Starting phenix.real_space_refine on Mon Jul 6 06:13:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ymv_73123/07_2026/9ymv_73123.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ymv_73123/07_2026/9ymv_73123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ymv_73123/07_2026/9ymv_73123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ymv_73123/07_2026/9ymv_73123.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ymv_73123/07_2026/9ymv_73123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ymv_73123/07_2026/9ymv_73123.map" } resolution = 2.6 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= 0.000 sd= 0.020 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 123 5.49 5 Mg 1 5.21 5 S 128 5.16 5 C 19217 2.51 5 N 5534 2.21 5 O 7418 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32423 Number of models: 1 Model: "" Number of chains: 20 Chain: "I" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "K" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 610 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "P" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1259 Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} Chain: "R" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Classifications: {'RNA': 2} Modifications used: {'rna3p_pyr': 2} Link IDs: {'rna3p': 1} Chain: "G" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 211} Chain breaks: 1 Chain: "H" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1710 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain breaks: 1 Chain: "J" Number of atoms: 10386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10386 Classifications: {'peptide': 1336} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1280} Chain breaks: 2 Chain: "L" Number of atoms: 3814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3814 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 15, 'TRANS': 452} Chain breaks: 3 Chain: "Q" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1116 Classifications: {'DNA': 55} Link IDs: {'rna3p': 54} Chain breaks: 1 Chain: "R" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 12 Unusual residues: {' MG': 1, ' ZN': 2, 'POP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 397 Classifications: {'water': 397} Link IDs: {None: 396} Chain: "K" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "P" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "G" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Chain: "H" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "J" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 404 Classifications: {'water': 404} Link IDs: {None: 403} Chain: "L" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 119 Classifications: {'water': 119} Link IDs: {None: 118} Chain: "Q" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16344 SG CYS J 70 51.243 53.389 118.007 1.00 57.61 S ATOM 16358 SG CYS J 72 53.373 52.398 120.913 1.00 74.11 S ATOM 16466 SG CYS J 85 49.759 52.871 121.419 1.00 67.66 S ATOM 16490 SG CYS J 88 51.955 55.825 120.817 1.00 67.12 S ATOM 22178 SG CYS J 814 23.624 108.902 87.927 1.00 53.64 S ATOM 22743 SG CYS J 888 26.908 107.545 89.073 1.00 37.02 S ATOM 22794 SG CYS J 895 25.362 106.353 85.913 1.00 34.59 S ATOM 22815 SG CYS J 898 26.737 109.807 86.063 1.00 48.34 S Time building chain proxies: 7.06, per 1000 atoms: 0.22 Number of scatterers: 32423 At special positions: 0 Unit cell: (154.8, 184.04, 194.36, 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 128 16.00 P 123 15.00 Mg 1 11.99 O 7418 8.00 N 5534 7.00 C 19217 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 70 " pdb=" ZN J1504 " pdb="ZN ZN J1504 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1504 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1504 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1504 " - pdb=" SG CYS J 898 " Number of angles added : 12 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6798 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 48 sheets defined 44.8% alpha, 16.3% beta 48 base pairs and 92 stacking pairs defined. Time for finding SS restraints: 4.88 Creating SS restraints... Processing helix chain 'I' and resid 4 through 9 removed outlier: 3.929A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 4.033A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.606A 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: 3.916A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 Processing helix chain 'I' and resid 270 through 280 Processing helix chain 'I' and resid 288 through 293 removed outlier: 3.692A pdb=" N ILE I 292 " --> pdb=" O VAL I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 327 removed outlier: 3.867A pdb=" N GLN I 327 " --> pdb=" O ALA I 323 " (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: 3.558A pdb=" N GLU I 382 " --> pdb=" O ARG I 378 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 397 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 482 removed outlier: 3.611A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 493 removed outlier: 3.610A pdb=" N MET I 492 " --> pdb=" O MET I 488 " (cutoff:3.500A) removed outlier: 3.615A 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: 3.628A pdb=" N ALA I 501 " --> pdb=" O PRO I 497 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL I 502 " --> pdb=" O ILE I 498 " (cutoff:3.500A) removed outlier: 3.573A 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 