 HIS Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1172 LYS Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1186 TYR Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1365 TYR Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 172 optimal weight: 0.0170 chunk 305 optimal weight: 4.9990 chunk 103 optimal weight: 0.1980 chunk 128 optimal weight: 0.9990 chunk 294 optimal weight: 50.0000 chunk 90 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 248 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 112 optimal weight: 20.0000 overall best weight: 0.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 762 ASN J1279 GLN G 147 GLN ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.075183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.051770 restraints weight = 134287.532| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 4.12 r_work: 0.2740 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 28855 Z= 0.113 Angle : 0.569 12.839 39366 Z= 0.295 Chirality : 0.042 0.273 4498 Planarity : 0.004 0.086 4849 Dihedral : 16.487 179.743 4747 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.53 % Favored : 97.44 % Rotamer: Outliers : 2.33 % Allowed : 26.25 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.15), residues: 3359 helix: 1.94 (0.15), residues: 1189 sheet: 0.12 (0.24), residues: 492 loop : -0.32 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 478 TYR 0.026 0.001 TYR I 123 PHE 0.014 0.001 PHE P 126 TRP 0.016 0.001 TRP J 115 HIS 0.004 0.001 HIS H 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (28847) covalent geometry : angle 0.56817 / 0.29 (39354) hydrogen bonds : bond 0.03532 / 2.37 ( 1243) hydrogen bonds : angle 4.26261 / 2.99 ( 3419) metal coordination : bond 0.00428 / 0.23 ( 8) metal coordination : angle 2.13841 / 1.30 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 215 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 76 SER cc_start: 0.9109 (t) cc_final: 0.8412 (m) REVERT: P 95 GLN cc_start: 0.9265 (mm-40) cc_final: 0.8776 (mm-40) REVERT: P 111 TYR cc_start: 0.7292 (m-80) cc_final: 0.6958 (m-80) REVERT: I 183 TRP cc_start: 0.8970 (m-10) cc_final: 0.8221 (m-10) REVERT: I 189 ASP cc_start: 0.9086 (t0) cc_final: 0.8834 (t0) REVERT: I 541 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8615 (mp0) REVERT: I 593 LYS cc_start: 0.9400 (OUTLIER) cc_final: 0.8931 (tptm) REVERT: I 654 ASP cc_start: 0.8455 (t0) cc_final: 0.8114 (t0) REVERT: I 704 MET cc_start: 0.9019 (mmm) cc_final: 0.8710 (tpp) REVERT: I 849 GLU cc_start: 0.9275 (pm20) cc_final: 0.8945 (pm20) REVERT: I 1240 ASP cc_start: 0.8830 (p0) cc_final: 0.8566 (p0) REVERT: I 1297 ASP cc_start: 0.8001 (t0) cc_final: 0.7674 (t0) REVERT: J 133 ARG cc_start: 0.8767 (mmm-85) cc_final: 0.8354 (tpt170) REVERT: J 177 ASP cc_start: 0.8585 (t0) cc_final: 0.8248 (p0) REVERT: J 180 MET cc_start: 0.7867 (ptt) cc_final: 0.7421 (ptt) REVERT: J 229 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8740 (tm-30) REVERT: J 298 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8381 (ttm) REVERT: J 304 ASP cc_start: 0.8953 (m-30) cc_final: 0.8705 (t0) REVERT: J 783 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9046 (mm) REVERT: J 792 ASN cc_start: 0.9031 (m-40) cc_final: 0.8618 (t0) REVERT: J 830 ASP cc_start: 0.8861 (t0) cc_final: 0.8564 (t0) REVERT: J 844 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8482 (p) REVERT: J 913 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8805 (mm-30) REVERT: J 922 SER cc_start: 0.9473 (m) cc_final: 0.9219 (p) REVERT: J 932 MET cc_start: 0.7480 (ptm) cc_final: 0.7263 (ptp) REVERT: J 933 ARG cc_start: 0.6359 (mmm-85) cc_final: 0.5247 (ptm160) REVERT: J 1054 THR cc_start: 0.5876 (OUTLIER) cc_final: 0.5663 (t) REVERT: J 1175 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7462 (pp) REVERT: J 1254 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8523 (mt-10) REVERT: K 7 GLN cc_start: 