Starting phenix.real_space_refine on Mon Aug 25 13:11:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8phk_17668/08_2025/8phk_17668.cif Found real_map, /net/cci-nas-00/data/ceres_data/8phk_17668/08_2025/8phk_17668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8phk_17668/08_2025/8phk_17668.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8phk_17668/08_2025/8phk_17668.map" model { file = "/net/cci-nas-00/data/ceres_data/8phk_17668/08_2025/8phk_17668.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8phk_17668/08_2025/8phk_17668.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.053 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 87 5.49 5 Mg 1 5.21 5 S 112 5.16 5 C 17421 2.51 5 N 4998 2.21 5 O 5604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28225 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: 10431 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: 10580 Chain: "J" Number of atoms: 10440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1342, 10440 Classifications: {'peptide': 1342} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1286} Chain breaks: 2 Chain: "K" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 655 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "G" Number of atoms: 1807 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 222} Conformer: "B" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 222} bond proxies already assigned to first conformer: 1812 Chain: "H" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1780 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "A" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 771 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "B" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 784 Classifications: {'DNA': 38} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 37} Chain: "R" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 260 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 5} Link IDs: {'rna3p': 11} Chain: "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 12174 SG CYS J 70 24.393 69.954 83.528 1.00119.04 S ATOM 12188 SG CYS J 72 23.310 66.311 83.232 1.00118.34 S ATOM 12296 SG CYS J 85 21.845 68.517 85.926 1.00117.72 S ATOM 12320 SG CYS J 88 25.534 67.472 86.117 1.00115.59 S ATOM 18008 SG CYS J 814 56.521 126.276 92.019 1.00108.47 S ATOM 18573 SG CYS J 888 58.636 123.461 91.132 1.00106.90 S ATOM 18624 SG CYS J 895 57.608 126.109 88.414 1.00 98.23 S ATOM 18645 SG CYS J 898 60.284 126.828 90.894 1.00 99.88 S Time building chain proxies: 7.80, per 1000 atoms: 0.28 Number of scatterers: 28225 At special positions: 0 Unit cell: (139.776, 169.728, 158.08, 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 112 16.00 P 87 15.00 Mg 1 11.99 O 5604 8.00 N 4998 7.00 C 17421 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: 2.52 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 88 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " Number of angles added : 12 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6238 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 51 sheets defined 38.5% alpha, 18.6% beta 38 base pairs and 60 stacking pairs defined. Time for finding SS restraints: 4.00 Creating SS restraints... Processing helix chain 'P' and resid 13 through 24 Processing helix chain 'P' and resid 38 through 42 Processing helix chain 'P' and resid 65 through 71 removed outlier: 3.620A pdb=" N ILE P 69 " --> pdb=" O HIS P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 98 removed outlier: 3.525A pdb=" N ILE P 93 " --> pdb=" O PRO P 89 " (cutoff:3.500A) Processing helix chain 'P' and resid 120 through 124 removed outlier: 3.967A pdb=" N PHE P 123 " --> pdb=" O GLU P 120 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU P 124 " --> pdb=" O GLY P 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 120 through 124' Processing helix chain 'P' and resid 155 through 157 No H-bonds generated for 'chain 'P' and resid 155 through 157' Processing helix chain 'I' and resid 4 through 9 Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.646A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.648A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 4.093A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 295 removed outlier: 3.829A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS I 295 " --> pdb=" O TYR I 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 288 through 295' Processing helix chain 'I' and resid 318 through 329 removed outlier: 3.557A pdb=" N GLY I 329 " --> pdb=" O LEU I 325 " (cutoff:3.500A) 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: 3.704A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 410 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: 4.179A pdb=" N MET I 492 " --> pdb=" O MET I 488 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE I 493 " --> pdb=" O PRO I 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 488 through 493' Processing helix chain 'I' and resid 495 through 509 removed outlier: 3.818A 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 544 through 549 removed outlier: 4.058A pdb=" N ARG I 548 " --> pdb=" O GLY I 544 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP I 549 " --> pdb=" O PHE I 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 