539 through 543 removed outlier: 3.918A pdb=" N ALA I 543 " --> pdb=" O ARG I 540 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.542A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 612 removed outlier: 3.982A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 612' Processing helix chain 'I' and resid 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.595A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 686 Processing helix chain 'I' and resid 687 through 689 No H-bonds generated for 'chain 'I' and resid 687 through 689' Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 896 through 907 Processing helix chain 'I' and resid 942 through 981 removed outlier: 3.961A pdb=" N ALA I 981 " --> pdb=" O ALA I 977 " (cutoff:3.500A) Processing helix chain 'I' and resid 988 through 992 Processing helix chain 'I' and resid 993 through 1000 removed outlier: 3.948A pdb=" N LEU I1000 " --> pdb=" O TRP I 997 " (cutoff:3.500A) Processing helix chain 'I' and resid 1010 through 1037 removed outlier: 3.716A pdb=" N GLU I1026 " --> pdb=" O LYS I1022 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 removed outlier: 3.523A pdb=" N MET I1085 " --> pdb=" O ILE I1082 " (cutoff:3.500A) Processing helix chain 'I' and resid 1099 through 1103 Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.711A pdb=" N GLY I1125 " --> pdb=" O ALA I1121 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.680A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.618A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1176 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1282 Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1297 through 1311 removed outlier: 3.569A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.825A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 15 through 32 removed outlier: 3.652A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN K 29 " --> pdb=" O ARG K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 78 Processing helix chain 'G' and resid 34 through 48 removed outlier: 3.739A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.634A 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 158 Processing helix chain 'G' and resid 212 through 228 Processing helix chain 'G' and resid 228 through 233 removed outlier: 3.672A pdb=" N ASP G 233 " --> pdb=" O GLU G 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.532A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.665A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 115 removed outlier: 3.638A pdb=" N ASP H 114 " --> pdb=" O THR H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 227 Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.711A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 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 192 removed outlier: 3.726A pdb=" N ALA J 184 " --> pdb=" O MET J 180 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET J 192 " --> pdb=" O LEU J 188 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 206 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 264 through 286 removed outlier: 3.712A pdb=" N LEU J 268 " --> pdb=" O ASP J 264 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 336 through 342 Processing helix chain 'J' and resid 370 through 377 removed outlier: 3.768A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) 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 removed outlier: 4.078A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 581 through 583 No H-bonds generated for 'chain 'J' and resid 581 through 583' Processing helix chain 'J' and resid 588 through 592 Processing helix chain 'J' and resid 597 through 613 Processing helix chain 'J' and resid 613 through 636 removed outlier: 3.726A pdb=" N THR J 617 " --> pdb=" O GLY J 613 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP J 622 " --> pdb=" O VAL J 618 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 671 Processing helix chain 'J' and resid 674 through 702 Processing helix chain 'J' and resid 720 through 729 removed outlier: 3.517A pdb=" N GLY J 729 " --> pdb=" O MET J 725 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 805 removed outlier: 3.974A pdb=" N LYS J 781 " --> pdb=" O HIS J 777 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY J 782 " --> pdb=" O GLY J 778 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 840 Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 884 through 888 removed outlier: 3.547A pdb=" N CYS J 888 " --> pdb=" O VAL J 885 " (cutoff:3.500A) 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 929 Processing helix chain 'J' and resid 1068 through 1074 removed outlier: 3.665A pdb=" N LEU J1074 " --> pdb=" O GLY J1070 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1146 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1243 removed outlier: 3.658A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU J1243 " --> pdb=" O ASP J1239 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.329A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1326 Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1353 removed outlier: 3.725A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1359 through 1361 No H-bonds generated for 'chain 'J' and resid 1359 through 1361' Processing helix chain 'J' and resid 1362 through 1374 Processing helix chain 'L' and resid 96 through 106 Processing helix chain 