0.8628 (tp40) cc_final: 0.8165 (tp40) REVERT: K 8 ASP cc_start: 0.9001 (p0) cc_final: 0.8782 (p0) REVERT: K 15 ASN cc_start: 0.8491 (t0) cc_final: 0.8118 (t0) REVERT: K 43 ASN cc_start: 0.9481 (t0) cc_final: 0.9022 (t0) REVERT: G 58 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8457 (mt-10) REVERT: G 80 GLU cc_start: 0.9126 (tt0) cc_final: 0.8751 (tm-30) REVERT: G 181 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8051 (pm20) REVERT: H 29 GLU cc_start: 0.8375 (tt0) cc_final: 0.7972 (tm-30) REVERT: H 117 HIS cc_start: 0.8532 (t-90) cc_final: 0.8229 (t-90) REVERT: H 142 MET cc_start: 0.8747 (ptp) cc_final: 0.8120 (pmm) REVERT: H 200 LYS cc_start: 0.9119 (ptmt) cc_final: 0.8629 (ttpp) outliers start: 65 outliers final: 50 residues processed: 273 average time/residue: 0.1703 time to fit residues: 75.7271 Evaluate side-chains 271 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 213 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 43 ARG Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 133 PRO Chi-restraints excluded: chain P residue 147 ASN Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 318 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 593 LYS Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 1012 GLU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1286 THR Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 721 SER Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 910 ASN Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1186 TYR Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 328 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 253 optimal weight: 9.9990 chunk 186 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 228 optimal weight: 8.9990 chunk 162 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 291 optimal weight: 50.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J1279 GLN ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.074729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.051418 restraints weight = 132529.557| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 4.06 r_work: 0.2731 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28855 Z= 0.134 Angle : 0.564 12.798 39366 Z= 0.291 Chirality : 0.042 0.267 4498 Planarity : 0.004 0.086 4849 Dihedral : 16.434 179.913 4738 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.53 % Favored : 97.44 % Rotamer: Outliers : 2.60 % Allowed : 26.18 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.15), residues: 3359 helix: 1.97 (0.15), residues: 1190 sheet: 0.00 (0.23), residues: 499 loop : -0.28 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 148 TYR 0.023 0.001 TYR I 123 PHE 0.022 0.001 PHE P 126 TRP 0.014 0.001 TRP J 115 HIS 0.003 0.001 HIS P 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (28847) covalent geometry : angle 0.56351 / 0.29 (39354) hydrogen bonds : bond 0.03468 / 2.32 ( 1243) hydrogen bonds : angle 4.22466 / 2.97 ( 3419) metal coordination : bond 0.00692 / 0.37 ( 8) metal coordination : angle 1.74572 / 1.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 214 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 11 ARG cc_start: 0.8173 (ttt180) cc_final: 0.7954 (ttt180) REVERT: P 32 MET cc_start: 0.9357 (mmm) cc_final: 0.9142 (mmm) REVERT: P 76 SER cc_start: 0.9148 (t) cc_final: 0.8426 (m) REVERT: P 95 GLN cc_start: 0.9275 (mm-40) cc_final: 0.8786 (mm-40) REVERT: P 111 TYR cc_start: 0.7304 (m-80) cc_final: 0.6895 (m-80) REVERT: I 183 TRP cc_start: 0.8998 (m-10) cc_final: 0.8215 (m-10) REVERT: I 189 ASP cc_start: 0.9086 (t0) cc_final: 0.8833 (t0) REVERT: I 403 MET cc_start: 0.9128 (tmm) cc_final: 0.8869 (tmm) REVERT: I 541 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8618 (mp0) REVERT: I 593 LYS cc_start: 0.9406 (OUTLIER) cc_final: 0.8949 (tptm) REVERT: I 654 ASP cc_start: 0.8446 (t0) cc_final: 0.8103 (t0) REVERT: I 704 MET cc_start: 0.9035 (mmm) cc_final: 0.8719 (tpp) REVERT: I 849 GLU cc_start: 0.9274 (pm20) cc_final: 0.8947 (pm20) REVERT: I 1240 ASP cc_start: 0.8836 (p0) cc_final: 0.8604 (p0) REVERT: I 1297 ASP cc_start: 0.8010 (t0) cc_final: 0.7693 (t0) REVERT: J 133 ARG cc_start: 0.8761 (mmm-85) cc_final: 0.8330 (tpt170) REVERT: J 177 ASP cc_start: 0.8603 (t0) cc_final: 0.8250 (p0) REVERT: J 180 MET cc_start: 0.7882 (ptt) cc_final: 0.7409 (ptt) REVERT: J 229 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8761 (tm-30) REVERT: J 298 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8431 (ttm) REVERT: J 304 ASP cc_start: 0.8982 (m-30) cc_final: 0.8549 (t0) REVERT: J 783 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9051 (mm) REVERT: J 792 ASN cc_start: 0.9038 (m-40) cc_final: 0.8625 (t0) REVERT: J 825 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8428 (p) REVERT: J 830 ASP cc_start: 0.8886 (t0) cc_final: 0.8590 (t0) REVERT: J 844 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8497 (p) REVERT: J 913 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8832 (mm-30) REVERT: J 932 MET cc_start: 0.7543 (ptm) cc_final: 0.7316 (ptp) REVERT: J 933 ARG cc_start: 0.6541 (mmm-85) cc_final: 0.5298 (ptm160) REVERT: J 1054 THR cc_start: 0.5895 (OUTLIER) cc_final: 0.5685 (t) REVERT: J 1165 PHE cc_start: 0.6532 (m-80) cc_final: 0.6120 (m-80) REVERT: J 1175 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7429 (pp) REVERT: K 7 GLN cc_start: 0.8658 (tp40) cc_final: 0.8213 (tp40) REVERT: K 15 ASN cc_start: 0.8481 (t0) cc_final: 0.8085 (t0) REVERT: K 43 ASN cc_start: 0.9423 (t0) cc_final: 0.8852 (t0) REVERT: G 58 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8400 (mt-10) REVERT: G 80 GLU cc_start: 0.9138 (tt0) cc_final: 0.8639 (tm-30) REVERT: G 181 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8046 (pm20) REVERT: H 13 LEU cc_start: 0.7598 (tt) cc_final: 0.7294 (tt) REVERT: H 29 GLU cc_start: 0.8365 (tt0) cc_final: 0.7942 (tm-30) REVERT: H 117 HIS cc_start: 0.8516 (t-90) cc_final: 0.8172 (t-90) REVERT: H 142 MET cc_start: 0.8768 (ptp) cc_final: 0.8154 (pmm) REVERT: H 200 LYS cc_start: 0.9114 (ptmt) cc_final: 0.8626 (ttpp) outliers start: 73 outliers final: 51 residues processed: 278 average time/residue: 0.1669 time to fit residues: 75.8516 Evaluate side-chains 268 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 208 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 43 ARG Chi-restraints excluded: chain P residue 133 PRO Chi-restraints excluded: chain P residue 147 ASN Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 318 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 593 LYS Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 1012 GLU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1286 THR Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 564 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 721 SER Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 910 ASN Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1186 TYR Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 223 optimal weight: 4.9990 chunk 276 optimal weight: 4.9990 chunk 288 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 315 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 250 optimal weight: 8.9990 chunk 322 optimal weight: 3.9990 chunk 316 optimal weight: 6.9990 chunk 184 optimal weight: 0.7980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J1279 GLN ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.074666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.051259 restraints weight = 142541.439| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 4.23 r_work: 0.2722 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28855 Z= 0.140 Angle : 0.575 12.627 39366 Z= 0.294 Chirality : 0.042 0.268 4498 Planarity : 0.004 0.088 4849 Dihedral : 16.435 179.881 4737 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.65 % Favored : 97.32 % Rotamer: Outliers : 2.50 % Allowed : 26.18 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.15), residues: 3359 helix: 1.98 (0.15), residues: 1189 sheet: 0.02 (0.23), residues: 491 loop : -0.29 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 43 TYR 0.025 0.001 TYR I 123 PHE 0.023 0.001 PHE P 126 TRP 0.013 0.001 TRP J 115 HIS 0.003 0.001 HIS P 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (28847) covalent geometry : angle 0.57417 / 0.29 (39354) hydrogen bonds : bond 0.03435 / 2.30 ( 1243) hydrogen bonds : angle 4.20773 / 2.95 ( 3419) metal coordination : bond 0.00728 / 0.39 ( 8) metal coordination : angle 1.65985 / 0.97 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 213 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 11 ARG cc_start: 0.8259 (ttt180) cc_final: 0.8045 (ttt180) REVERT: P 32 MET cc_start: 0.9363 (mmm) cc_final: 0.9078 (mmm) REVERT: P 76 SER cc_start: 0.9188 (t) cc_final: 0.8467 (m) REVERT: P 95 GLN cc_start: 0.9300 (mm-40) cc_final: 0.8794 (mm-40) REVERT: P 111 TYR cc_start: 0.7332 (m-80) cc_final: 0.6827 (m-80) REVERT: I 142 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8766 (mt-10) REVERT: I 183 TRP cc_start: 0.9023 (m-10) cc_final: 0.8229 (m-10) REVERT: I 189 ASP cc_start: 0.9092 (t0) cc_final: 0.8831 (t0) REVERT: I 403 MET cc_start: 0.9146 (tmm) cc_final: 0.8886 (tmm) REVERT: I 541 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8642 (mp0) REVERT: I 593 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.9190 (tptm) REVERT: I 654 ASP cc_start: 0.8483 (t0) cc_final: 0.8134 (t0) REVERT: I 704 MET cc_start: 0.9042 (mmm) cc_final: 0.8729 (tpp) REVERT: I 849 GLU cc_start: 0.9279 (pm20) cc_final: 0.8955 (pm20) REVERT: I 1240 ASP cc_start: 0.8865 (p0) cc_final: 0.8635 (p0) REVERT: I 1297 ASP cc_start: 0.8046 (t0) cc_final: 0.7742 (t0) REVERT: J 133 ARG cc_start: 0.8796 (mmm-85) cc_final: 0.8582 (mmm-85) REVERT: J 177 ASP cc_start: 0.8645 (t0) cc_final: 0.8271 (p0) REVERT: J 180 MET cc_start: 0.7874 (ptt) cc_final: 0.7429 (ptt) REVERT: J 229 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8776 (tm-30) REVERT: J 298 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8461 (ttm) REVERT: J 304 ASP cc_start: 0.8971 (m-30) cc_final: 0.8541 (t0) REVERT: J 541 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9338 (mp) REVERT: J 563 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8385 (mm) REVERT: J 783 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9043 (mm) REVERT: J 792 ASN cc_start: 0.9042 (m-40) cc_final: 0.8630 (t0) REVERT: J 825 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8434 (p) REVERT: J 844 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8508 (p) REVERT: J 913 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8843 (mm-30) REVERT: J 922 SER cc_start: 0.9480 (m) cc_final: 0.9217 (p) REVERT: J 932 MET cc_start: 0.7530 (ptm) cc_final: 0.7290 (ptp) REVERT: J 933 ARG cc_start: 0.6738 (mmm-85) cc_final: 0.5354 (ptm160) REVERT: J 1054 THR cc_start: 0.5866 (OUTLIER) cc_final: 0.5652 (t) REVERT: J 1175 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7546 (pp) REVERT: J 1254 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8626 (mt-10) REVERT: K 7 GLN cc_start: 0.8581 (tp40) cc_final: 0.8134 (tp40) REVERT: K 8 ASP cc_start: 0.8892 (p0) cc_final: 0.8663 (p0) REVERT: K 15 ASN cc_start: 0.8455 (t0) cc_final: 0.8089 (t0) REVERT: K 43 ASN cc_start: 0.9416 (t0) cc_final: 0.8765 (t0) REVERT: K 68 GLU cc_start: 0.9423 (tp30) cc_final: 0.9176 (tp30) REVERT: G 58 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8414 (mt-10) REVERT: G 80 GLU cc_start: 0.9172 (tt0) cc_final: 0.8667 (tm-30) REVERT: G 181 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8053 (pm20) REVERT: H 13 LEU cc_start: 0.7627 (tt) cc_final: 0.7335 (tt) REVERT: H 29 GLU cc_start: 0.8387 (tt0) cc_final: 0.7947 (tm-30) REVERT: H 117 HIS cc_start: 0.8504 (t-90) cc_final: 0.8171 (t-90) REVERT: H 142 MET cc_start: 0.8790 (ptp) cc_final: 0.8148 (pmm) REVERT: H 200 LYS cc_start: 0.9129 (ptmt) cc_final: 0.8645 (ttpp) outliers start: 70 outliers final: 51 residues processed: 276 average time/residue: 0.1828 time to fit residues: 82.5602 Evaluate side-chains 270 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 208 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 43 ARG Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 133 PRO Chi-restraints excluded: chain P residue 147 ASN Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 318 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 593 LYS Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 1012 GLU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1286 THR Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 564 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 721 SER Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 910 ASN Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1186 TYR Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 225 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 285 optimal weight: 4.9990 chunk 202 optimal weight: 6.9990 chunk 259 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 206 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J1279 GLN G 147 GLN G 160 HIS ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.074131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.050590 restraints weight = 146810.990| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 4.28 r_work: 0.2706 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28855 Z= 0.167 Angle : 0.587 12.530 39366 Z= 0.300 Chirality : 0.042 0.265 4498 Planarity : 0.004 0.089 4849 Dihedral : 16.433 179.537 4736 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.71 % Favored : 97.26 % Rotamer: Outliers : 2.33 % Allowed : 26.28 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.15), residues: 3359 helix: 1.98 (0.15), residues: 1189 sheet: 0.01 (0.23), residues: 482 loop : -0.30 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 43 TYR 0.021 0.001 TYR I 123 PHE 0.018 0.001 PHE P 126 TRP 0.010 0.001 TRP J 115 HIS 0.004 0.001 HIS I 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (28847) covalent geometry : angle 0.58603 / 0.30 (39354) hydrogen bonds : bond 0.03511 / 2.35 ( 1243) hydrogen bonds : angle 4.21873 / 2.95 ( 3419) metal coordination : bond 0.00915 / 0.49 ( 8) metal coordination : angle 1.70695 / 0.98 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 213 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 11 ARG cc_start: 0.8300 (ttt180) cc_final: 0.8090 (ttt180) REVERT: P 32 MET cc_start: 0.9388 (mmm) cc_final: 0.9090 (mmm) REVERT: P 76 SER cc_start: 0.9204 (t) cc_final: 0.8473 (m) REVERT: P 95 GLN cc_start: 0.9311 (mm-40) cc_final: 0.8815 (mm-40) REVERT: P 111 TYR cc_start: 0.7474 (m-80) cc_final: 0.6963 (m-80) REVERT: I 183 TRP cc_start: 0.9059 (m-10) cc_final: 0.8228 (m-10) REVERT: I 189 ASP cc_start: 0.9098 (t0) cc_final: 0.8833 (t0) REVERT: I 403 MET cc_start: 0.9142 (tmm) cc_final: 0.8873 (tmm) REVERT: I 541 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8655 (mp0) REVERT: I 593 LYS cc_start: 0.9441 (OUTLIER) cc_final: 0.9221 (tptm) REVERT: I 654 ASP cc_start: 0.8501 (t0) cc_final: 0.8174 (t0) REVERT: I 704 MET cc_start: 0.9059 (mmm) cc_final: 0.8752 (tpp) REVERT: I 849 GLU cc_start: 0.9304 (pm20) cc_final: 0.8964 (pm20) REVERT: I 1240 ASP cc_start: 0.8875 (p0) cc_final: 0.8653 (p0) REVERT: I 1297 ASP cc_start: 0.8094 (t0) cc_final: 0.7797 (t0) REVERT: J 133 ARG cc_start: 0.8833 (mmm-85) cc_final: 0.8620 (mmm-85) REVERT: J 177 ASP cc_start: 0.8658 (t0) cc_final: 0.8289 (p0) REVERT: J 180 MET cc_start: 0.7885 (ptt) cc_final: 0.7443 (ptt) REVERT: J 229 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8804 (tm-30) REVERT: J 298 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8471 (ttm) REVERT: J 304 ASP cc_start: 