544 through 549' Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.529A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 614 removed outlier: 3.840A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.852A 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: 4.289A 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 675 through 687 removed outlier: 4.000A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 826 Processing helix chain 'I' and resid 858 through 863 removed outlier: 3.660A pdb=" N LEU I 862 " --> pdb=" O GLY I 858 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 983 Processing helix chain 'I' and resid 985 through 992 removed outlier: 3.573A pdb=" N LEU I 992 " --> pdb=" O LYS I 988 " (cutoff:3.500A) Processing helix chain 'I' and resid 993 through 997 removed outlier: 4.027A pdb=" N ARG I 996 " --> pdb=" O PRO I 993 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 4.127A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 3.808A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.754A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.518A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1177 removed outlier: 3.646A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1243 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1297 through 1311 Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.812A 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 77 through 81 Processing helix chain 'J' and resid 94 through 100 Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.656A 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 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 180 through 191 removed outlier: 3.664A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 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 341 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 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 485 through 489 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.757A 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: 3.855A 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: 3.566A pdb=" N VAL J 618 " --> pdb=" O LEU J 614 " (cutoff:3.500A) removed outlier: 4.096A 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: 4.096A 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: 4.115A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA J 779 " --> pdb=" O SER J 775 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.828A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 875 removed outlier: 3.688A pdb=" N ASN J 875 " --> pdb=" O LEU J 871 " (cutoff:3.500A) Processing helix chain 'J' and resid 884 through 888 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 928 No H-bonds generated for 'chain 'J' and resid 926 through 928' Processing helix chain 'J' and resid 1137 through 1146 Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.587A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.326A 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: 3.714A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN J1326 " --> pdb=" O ALA J1322 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 removed outlier: 3.648A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1360 through 1373 removed outlier: 3.768A pdb=" N ALA J1364 " --> pdb=" O GLY J1360 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 17 through 34 removed outlier: 3.661A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY K 34 " --> pdb=" O MET K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.748A 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 34 through 48 removed outlier: 4.360A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.631A 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 162 removed outlier: 3.788A pdb=" N ARG G 158 " --> pdb=" O PRO G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 234 removed outlier: 4.212A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 Processing helix chain 'H' and resid 77 through 88 Processing helix chain 'H' and resid 154 through 160 removed outlier: 3.616A pdb=" N ARG H 158 " --> pdb=" O PRO H 154 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N HIS H 160 " --> pdb=" O SER H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 228 removed outlier: 3.772A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 232 removed outlier: 3.565A pdb=" N VAL H 232 " --> pdb=" O GLU H 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 229 through 232' Processing sheet with id=AA1, first strand: chain 'P' and resid 27 through 29 Processing sheet with id=AA2, first strand: chain 'P' and resid 32 through 37 Processing sheet with id=AA3, first strand: chain 'P' and resid 149 through 153 removed outlier: 7.490A pdb=" N MET P 140 " --> pdb=" O THR P 131 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE P 129 " --> pdb=" O LEU P 142 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ASN P 144 " --> pdb=" O GLN P 127 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLN P 127 " --> pdb=" O ASN P 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.586A 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: 6.030A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ALA I 94 " --> pdb=" O GLY I 125 