'L' and resid 112 through 136 Processing helix chain 'L' and resid 137 through 153 Processing helix chain 'L' and resid 157 through 162 Processing helix chain 'L' and resid 215 through 234 Processing helix chain 'L' and resid 245 through 259 Processing helix chain 'L' and resid 262 through 296 removed outlier: 3.571A pdb=" N CYS L 291 " --> pdb=" O ILE L 287 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLN L 294 " --> pdb=" O LEU L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 307 Processing helix chain 'L' and resid 312 through 319 removed outlier: 4.806A pdb=" N PHE L 316 " --> pdb=" O SER L 312 " (cutoff:3.500A) Processing helix chain 'L' and resid 320 through 322 No H-bonds generated for 'chain 'L' and resid 320 through 322' Processing helix chain 'L' and resid 324 through 330 Processing helix chain 'L' and resid 333 through 352 Processing helix chain 'L' and resid 354 through 382 removed outlier: 3.706A pdb=" N ASP L 360 " --> pdb=" O GLU L 356 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG L 363 " --> pdb=" O LYS L 359 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA L 382 " --> pdb=" O GLU L 378 " (cutoff:3.500A) Processing helix chain 'L' and resid 383 through 393 removed outlier: 3.667A pdb=" N VAL L 387 " --> pdb=" O ASN L 383 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 419 removed outlier: 3.561A pdb=" N ILE L 410 " --> pdb=" O GLN L 406 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY L 411 " --> pdb=" O GLU L 407 " (cutoff:3.500A) Processing helix chain 'L' and resid 420 through 424 removed outlier: 3.695A pdb=" N ARG L 423 " --> pdb=" O GLU L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 426 through 447 removed outlier: 3.877A pdb=" N TYR L 430 " --> pdb=" O LYS L 426 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 475 removed outlier: 3.726A pdb=" N GLN L 472 " --> pdb=" O ARG L 468 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU L 473 " --> pdb=" O GLN L 469 " (cutoff:3.500A) Processing helix chain 'L' and resid 479 through 488 removed outlier: 3.590A pdb=" N ALA L 484 " --> pdb=" O PRO L 480 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N GLU L 485 " --> pdb=" O GLU L 481 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG L 486 " --> pdb=" O GLU L 482 " (cutoff:3.500A) Processing helix chain 'L' and resid 490 through 499 Processing helix chain 'L' and resid 518 through 523 removed outlier: 3.778A pdb=" N ILE L 523 " --> pdb=" O GLY L 520 " (cutoff:3.500A) Processing helix chain 'L' and resid 530 through 549 Processing helix chain 'L' and resid 552 through 564 removed outlier: 3.579A pdb=" N LEU L 559 " --> pdb=" O GLU L 555 " (cutoff:3.500A) Processing helix chain 'L' and resid 572 through 581 Processing helix chain 'L' and resid 583 through 600 removed outlier: 3.952A pdb=" N HIS L 600 " --> pdb=" O ARG L 596 " (cutoff:3.500A) Processing helix chain 'L' and resid 606 through 611 removed outlier: 3.693A pdb=" N LEU L 611 " --> pdb=" O ARG L 608 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.521A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 59 through 60 removed outlier: 5.963A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 136 through 138 Processing sheet with id=AA4, first strand: chain 'I' and resid 451 through 454 removed outlier: 3.587A pdb=" N SER I 147 " --> pdb=" O ARG I 529 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 154 through 159 removed outlier: 5.310A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 285 through 287 removed outlier: 4.186A pdb=" N LEU I 237 " --> pdb=" O VAL I 287 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 255 through 257 removed outlier: 7.128A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 296 through 297 removed outlier: 4.012A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 301 through 303 removed outlier: 6.801A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU I 308 " --> pdb=" O ASP I 303 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 580 through 581 removed outlier: 7.207A pdb=" N LEU I 587 " --> pdb=" O LEU I 606 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU I 606 " --> pdb=" O LEU I 587 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR I 589 " --> pdb=" O HIS I 604 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N HIS I 604 " --> pdb=" O THR I 589 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TYR I 591 " --> pdb=" O GLU I 602 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLU I 602 " --> pdb=" O TYR I 591 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LYS I 593 " --> pdb=" O THR I 600 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AB3, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.448A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 748 through 752 removed outlier: 3.752A pdb=" N ARG I 731 " --> pdb=" O ASP I 728 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AB6, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AB7, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.104A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 830 through 841 removed outlier: 6.434A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.687A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 887 through 889 Processing sheet with id=AC2, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AC3, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.837A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 