0.8986 (m-30) cc_final: 0.8549 (t0) REVERT: J 563 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8390 (mm) REVERT: J 783 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9054 (mm) REVERT: J 792 ASN cc_start: 0.9047 (m-40) cc_final: 0.8629 (t0) REVERT: J 913 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8848 (mm-30) REVERT: J 922 SER cc_start: 0.9490 (m) cc_final: 0.9228 (p) REVERT: J 1054 THR cc_start: 0.5926 (OUTLIER) cc_final: 0.5718 (t) REVERT: J 1175 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7575 (pp) REVERT: K 7 GLN cc_start: 0.8598 (tp40) cc_final: 0.8177 (tp40) REVERT: K 8 ASP cc_start: 0.8838 (p0) cc_final: 0.8633 (p0) REVERT: K 15 ASN cc_start: 0.8486 (t0) cc_final: 0.8136 (t0) REVERT: K 43 ASN cc_start: 0.9385 (t0) cc_final: 0.8722 (t0) REVERT: K 62 GLN cc_start: 0.9235 (tp-100) cc_final: 0.8978 (tm-30) REVERT: K 68 GLU cc_start: 0.9435 (tp30) cc_final: 0.9216 (tp30) REVERT: G 80 GLU cc_start: 0.9177 (tt0) cc_final: 0.8734 (tm-30) REVERT: G 181 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8069 (pm20) REVERT: H 13 LEU cc_start: 0.7642 (tt) cc_final: 0.7362 (tt) REVERT: H 29 GLU cc_start: 0.8404 (tt0) cc_final: 0.7949 (tm-30) REVERT: H 117 HIS cc_start: 0.8565 (t-90) cc_final: 0.8207 (t-90) REVERT: H 142 MET cc_start: 0.8784 (ptp) cc_final: 0.8156 (pmm) REVERT: H 200 LYS cc_start: 0.9131 (ptmt) cc_final: 0.8638 (ttpp) outliers start: 65 outliers final: 51 residues processed: 271 average time/residue: 0.1756 time to fit residues: 78.6905 Evaluate side-chains 266 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 207 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 43 ARG Chi-restraints excluded: chain P residue 133 PRO Chi-restraints excluded: chain P residue 147 ASN Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 318 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 593 LYS Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 1012 GLU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1286 THR Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 564 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 721 SER Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 910 ASN Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1186 TYR Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 108 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 273 optimal weight: 0.9980 chunk 259 optimal weight: 5.9990 chunk 180 optimal weight: 0.3980 chunk 204 optimal weight: 0.9980 chunk 209 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 198 optimal weight: 5.9990 chunk 224 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 147 GLN ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.074779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.051768 restraints weight = 113193.074| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.73 r_work: 0.2754 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28855 Z= 0.123 Angle : 0.570 12.662 39366 Z= 0.291 Chirality : 0.042 0.268 4498 Planarity : 0.004 0.089 4849 Dihedral : 16.403 179.771 4736 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.62 % Favored : 97.32 % Rotamer: Outliers : 2.19 % Allowed : 26.56 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.15), residues: 3359 helix: 2.00 (0.15), residues: 1188 sheet: -0.00 (0.23), residues: 488 loop : -0.26 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 43 TYR 0.025 0.001 TYR I 123 PHE 0.019 0.001 PHE P 126 TRP 0.012 0.001 TRP J 115 HIS 0.004 0.001 HIS P 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (28847) covalent geometry : angle 0.56931 / 0.29 (39354) hydrogen bonds : bond 0.03333 / 2.23 ( 1243) hydrogen bonds : angle 4.15476 / 2.91 ( 3419) metal coordination : bond 0.00593 / 0.32 ( 8) metal coordination : angle 1.65403 / 0.97 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6777.79 seconds wall clock time: 116 minutes 47.81 seconds (7007.81 seconds total)