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLY I 125 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU I 96 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR I 123 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL I 98 " --> pdb=" O GLU I 121 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU I 121 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU I 100 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLU I 119 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU I 102 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE I 117 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE I 104 " --> pdb=" O LYS I 115 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 136 through 138 Processing sheet with id=AA7, first strand: chain 'I' and resid 148 through 151 Processing sheet with id=AA8, first strand: chain 'I' and resid 154 through 159 removed outlier: 4.872A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 226 through 231 removed outlier: 4.790A pdb=" N GLU I 226 " --> pdb=" O PHE I 337 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AB2, first strand: chain 'I' and resid 296 through 297 removed outlier: 4.090A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 301 through 303 removed outlier: 6.613A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 529 through 531 Processing sheet with id=AB5, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.681A pdb=" N LYS I 593 " --> pdb=" O GLU I 602 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AB7, first strand: chain 'I' and resid 716 through 717 removed outlier: 4.122A pdb=" N ALA I 784 " --> pdb=" O ALA I 716 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.123A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC1, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC2, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.524A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 9.697A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.724A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 849 through 850 removed outlier: 3.551A pdb=" N GLU I 849 " --> pdb=" O VAL I 887 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 882 through 884 removed outlier: 3.972A pdb=" N VAL I 884 " --> pdb=" O LEU I 918 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AC7, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AC8, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AC9, first strand: chain 'I' and resid 1335 through 1340 Processing sheet with id=AD1, first strand: chain 'J' and resid 103 through 112 removed outlier: 10.029A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.816A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 159 through 160 removed outlier: 6.682A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 253 through 254 removed outlier: 4.081A pdb=" N VAL J 253 " --> pdb=" O ALA J 261 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD5, first strand: chain 'J' and resid 705 through 709 removed outlier: 3.687A pdb=" N THR J 705 " --> pdb=" O GLN J 716 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AD7, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AD8, first strand: chain 'J' and resid 825 through 827 removed outlier: 3.911A pdb=" N GLU J 833 " --> pdb=" O VAL J 825 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLU J 827 " --> pdb=" O VAL J 831 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N VAL J 831 " --> pdb=" O GLU J 827 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 842 through 843 removed outlier: 4.096A pdb=" N ARG J 842 " --> pdb=" O LEU J 864 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.396A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.635A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 957 through 961 removed outlier: 4.265A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 1024 through 1028 removed outlier: 6.379A pdb=" N MET J1025 " --> pdb=" O ARG J1123 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG J1123 " --> pdb=" O MET J1025 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N VAL J1027 " --> pdb=" O LEU J1121 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 1098 through 1100 Processing sheet with id=AE6, first strand: chain 'J' and resid 1186 through 1191 removed outlier: 4.512A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.474A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 12 through 17 removed outlier: 5.001A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.571A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AF2, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.948A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AF4, first strand: chain 'H' and resid 15 through 20 removed outlier: 6.732A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU H 206 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 97 through 105 removed outlier: 7.938A pdb=" N SER H 141 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ILE H 61 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 108 through 111 removed outlier: 6.592A pdb=" N GLY H 108 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS H 132 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL H 110 " --> pdb=" O ILE H 130 " (cutoff:3.500A) 1143 hydrogen bonds defined for protein. 