1335 through 1340 Processing sheet with id=AC5, first strand: chain 'G' and resid 12 through 18 removed outlier: 5.027A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 97 through 105 removed outlier: 7.503A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AC8, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.527A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL G 110 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AD1, first strand: chain 'H' and resid 13 through 18 removed outlier: 6.411A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU H 198 " --> pdb=" O ALA H 190 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 97 through 105 removed outlier: 6.616A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AD4, first strand: chain 'H' and resid 108 through 110 removed outlier: 3.614A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AD6, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.590A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 10.103A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.524A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 159 through 160 removed outlier: 6.735A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 252 through 254 removed outlier: 6.547A pdb=" N PHE J 260 " --> pdb=" O ILE L 505 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AE1, first strand: chain 'J' and resid 703 through 707 Processing sheet with id=AE2, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE3, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE4, first strand: chain 'J' and resid 825 through 826 removed outlier: 6.427A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.676A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 949 through 952 removed outlier: 4.312A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL J 952 " --> pdb=" O THR J1016 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N THR J1016 " --> pdb=" O VAL J 952 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.994A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 1025 through 1028 removed outlier: 5.264A pdb=" N MET J1025 " --> pdb=" O ARG J1123 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG J1123 " --> pdb=" O MET J1025 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL J1027 " --> pdb=" O LEU J1121 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 1034 through 1038 removed outlier: 3.539A pdb=" N ARG J1036 " --> pdb=" O LYS J1079 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR J1038 " --> pdb=" O ALA J1077 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA J1077 " --> pdb=" O THR J1038 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1046 through 1051 removed outlier: 3.818A pdb=" N VAL J1060 " --> pdb=" O THR J1047 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU J1056 " --> pdb=" O ASP J1051 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 1186 through 1191 Processing sheet with id=AF3, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.995A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1339 hydrogen bonds defined for protein. 3759 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 118 hydrogen bonds 236 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 92 stacking parallelities Total time for adding SS restraints: 12.52 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 9221 1.33 - 1.45: 4865 1.45 - 1.57: 17410 1.57 - 1.69: 239 1.69 - 1.81: 225 Bond restraints: 31960 Sorted by residual: bond pdb=" C1' DC P 65 " pdb=" N1 DC P 65 " ideal model delta sigma weight residual 1.468 1.524 -0.056 1.40e-02 5.10e+03 1.63e+01 bond pdb=" C3' DA P 45 " pdb=" C2' DA P 45 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DT Q 69 " pdb=" C2' DT Q 69 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DC Q 46 " pdb=" C2' DC Q 46 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DG P 52 " pdb=" C2' DG P 52 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 31955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 43621 3.69 - 7.38: 28 7.38 - 11.07: 3 11.07 - 14.76: 0 14.76 - 18.45: 1 Bond angle restraints: 43653 Sorted by residual: angle pdb=" P1 POP J1501 " pdb=" O POP J1501 " pdb=" P2 POP J1501 " ideal model delta sigma weight residual 139.66 121.21 18.45 3.00e+00 1.11e-01 3.78e+01 angle pdb=" N3 DT P 31 " pdb=" C4 DT P 31 " pdb=" O4 DT P 31 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" O4' DG Q 30 " pdb=" C4' DG Q 30 " pdb=" C3' DG Q 30 " ideal model delta sigma weight residual 106.00 103.33 2.67 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT Q 13 " pdb=" C4 DT Q 13 " pdb=" O4 DT Q 13 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT Q 14 " pdb=" C4 DT Q 14 " pdb=" O4 DT Q 14 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 ... (remaining 43648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 18741 35.50 - 70.99: 661 70.99 - 106.49: 13 106.49 - 141.99: 0 141.99 - 177.49: 1 Dihedral angle restraints: 19416 sinusoidal: 8871 harmonic: 10545 Sorted by residual: dihedral pdb=" CA VAL H 192 " pdb=" C VAL H 192 " pdb=" N GLU H 193 " pdb=" CA GLU H 193 " ideal model delta harmonic sigma weight residual -180.00 -156.23 -23.77 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA ARG H 191 " pdb=" C ARG H 191 " pdb=" N VAL H 192 " pdb=" CA VAL H 192 " ideal model delta harmonic sigma weight residual 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" C4' DA Q 55 " pdb=" C3' DA Q 55 " pdb=" O3' DA Q 55 " pdb=" P DG Q 56 " ideal model delta sinusoidal sigma weight residual -140.00 37.49 -177.49 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 19413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 3124 0.032 - 0.064: 1250 0.064 - 0.097: 374 0.097 - 0.129: 206 0.129 - 0.161: 23 Chirality restraints: 4977 Sorted by residual: chirality pdb=" C3' DA P 62 " pdb=" C4' DA P 62 " pdb=" O3' DA P 62 " pdb=" C2' DA P 62 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CA VAL H 192 " pdb=" N VAL H 192 " pdb=" C VAL H 192 " pdb=" CB VAL H 192 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA ILE J1124 " pdb=" N ILE J1124 " pdb=" C ILE J1124 " pdb=" CB ILE J1124 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 4974 not shown) Planarity restraints: 5281 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR I 589 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO I 590 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO I 590 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 590 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS I 551 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO I 552 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO I 552 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO I 552 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 858 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.40e+00 pdb=" N PRO J 859 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO J 859 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 859 " -0.022 5.00e-02 4.00e+02 ... (remaining 5278 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 416 2.56 - 3.15: 23822 3.15 - 3.73: 49830 3.73 - 4.32: 74128 4.32 - 4.90: 119216 Nonbonded interactions: 267412 Sorted by model distance: nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1502 " model vdw 1.978 2.170 nonbonded pdb=" OG1 THR I 843 " pdb=" O GLY I 846 " model vdw 2.177 3.040 nonbonded pdb=" O HOH J1746 " pdb=" O HOH Q 127 " model vdw 2.181 3.040 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1502 " model vdw 2.186 2.170 nonbonded pdb=" O HOH J1734 " pdb=" O HOH J1948 " model vdw 2.207 3.040 ... (remaining 267407 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 7 through 158 or resid 167 through 233)) selection = (chain 'H' and resid 7 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.710 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 44.900 Find NCS groups from input model: 0.320 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:8.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 31969 Z= 0.235 Angle : 0.530 18.447 43665 Z= 0.360 Chirality : 0.042 0.161 4977 Planarity : 0.004 0.041 5281 Dihedral : 15.035 177.486 12618 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.21 % Allowed : 5.68 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.14), residues: 3638 helix: 1.67 (0.14), residues: 1439 sheet: 0.57 (0.23), residues: 467 loop : -0.42 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 798 TYR 0.012 0.001 TYR J 631 PHE 0.013 0.001 PHE I 514 TRP 0.006 0.001 TRP J 686 HIS 0.003 0.001 HIS L 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.23 (31960) covalent geometry : angle 0.53036 / 0.36 (43653) hydrogen bonds : bond 0.13617 / 8.90 ( 1455) hydrogen bonds : angle 5.15942 / 3.54 ( 3995) metal coordination : bond 0.05481 / 2.54 ( 8) metal coordination : angle 0.13562 / 0.07 ( 12) Misc. bond : bond 0.04266 / 2.25 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 375 time to evaluate : 1.462 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: I 903 ARG cc_start: 0.8931 (mmt90) cc_final: 0.8669 (mmt90) REVERT: I 1028 LYS cc_start: 0.8932 (mtmt) cc_final: 0.8689 (mtmt) REVERT: J 153 ASN cc_start: 0.8355 (t0) cc_final: 0.7790 (t0) REVERT: J 1040 MET cc_start: -0.1500 (mtt) cc_final: -0.3328 (ptp) REVERT: J 1051 ASP cc_start: 0.1379 (OUTLIER) cc_final: 0.0002 (p0) REVERT: J 1196 LEU cc_start: 0.9255 (mm) cc_final: 0.8860 (tp) REVERT: L 144 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8844 (pp) REVERT: L 277 MET cc_start: 0.8904 (tpt) cc_final: 0.8548 (tpp) REVERT: L 458 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: L 602 SER cc_start: 0.8967 (OUTLIER) cc_final: 0.8627 (p) outliers start: 38 outliers final: 12 residues processed: 407 average time/residue: 0.9493 time to fit residues: 441.9068 Evaluate side-chains 255 residues out of total 3135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 239 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 1051 ASP Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 267 ASP Chi-restraints excluded: chain L residue 458 GLU Chi-restraints excluded: chain L residue 602 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 20.