3212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 192 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 60 stacking parallelities Total time for adding SS restraints: 6.67 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9269 1.34 - 1.46: 4631 1.46 - 1.58: 14577 1.58 - 1.70: 172 1.70 - 1.82: 194 Bond restraints: 28843 Sorted by residual: bond pdb=" CB GLU J 925 " pdb=" CG GLU J 925 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.99e+00 bond pdb=" CB ASP I1126 " pdb=" CG ASP I1126 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.39e+00 bond pdb=" CB LYS J 599 " pdb=" CG LYS J 599 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.35e+00 bond pdb=" CB GLN K 75 " pdb=" CG GLN K 75 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.28e+00 bond pdb=" CB ASP J 751 " pdb=" CG ASP J 751 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.23e+00 ... (remaining 28838 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 39155 2.89 - 5.78: 174 5.78 - 8.68: 20 8.68 - 11.57: 5 11.57 - 14.46: 1 Bond angle restraints: 39355 Sorted by residual: angle pdb=" CB MET I 488 " pdb=" CG MET I 488 " pdb=" SD MET I 488 " ideal model delta sigma weight residual 112.70 127.16 -14.46 3.00e+00 1.11e-01 2.32e+01 angle pdb=" CG ARG I1034 " pdb=" CD ARG I1034 " pdb=" NE ARG I1034 " ideal model delta sigma weight residual 112.00 122.32 -10.32 2.20e+00 2.07e-01 2.20e+01 angle pdb=" C PHE H 8 " pdb=" CA PHE H 8 " pdb=" CB PHE H 8 " ideal model delta sigma weight residual 115.79 110.33 5.46 1.19e+00 7.06e-01 2.10e+01 angle pdb=" C PHE P 130 " pdb=" N THR P 131 " pdb=" CA THR P 131 " ideal model delta sigma weight residual 122.08 116.44 5.64 1.53e+00 4.27e-01 1.36e+01 angle pdb=" CA GLN K 75 " pdb=" CB GLN K 75 " pdb=" CG GLN K 75 " ideal model delta sigma weight residual 114.10 121.12 -7.02 2.00e+00 2.50e-01 1.23e+01 ... (remaining 39350 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.24: 16170 29.24 - 58.47: 1248 58.47 - 87.71: 122 87.71 - 116.95: 6 116.95 - 146.19: 3 Dihedral angle restraints: 17549 sinusoidal: 7856 harmonic: 9693 Sorted by residual: dihedral pdb=" CA ARG I 994 " pdb=" C ARG I 994 " pdb=" N ASP I 995 " pdb=" CA ASP I 995 " ideal model delta harmonic sigma weight residual -180.00 -160.59 -19.41 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA PRO I 993 " pdb=" C PRO I 993 " pdb=" N ARG I 994 " pdb=" CA ARG I 994 " ideal model delta harmonic sigma weight residual -180.00 -161.00 -19.00 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" C4' DC A 39 " pdb=" C3' DC A 39 " pdb=" O3' DC A 39 " pdb=" P DC A 40 " ideal model delta sinusoidal sigma weight residual 220.00 73.81 146.19 1 3.50e+01 8.16e-04 1.43e+01 ... (remaining 17546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3292 0.036 - 0.072: 801 0.072 - 0.109: 318 0.109 - 0.145: 79 0.145 - 0.181: 5 Chirality restraints: 4495 Sorted by residual: chirality pdb=" CB ILE P 117 " pdb=" CA ILE P 117 " pdb=" CG1 ILE P 117 " pdb=" CG2 ILE P 117 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" CA MET I 488 " pdb=" N MET I 488 " pdb=" C MET I 488 " pdb=" CB MET I 488 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CA ILE H 107 " pdb=" N ILE H 107 " pdb=" C ILE H 107 " pdb=" CB ILE H 107 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 ... (remaining 4492 not shown) Planarity restraints: 4843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP P 106 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO P 107 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO P 107 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO P 107 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 137 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.91e+00 pdb=" C ASN G 137 " 0.034 2.00e-02 2.50e+03 pdb=" O ASN G 137 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA G 138 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU J 925 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" CD GLU J 925 " -0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU J 925 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU J 925 " 0.012 2.00e-02 2.50e+03 ... (remaining 4840 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 274 2.60 - 3.18: 23617 3.18 - 3.75: 46241 3.75 - 4.33: 60553 4.33 - 4.90: 99606 Nonbonded interactions: 230291 Sorted by model distance: nonbonded pdb=" OP1 U R 17 " pdb="MG MG J1503 " model vdw 2.027 2.170 nonbonded pdb=" P U R 17 " pdb="MG MG J1503 " model vdw 2.031 2.530 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1503 " model vdw 2.072 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1503 " model vdw 2.087 2.170 nonbonded pdb=" OD2 ASP J 460 " pdb="MG MG J1503 " model vdw 2.091 2.170 ... (remaining 230286 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 4 through 218 or resid 220 through 233)) selection = (chain 'H' and (resid 4 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: 3.