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 276 GLN ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN J 365 GLN J 430 HIS J 651 HIS J 777 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.113243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.068337 restraints weight = 62553.028| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.52 r_work: 0.2839 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31969 Z= 0.132 Angle : 0.556 11.410 43665 Z= 0.304 Chirality : 0.042 0.215 4977 Planarity : 0.004 0.050 5281 Dihedral : 16.433 175.255 5390 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.47 % Allowed : 11.04 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.14), residues: 3638 helix: 1.80 (0.14), residues: 1469 sheet: 0.76 (0.25), residues: 417 loop : -0.27 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I1034 TYR 0.013 0.001 TYR H 152 PHE 0.016 0.001 PHE L 256 TRP 0.019 0.001 TRP J1193 HIS 0.004 0.001 HIS L 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (31960) covalent geometry : angle 0.55525 / 0.30 (43653) hydrogen bonds : bond 0.04539 / 2.94 ( 1455) hydrogen bonds : angle 4.34563 / 2.98 ( 3995) metal coordination : bond 0.00495 / 0.23 ( 8) metal coordination : angle 1.96010 / 0.96 ( 12) Misc. bond : bond 0.00489 / 0.26 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 256 time to evaluate : 1.310 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: I 247 ARG cc_start: 0.8855 (ttm110) cc_final: 0.8640 (ttm110) REVERT: I 265 LYS cc_start: 0.9189 (ptpt) cc_final: 0.8893 (tmtm) REVERT: I 425 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8568 (mp) REVERT: I 643 SER cc_start: 0.8599 (t) cc_final: 0.8336 (m) REVERT: I 903 ARG cc_start: 0.9127 (mmt90) cc_final: 0.8755 (mmt90) REVERT: I 1028 LYS cc_start: 0.9031 (mtmt) cc_final: 0.8806 (mtmt) REVERT: K 11 GLU cc_start: 0.8568 (pp20) cc_final: 0.8321 (pp20) REVERT: G 127 GLN cc_start: 0.8987 (mp10) cc_final: 0.8762 (mp10) REVERT: H 17 GLU cc_start: 0.8328 (tt0) cc_final: 0.7863 (tm-30) REVERT: H 80 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8317 (mm-30) REVERT: J 153 ASN cc_start: 0.8416 (t0) cc_final: 0.8213 (t0) REVERT: J 386 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8315 (mm-30) REVERT: J 818 GLU cc_start: 0.8469 (mp0) cc_final: 0.8143 (mp0) REVERT: J 1040 MET cc_start: -0.0198 (mtt) cc_final: -0.2411 (ptp) REVERT: J 1196 LEU cc_start: 0.9218 (mm) cc_final: 0.8769 (tp) REVERT: J 1267 VAL cc_start: 0.9476 (t) cc_final: 0.9268 (m) REVERT: L 144 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9036 (pp) REVERT: L 273 MET cc_start: 0.9116 (tmm) cc_final: 0.8831 (mmt) REVERT: L 277 MET cc_start: 0.8998 (tpt) cc_final: 0.8678 (tpp) REVERT: L 288 MET cc_start: 0.8888 (tmm) cc_final: 0.8528 (pp-130) outliers start: 46 outliers final: 16 residues processed: 291 average time/residue: 0.8456 time to fit residues: 285.4503 Evaluate side-chains 254 residues out of total 3135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 235 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 425 ILE Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 266 PHE Chi-restraints excluded: chain L residue 267 ASP Chi-restraints excluded: chain L residue 468 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 59 optimal weight: 0.7980 chunk 273 optimal weight: 0.1980 chunk 344 optimal weight: 30.0000 chunk 51 optimal weight: 1.9990 chunk 61 optimal weight: 0.1980 chunk 218 optimal weight: 1.9990 chunk 247 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 354 optimal weight: 5.9990 chunk 270 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 65 ASN ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN J 430 HIS J 651 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.113445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.068852 restraints weight = 62835.103| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.52 r_work: 0.2853 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 31969 Z= 0.110 Angle : 0.500 9.682 43665 Z= 0.275 Chirality : 0.041 0.231 4977 Planarity : 0.004 0.049 5281 Dihedral : 16.433 177.215 5379 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.24 % Allowed : 11.48 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.14), residues: 3638 helix: 1.97 (0.14), residues: 1469 sheet: 0.99 (0.25), residues: 425 loop : -0.23 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I1034 TYR 0.012 0.001 TYR J 631 PHE 0.010 0.001 PHE I 514 TRP 0.025 0.001 TRP J1193 HIS 0.006 0.001 HIS L 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (31960) covalent geometry : angle 0.49925 / 0.28 (43653) hydrogen bonds : bond 0.04010 / 2.58 ( 1455) hydrogen bonds : angle 4.15278 / 2.85 ( 3995) metal coordination : bond 0.00406 / 0.20 ( 8) metal coordination : angle 1.95842 / 0.97 ( 12) Misc. bond : bond 0.00087 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 243 time to evaluate : 1.084 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: I 247 ARG cc_start: 0.8837 (ttm110) cc_final: 0.8601 (ttm110) REVERT: I 265 LYS cc_start: 0.9215 (ptpt) cc_final: 0.8950 (tmtm) REVERT: I 425 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8571 (mp) REVERT: I 542 ARG cc_start: 0.7694 (mmm-85) cc_final: 0.7119 (ttt-90) REVERT: I 546 GLU cc_start: 0.8520 (pm20) cc_final: 0.8122 (pm20) REVERT: I 643 SER cc_start: 0.8580 (t) cc_final: 0.8316 (m) REVERT: I 1028 LYS cc_start: 0.9093 (mtmt) cc_final: 0.8502 (mtmt) REVERT: I 1032 LYS cc_start: 0.9160 (mmmm) cc_final: 0.8839 (mtmm) REVERT: K 70 GLN cc_start: 0.8457 (tm-30) cc_final: 0.7903 (tm-30) REVERT: K 72 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8632 (tm-30) REVERT: G 95 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8348 (ptmt) REVERT: H 66 HIS cc_start: 0.8904 (t-90) cc_final: 0.8555 (t-90) REVERT: H 80 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8339 (mm-30) REVERT: H 95 LYS cc_start: 0.8794 (ttmt) cc_final: 0.8571 (mtmm) REVERT: J 153 ASN cc_start: 0.8438 (t0) cc_final: 0.8216 (t0) REVERT: J 818 GLU cc_start: 0.8583 (mp0) cc_final: 0.8222 (mp0) REVERT: J 1040 MET cc_start: 0.0101 (mtt) cc_final: -0.2191 (ptp) REVERT: J 1193 TRP cc_start: 0.8234 (p-90) cc_final: 0.7826 (p-90) REVERT: J 1196 LEU cc_start: 0.9346 (mm) cc_final: 0.8841 (tp) REVERT: L 144 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9035 (pp) REVERT: L 273 MET cc_start: 0.9136 (tmm) cc_final: 0.8815 (mmt) REVERT: L 277 MET cc_start: 0.9009 (tpt) cc_final: 0.8679 (tpp) REVERT: L 288 MET cc_start: 0.8889 (tmm) cc_final: 0.8477 (pp-130) outliers start: 39 outliers final: 18 residues processed: 272 average time/residue: 0.8249 time to fit residues: 259.3641 Evaluate side-chains 248 residues out of total 3135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 227 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 279 LYS Chi-restraints excluded: chain I residue 425 ILE Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1131 MET Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 267 ASP Chi-restraints excluded: chain L residue 468 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 323 optimal weight: 8.9990 chunk 220 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 252 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 35 optimal weight: 0.5980 chunk 207 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 65 ASN ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 430 HIS J 651 HIS J 777 HIS J1108 GLN ** L 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.109985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.065414 restraints weight = 62736.200| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.46 r_work: 0.2774 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9050 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 31969 Z= 0.245 Angle : 0.578 9.122 43665 Z= 0.314 Chirality : 0.045 0.236 4977 Planarity : 0.004 0.051 5281 Dihedral : 16.582 179.738 5379 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.79 % Allowed : 11.83 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.14), residues: 3638 helix: 1.76 (0.14), residues: 1479 sheet: 0.78 (0.25), residues: 445 loop : -0.34 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I1034 TYR 0.017 0.001 TYR J 631 PHE 0.014 0.002 PHE I 405 TRP 0.022 0.002 TRP J1193 HIS 0.015 0.001 HIS L 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.25 (31960) covalent geometry : angle 0.57706 / 0.31 (43653) hydrogen bonds : bond 0.05533 / 3.58 ( 1455) hydrogen bonds : angle 4.25207 / 2.93 ( 3995) metal coordination : bond 0.01002 / 0.47 ( 8) metal coordination : angle 2.28581 / 1.19 ( 12) Misc. bond : bond 0.00164 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 238 time to evaluate : 1.038 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: I 425 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8685 (mp) REVERT: I 488 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8534 (mmp) REVERT: I 542 ARG cc_start: 0.7858 (mmm-85) cc_final: 0.7245 (mtp180) REVERT: I 546 GLU cc_start: 0.8536 (pm20) cc_final: 0.8169 (pm20) REVERT: I 643 SER cc_start: 0.8682 (t) cc_final: 0.8424 (m) REVERT: I 1019 ASP cc_start: -0.2802 (OUTLIER) cc_final: -0.3197 (m-30) REVERT: I 1028 LYS cc_start: 0.9113 (mtmt) cc_final: 0.8502 (mtmm) REVERT: I 1032 LYS cc_start: 0.9161 (mmmm) cc_final: 0.8827 (mtmm) REVERT: K 11 GLU cc_start: 0.8635 (pp20) cc_final: 0.8347 (pp20) REVERT: K 55 GLU cc_start: 0.8893 (pt0) cc_final: 0.8683 (pt0) REVERT: H 95 LYS cc_start: 0.8888 (ttmt) cc_final: 0.8615 (mtmm) REVERT: J 153 ASN cc_start: 0.8530 (t0) cc_final: 0.8295 (t0) REVERT: J 216 LYS cc_start: 0.9050 (mtpm) cc_final: 0.8818 (mmpt) REVERT: J 818 GLU cc_start: 0.8677 (mp0) cc_final: 0.8386 (mp0) REVERT: J 1040 MET cc_start: -0.0167 (mtt) cc_final: -0.2668 (ptp) REVERT: J 1196 LEU cc_start: 0.9354 (mm) cc_final: 0.8819 (tp) REVERT: L 144 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9032 (pp) REVERT: L 273 MET cc_start: 0.9172 (tmm) cc_final: 0.8843 (mmt) REVERT: L 277 MET cc_start: 0.9026 (tpt) cc_final: 0.8693 (tpp) REVERT: L 458 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8882 (mt-10) outliers start: 56 outliers final: 25 residues processed: 282 average time/residue: 0.7920 time to fit residues: 259.9105 Evaluate side-chains 257 residues out of total 3135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 227 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 425 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1019 ASP Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 319 SER Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 749 LYS Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain L residue 132 CYS Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 267 ASP Chi-restraints excluded: chain L residue 458 GLU Chi-restraints excluded: chain L residue 552 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 336 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 356 optimal weight: 5.9990 chunk 258 optimal weight: 0.9980 chunk 287 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 55 optimal weight: 0.0050 chunk 162 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 235 optimal weight: 0.9980 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 65 ASN H 186 ASN J 430 HIS J 651 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.111565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.066617 restraints weight = 