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 34.930 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 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 : 0.002 0.043 28851 Z= 0.103 Angle : 0.531 14.462 39367 Z= 0.272 Chirality : 0.039 0.181 4495 Planarity : 0.004 0.054 4843 Dihedral : 18.805 146.185 11311 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.54 % Favored : 97.43 % Rotamer: Outliers : 0.10 % Allowed : 24.54 % Favored : 75.36 % 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 aren not related in a simple way. whole: 1.00 (0.15), residues: 3354 helix: 2.08 (0.16), residues: 1161 sheet: 0.24 (0.23), residues: 518 loop : -0.16 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 473 TYR 0.006 0.001 TYR J 140 PHE 0.012 0.001 PHE G 231 TRP 0.028 0.001 TRP I 183 HIS 0.007 0.000 HIS I1023 Details of bonding type rmsd covalent geometry : bond 0.00226 (28843) covalent geometry : angle 0.52729 (39355) hydrogen bonds : bond 0.13107 ( 1235) hydrogen bonds : angle 5.27760 ( 3404) metal coordination : bond 0.00406 ( 8) metal coordination : angle 3.66457 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 476 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 127 GLN cc_start: 0.7905 (pm20) cc_final: 0.7643 (pm20) REVERT: I 515 MET cc_start: 0.7628 (ttm) cc_final: 0.7058 (ttp) REVERT: I 516 ASP cc_start: 0.7910 (p0) cc_final: 0.7415 (p0) REVERT: I 1188 ASP cc_start: 0.7901 (t0) cc_final: 0.7618 (t0) REVERT: I 1273 MET cc_start: 0.8710 (mtt) cc_final: 0.8352 (mtt) REVERT: J 329 ASP cc_start: 0.8162 (m-30) cc_final: 0.7728 (m-30) REVERT: J 485 MET cc_start: 0.8770 (tpp) cc_final: 0.8322 (tpt) REVERT: J 724 MET cc_start: 0.8329 (ttm) cc_final: 0.8039 (ttp) REVERT: J 878 ASP cc_start: 0.7725 (p0) cc_final: 0.7241 (t70) REVERT: K 61 ASN cc_start: 0.9346 (t0) cc_final: 0.9131 (t0) REVERT: K 79 GLU cc_start: 0.8548 (pt0) cc_final: 0.8287 (pt0) REVERT: H 65 LEU cc_start: 0.9409 (tp) cc_final: 0.9145 (tt) REVERT: H 66 HIS cc_start: 0.8096 (m170) cc_final: 0.7669 (m170) REVERT: H 182 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7611 (tpt-90) outliers start: 1 outliers final: 0 residues processed: 476 average time/residue: 0.2150 time to fit residues: 153.0593 Evaluate side-chains 247 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 53 ASN I 193 ASN I 273 HIS J 206 ASN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 341 ASN J 488 ASN J 792 ASN J 921 GLN J1279 GLN K 43 ASN K 73 GLN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.071864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.049889 restraints weight = 109816.156| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 3.34 r_work: 0.2711 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 28851 Z= 0.258 Angle : 0.647 11.360 39367 Z= 0.338 Chirality : 0.044 0.237 4495 Planarity : 0.005 0.067 4843 Dihedral : 15.760 149.145 4706 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.01 % Favored : 96.96 % Rotamer: Outliers : 3.27 % Allowed : 22.45 % Favored : 74.28 % 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 aren not related in a simple way. whole: 0.85 (0.15), residues: 3354 helix: 1.93 (0.15), residues: 1161 sheet: 0.24 (0.22), residues: 523 loop : -0.27 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 378 TYR 0.017 0.002 TYR J 631 PHE 0.021 0.002 PHE I 389 TRP 0.042 0.002 TRP I 183 HIS 0.006 0.001 HIS P 65 Details of bonding type rmsd covalent geometry : bond 0.00583 (28843) covalent geometry : angle 0.63774 (39355) hydrogen bonds : bond 0.04371 ( 1235) hydrogen bonds : angle 4.41185 ( 3404) metal coordination : bond 0.01320 ( 8) metal coordination : angle 6.36859 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 246 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 15 GLN cc_start: 0.9198 (tp40) cc_final: 0.8833 (tm-30) REVERT: P 37 LYS cc_start: 0.8053 (mppt) cc_final: 0.7706 (mptt) REVERT: P 127 GLN cc_start: 0.7997 (pm20) cc_final: 0.7645 (pm20) REVERT: I 142 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8246 (mt-10) REVERT: I 503 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8819 (ptpp) REVERT: I 516 ASP cc_start: 0.8608 (p0) cc_final: 0.8314 (p0) REVERT: I 1188 ASP cc_start: 0.8857 (t0) cc_final: 0.8335 (t0) REVERT: I 1273 MET cc_start: 0.9120 (mtt) cc_final: 0.8916 (mtt) REVERT: J 129 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8309 (m-30) REVERT: J 301 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8690 (mt-10) REVERT: J 503 SER cc_start: 0.8819 (m) cc_final: 0.8556 (t) REVERT: J 811 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8677 (mt-10) REVERT: K 8 ASP cc_start: 0.8339 (p0) cc_final: 0.7928 (p0) REVERT: K 43 ASN cc_start: 0.8937 (t0) cc_final: 0.8427 (t0) REVERT: H 10 LYS cc_start: 0.8652 (mmmm) cc_final: 0.8371 (mmtm) REVERT: H 25 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8492 (tttm) REVERT: H 65 LEU cc_start: 0.9526 (tp) cc_final: 0.9216 (tt) REVERT: H 66 HIS cc_start: 0.8725 (m170) cc_final: 0.8260 (m170) REVERT: H 80 GLU cc_start: 0.8775 (tp30) cc_final: 0.8544 (tp30) REVERT: H 165 GLU cc_start: 0.4658 (OUTLIER) cc_final: 0.3827 (tm-30) outliers start: 91 outliers final: 39 residues processed: 318 average time/residue: 0.1703 time to fit residues: 84.7847 Evaluate side-chains 258 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 215 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 421 SER Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1034 ARG Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 129 ASP Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 67 ARG Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 192 VAL 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 319 optimal weight: 10.0000 chunk 271 optimal weight: 0.5980 chunk 130 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 268 optimal weight: 0.9990 chunk 257 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 70 ASN I 165 HIS ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.070776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.049243 restraints weight = 99702.957| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.11 r_work: 0.2691 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 28851 Z= 0.220 Angle : 0.586 11.033 39367 Z= 0.305 Chirality : 0.042 0.216 4495 Planarity : 0.004 0.043 4843 Dihedral : 15.783 147.188 4706 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.04 % Favored : 96.93 % Rotamer: Outliers : 2.95 % Allowed : 22.25 % Favored : 74.80 % 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 aren not related in a simple way. whole: 0.78 (0.15), residues: 3354 helix: 1.96 (0.15), residues: 1163 sheet: 0.24 (0.23), residues: 498 loop : -0.39 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 247 TYR 0.013 0.001 TYR J 631 PHE 0.018 0.002 PHE I 385 TRP 0.038 0.002 TRP I 183 HIS 0.005 0.001 HIS P 77 Details of bonding type rmsd covalent geometry : bond 0.00507 (28843) covalent geometry : angle 0.57451 (39355) hydrogen bonds : bond 0.04155 ( 1235) hydrogen bonds : angle 4.30537 ( 3404) metal coordination : bond 0.01377 ( 8) metal coordination : angle 6.63589 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 218 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 15 GLN cc_start: 0.9147 (tp40) cc_final: 0.8835 (tm-30) REVERT: P 127 GLN cc_start: 0.7962 (pm20) cc_final: 0.7289 (pp30) REVERT: P 138 ARG cc_start: 0.9347 (mtp-110) cc_final: 0.8961 (ttp-110) REVERT: I 503 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8801 (ptpp) REVERT: I 1170 MET cc_start: 0.9400 (mmm) cc_final: 0.9200 (mmm) REVERT: I 1188 ASP cc_start: 0.8862 (t0) cc_final: 0.8280 (t0) REVERT: J 443 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8147 (mm-30) REVERT: J 503 SER cc_start: 0.8843 (m) cc_final: 0.8583 (t) REVERT: J 811 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8675 (mt-10) REVERT: K 43 ASN cc_start: 0.8846 (t0) cc_final: 0.8271 (t0) REVERT: K 73 GLN cc_start: 0.8483 (mm-40) cc_final: 0.8024 (mm-40) REVERT: H 10 LYS cc_start: 0.8770 (mmmm) cc_final: 0.8515 (mmtm) REVERT: H 25 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8468 (tttm) REVERT: H 65 LEU cc_start: 0.9515 (tp) cc_final: 0.9244 (tp) REVERT: H 165 GLU cc_start: 0.4743 (OUTLIER) cc_final: 0.4530 (tp30) outliers start: 83 outliers final: 46 residues processed: 290 average time/residue: 0.1835 time to fit residues: 83.7119 Evaluate side-chains 254 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 205 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1034 ARG Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 894 VAL 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 1144 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 192 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 196 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 23 optimal weight: 0.0050 chunk 136 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 193 ASN J 266 ASN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.071885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.050311 restraints weight = 104791.451| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.22 r_work: 0.2717 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28851 Z= 0.125 Angle : 0.542 12.812 39367 Z= 0.280 Chirality : 0.041 0.184 4495 Planarity : 0.004 0.041 4843 Dihedral : 15.728 148.035 4706 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.23 % Rotamer: Outliers : 2.88 % Allowed : 22.45 % Favored : 74.66 % 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 aren not related in a simple way. whole: 0.82 (0.15), residues: 3354 helix: 2.02 (0.15), residues: 1163 sheet: 0.33 (0.23), residues: 476 loop : -0.41 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 160 TYR 0.013 0.001 TYR J 140 PHE 0.013 0.001 PHE P 130 TRP 0.031 0.001 TRP I 183 HIS 0.004 0.000 HIS P 77 Details of bonding type rmsd covalent geometry : bond 0.00284 (28843) covalent geometry : angle 0.53234 (39355) hydrogen bonds : bond 0.03546 ( 1235) hydrogen bonds : angle 4.11401 ( 3404) metal coordination : bond 0.00701 ( 8) metal coordination : angle 5.99974 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 218 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 2 GLN cc_start: 0.8732 (mt0) cc_final: 0.8449 (tt0) REVERT: P 15 GLN cc_start: 0.9143 (tp40) cc_final: 0.8844 (tm-30) REVERT: P 127 GLN cc_start: 0.7956 (pm20) cc_final: 0.7296 (pp30) REVERT: P 134 ASP cc_start: 0.9065 (t0) cc_final: 0.8293 (t0) REVERT: P 138 ARG cc_start: 0.9356 (mtp-110) cc_final: 0.8854 (ttp-110) REVERT: P 140 MET cc_start: 0.8779 (tmm) cc_final: 0.8084 (tmm) REVERT: P 151 LYS cc_start: 0.8670 (tptp) cc_final: 0.8098 (tppt) REVERT: P 161 LYS cc_start: 0.7406 (mppt) cc_final: 0.6903 (mttp) REVERT: I 465 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7773 (tpt170) REVERT: I 503 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8802 (ptpp) REVERT: I 1188 ASP cc_start: 0.8824 (t0) cc_final: 0.8215 (t0) REVERT: J 443 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8210 (mm-30) REVERT: J 811 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8680 (mt-10) REVERT: J 1189 MET cc_start: 0.8684 (mmp) cc_final: 0.8199 (tpp) REVERT: K 43 ASN cc_start: 0.8820 (t0) cc_final: 0.8232 (t0) REVERT: K 73 GLN cc_start: 0.8598 (mm-40) cc_final: 0.8164 (mt0) REVERT: K 75 GLN cc_start: 0.9252 (tp40) cc_final: 0.8928 (tp40) REVERT: H 25 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8474 (tttm) REVERT: H 65 LEU cc_start: 0.9400 (tp) cc_final: 0.9055 (tp) REVERT: H 66 HIS cc_start: 0.8707 (m-70) cc_final: 0.8424 (m90) REVERT: H 76 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7870 (mp0) REVERT: H 93 GLN cc_start: 0.8151 (pm20) cc_final: 0.7811 (pm20) REVERT: H 95 LYS cc_start: 0.8710 (pttm) cc_final: 0.8387 (pttp) REVERT: H 165 GLU cc_start: 0.4673 (OUTLIER) cc_final: 0.4397 (tp30) outliers start: 81 outliers final: 43 residues processed: 290 average time/residue: 0.1669 time to fit residues: 76.0123 Evaluate side-chains 253 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 205 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 421 SER Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1034 ARG Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 192 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 296 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 193 ASN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.071503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.049699 restraints weight = 116890.850| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 3.40 r_work: 0.2695 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28851 Z= 0.139 Angle : 0.536 11.418 39367 Z= 0.277 Chirality : 0.040 0.154 4495 Planarity : 0.004 0.041 4843 Dihedral : 15.718 147.629 4706 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.89 % Favored : 97.08 % Rotamer: Outliers : 2.71 % Allowed : 22.14 % Favored : 75.15 % 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 aren not related in a simple way. whole: 0.84 (0.15), residues: 3354 helix: 2.05 (0.15), residues: 1163 sheet: 0.33 (0.23), residues: 476 loop : -0.41 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 69 TYR 0.011 0.001 TYR J 140 PHE 0.014 0.001 PHE I 385 TRP 0.027 0.001 TRP I 183 HIS 0.004 0.001 HIS P 77 Details of bonding type rmsd covalent geometry : bond 0.00318 (28843) covalent geometry : angle 0.52674 (39355) hydrogen bonds : bond 0.03531 ( 1235) hydrogen bonds : angle 4.07122 ( 3404) metal coordination : bond 0.00827 ( 8) metal coordination : angle 5.84162 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 215 time to evaluate : 0.983 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 15 GLN cc_start: 0.9144 (tp40) cc_final: 0.8849 (tm-30) REVERT: P 111 TYR cc_start: 0.8870 (m-10) cc_final: 0.8537 (m-10) REVERT: P 127 GLN cc_start: 0.7990 (pm20) cc_final: 0.7324 (pp30) REVERT: P 138 ARG cc_start: 0.9373 (mtp-110) cc_final: 0.9062 (tmm-80) REVERT: P 140 MET cc_start: 0.8929 (tmm) cc_final: 0.8157 (tmm) REVERT: P 151 LYS cc_start: 0.8737 (tptp) cc_final: 0.8110 (tppt) REVERT: I 465 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7788 (tpt170) REVERT: I 503 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8845 (ptpp) REVERT: I 805 MET cc_start: 0.9245 (ptm) cc_final: 0.9033 (ptp) REVERT: I 1188 ASP cc_start: 0.8838 (t0) cc_final: 0.8214 (t0) REVERT: J 443 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8261 (mm-30) REVERT: J 698 MET cc_start: 0.9108 (mmm) cc_final: 0.8852 (tpp) REVERT: J 811 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8687 (mt-10) REVERT: K 43 ASN cc_start: 0.8859 (t0) cc_final: 0.8266 (t0) REVERT: K 73 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8135 (mt0) REVERT: H 25 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8501 (tttm) REVERT: H 65 LEU cc_start: 0.9402 (tp) cc_final: 0.9038 (tp) REVERT: H 66 HIS cc_start: 0.8756 (m-70) cc_final: 0.8456 (m90) REVERT: H 76 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7864 (mp0) REVERT: H 93 GLN cc_start: 0.8184 (pm20) cc_final: 0.7878 (pm20) REVERT: H 95 LYS cc_start: 0.8671 (pttm) cc_final: 0.8438 (pttp) REVERT: H 125 LYS cc_start: 0.8867 (mtpp) cc_final: 0.8518 (mmmm) outliers start: 76 outliers final: 52 residues processed: 280 average time/residue: 0.1827 time to fit residues: 80.2624 Evaluate side-chains 257 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 201 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 183 TRP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 421 SER Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 903 LEU 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 1144 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 192 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 174 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 193 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 chunk 306 optimal weight: 4.9990 chunk 64 optimal weight: 0.3980 chunk 238 optimal weight: 0.6980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 762 ASN H 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.071048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.049262 restraints weight = 116425.232| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.38 r_work: 0.2684 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28851 Z= 0.157 Angle : 0.541 10.423 39367 Z= 0.280 Chirality : 0.041 0.150 4495 Planarity : 0.004 0.039 4843 Dihedral : 15.722 147.677 4706 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.98 % Favored : 96.99 % Rotamer: Outliers : 2.82 % Allowed : 22.38 % Favored : 74.80 % 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 aren not related in a simple way. whole: 0.85 (0.15), residues: 3354 helix: 2.11 (0.15), residues: 1157 sheet: 0.31 (0.23), residues: 476 loop : -0.43 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 69 TYR 0.011 0.001 TYR J1186 PHE 0.015 0.001 PHE I 385 TRP 0.029 0.001 TRP I 183 HIS 0.004 0.001 HIS P 77 Details of bonding type rmsd covalent geometry : bond 0.00363 (28843) covalent geometry : angle 0.53121 (39355) hydrogen bonds : bond 0.03569 ( 1235) hydrogen bonds : angle 4.07300 ( 3404) metal coordination : bond 0.00959 ( 8) metal coordination : angle 5.87558 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 210 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 15 GLN cc_start: 0.9131 (tp40) cc_final: 0.8849 (tm-30) REVERT: P 111 TYR cc_start: 0.8907 (m-10) cc_final: 0.8595 (m-10) REVERT: P 127 GLN cc_start: 0.7980 (pm20) cc_final: 0.7325 (pp30) REVERT: P 140 MET cc_start: 0.8975 (tmm) cc_final: 0.8345 (tmm) REVERT: P 151 LYS cc_start: 0.8717 (tptp) cc_final: 0.8111 (tppt) REVERT: I 465 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7789 (tpt170) REVERT: I 503 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8827 (ptpp) REVERT: I 805 MET cc_start: 0.9266 (ptm) cc_final: 0.9057 (ptp) REVERT: I 1188 ASP cc_start: 0.8852 (t0) cc_final: 0.8219 (t0) REVERT: J 811 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8685 (mt-10) REVERT: J 1189 MET cc_start: 0.8696 (mmp) cc_final: 0.8210 (tpt) REVERT: K 43 ASN cc_start: 0.8828 (t0) cc_final: 0.8243 (t0) REVERT: K 73 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8116 (mt0) REVERT: K 75 GLN cc_start: 0.9230 (tp40) cc_final: 0.8921 (tm-30) REVERT: H 65 LEU cc_start: 0.9391 (tp) cc_final: 0.8972 (tp) REVERT: H 66 HIS cc_start: 0.8748 (m-70) cc_final: 0.8393 (m90) REVERT: H 76 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: H 93 GLN cc_start: 0.8144 (pm20) cc_final: 0.7829 (pm20) REVERT: H 95 LYS cc_start: 0.8667 (pttm) cc_final: 0.8430 (pttp) outliers start: 79 outliers final: 60 residues processed: 278 average time/residue: 0.1719 time to fit residues: 75.9675 Evaluate side-chains 263 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 200 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 183 TRP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 421 SER Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 626 GLU Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 434 ILE 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 814 CYS Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 903 LEU 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 1144 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 67 ARG Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 192 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.2951 > 50: distance: 10 - 121: 35.456 distance: 13 - 118: 31.614 distance: 23 - 108: 26.309 distance: 26 - 105: 32.718 distance: 36 - 96: 33.428 distance: 39 - 93: 32.420 distance: 48 - 69: 16.504 distance: 53 - 58: 3.434 distance: 54 - 73: 30.593 distance: 58 - 59: 11.317 distance: 59 - 60: 10.452 distance: 59 - 62: 17.821 distance: 60 - 61: 13.354 distance: 60 - 69: 29.276 distance: 62 - 63: 27.554 distance: 63 - 64: 23.805 distance: 64 - 65: 13.425 distance: 65 - 66: 16.144 distance: 66 - 67: 6.249 distance: 66 - 68: 12.622 distance: 69 - 70: 7.328 distance: 70 - 71: 19.276 distance: 71 - 72: 39.905 distance: 71 - 73: 25.033 distance: 73 - 74: 27.952 distance: 74 - 75: 41.417 distance: 74 - 77: 14.872 distance: 75 - 76: 44.821 distance: 75 - 82: 32.574 distance: 77 - 78: 34.059 distance: 78 - 79: 35.607 distance: 79 - 80: 20.920 distance: 80 - 81: 52.877 distance: 82 - 83: 33.254 distance: 83 - 84: 18.632 distance: 83 - 86: 12.112 distance: 84 - 85: 21.965 distance: 84 - 93: 23.629 distance: 86 - 87: 11.324 distance: 87 - 88: 9.676 distance: 88 - 89: 4.383 distance: 89 - 90: 45.510 distance: 90 - 91: 8.550 distance: 90 - 92: 41.885 distance: 94 - 95: 21.839 distance: 94 - 97: 10.301 distance: 95 - 96: 44.184 distance: 95 - 100: 26.438 distance: 97 - 98: 11.668 distance: 100 - 101: 47.390 distance: 101 - 102: 59.032 distance: 101 - 104: 39.426 distance: 102 - 103: 33.989 distance: 102 - 105: 18.260 distance: 105 - 106: 40.918 distance: 106 - 107: 59.792 distance: 106 - 109: 41.057 distance: 107 - 108: 31.496 distance: 107 - 112: 20.462 distance: 109 - 110: 38.620 distance: 112 - 113: 42.102 distance: 113 - 114: 12.117 distance: 113 - 116: 64.660 distance: 114 - 115: 18.201 distance: 114 - 118: 30.406 distance: 116 - 117: 30.933 distance: 118 - 119: 39.939 distance: 119 - 120: 40.251 distance: 119 - 122: 11.797 distance: 120 - 121: 40.224 distance: 120 - 127: 36.769 distance: 122 - 123: 31.196 distance: 123 - 124: 13.965 distance: 124 - 125: 36.324 distance: 127 - 128: 37.351 distance: 129 - 130: 48.447 distance: 129 - 134: 35.057 distance: 132 - 133: 40.307