62998.648| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.53 r_work: 0.2824 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 31969 Z= 0.116 Angle : 0.507 10.578 43665 Z= 0.278 Chirality : 0.041 0.245 4977 Planarity : 0.004 0.054 5281 Dihedral : 16.488 178.690 5377 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.40 % Allowed : 12.76 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.14), residues: 3638 helix: 1.99 (0.14), residues: 1474 sheet: 0.95 (0.26), residues: 422 loop : -0.21 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I1034 TYR 0.013 0.001 TYR J 631 PHE 0.019 0.001 PHE L 302 TRP 0.035 0.001 TRP J1193 HIS 0.005 0.001 HIS J 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (31960) covalent geometry : angle 0.50631 / 0.28 (43653) hydrogen bonds : bond 0.04046 / 2.60 ( 1455) hydrogen bonds : angle 4.05576 / 2.80 ( 3995) metal coordination : bond 0.00379 / 0.21 ( 8) metal coordination : angle 1.95030 / 0.98 ( 12) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 239 time to evaluate : 1.235 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: I 425 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8602 (mp) REVERT: I 542 ARG cc_start: 0.7767 (mmm-85) cc_final: 0.7149 (ttt-90) REVERT: I 546 GLU cc_start: 0.8509 (pm20) cc_final: 0.8126 (pm20) REVERT: I 643 SER cc_start: 0.8603 (t) cc_final: 0.8358 (m) REVERT: I 914 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8650 (ttpp) REVERT: I 1028 LYS cc_start: 0.9117 (mtmt) cc_final: 0.8444 (mtmm) REVERT: I 1032 LYS cc_start: 0.9169 (mmmm) cc_final: 0.8848 (mtmm) REVERT: I 1034 ARG cc_start: 0.9104 (ttm-80) cc_final: 0.8804 (mmm160) REVERT: K 70 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8051 (tm-30) REVERT: G 33 ARG cc_start: 0.8957 (tpp-160) cc_final: 0.8591 (tpp-160) REVERT: H 66 HIS cc_start: 0.8923 (t-90) cc_final: 0.8555 (t-90) REVERT: H 93 GLN cc_start: 0.7583 (mp10) cc_final: 0.7350 (mp10) REVERT: J 216 LYS cc_start: 0.9009 (mtpm) cc_final: 0.8785 (mmpt) REVERT: J 818 GLU cc_start: 0.8677 (mp0) cc_final: 0.8197 (mp0) REVERT: J 1040 MET cc_start: -0.0060 (mtt) cc_final: -0.2449 (ptp) REVERT: J 1196 LEU cc_start: 0.9392 (mm) cc_final: 0.8947 (tp) REVERT: L 144 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9024 (pp) REVERT: L 273 MET cc_start: 0.9138 (tmm) cc_final: 0.8803 (mmt) REVERT: L 277 MET cc_start: 0.9030 (tpt) cc_final: 0.8664 (tpp) REVERT: L 288 MET cc_start: 0.8909 (tmm) cc_final: 0.8555 (pp-130) REVERT: L 297 MET cc_start: 0.2123 (OUTLIER) cc_final: 0.1655 (ppp) REVERT: L 458 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.8863 (mt-10) outliers start: 44 outliers final: 20 residues processed: 273 average time/residue: 0.7658 time to fit residues: 243.1717 Evaluate side-chains 254 residues out of total 3135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 229 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 279 LYS Chi-restraints excluded: chain I residue 425 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 914 LYS Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 749 LYS Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain L residue 132 CYS Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 267 ASP Chi-restraints excluded: chain L residue 297 MET Chi-restraints excluded: chain L residue 458 GLU Chi-restraints excluded: chain L residue 464 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 319 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 279 optimal weight: 0.6980 chunk 311 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 329 optimal weight: 20.0000 chunk 105 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 328 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 65 ASN H 186 ASN J 206 ASN J 430 HIS J 651 HIS J 777 HIS ** L 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.111156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.066826 restraints weight = 62738.078| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.48 r_work: 0.2809 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31969 Z= 0.143 Angle : 0.512 10.886 43665 Z= 0.279 Chirality : 0.042 0.245 4977 Planarity : 0.004 0.055 5281 Dihedral : 16.491 179.999 5377 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.37 % Allowed : 13.46 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.14), residues: 3638 helix: 2.02 (0.14), residues: 1473 sheet: 1.01 (0.26), residues: 422 loop : -0.20 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 77 TYR 0.014 0.001 TYR J 631 PHE 0.014 0.001 PHE L 302 TRP 0.038 0.001 TRP J1193 HIS 0.007 0.001 HIS J 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (31960) covalent geometry : angle 0.51143 / 0.28 (43653) hydrogen bonds : bond 0.04226 / 2.72 ( 1455) hydrogen bonds : angle 4.03631 / 2.79 ( 3995) metal coordination : bond 0.00592 / 0.29 ( 8) metal coordination : angle 1.99072 / 1.02 ( 12) Misc. bond : bond 0.00001 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 229 time to evaluate : 1.361 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: I 425 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8638 (mp) REVERT: I 542 ARG cc_start: 0.7701 (mmm-85) cc_final: 0.7167 (mtp180) REVERT: I 546 GLU cc_start: 0.8517 (pm20) cc_final: 0.8149 (pm20) REVERT: I 643 SER cc_start: 0.8621 (t) cc_final: 0.8378 (m) REVERT: I 914 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8623 (ttpp) REVERT: I 1028 LYS cc_start: 0.9101 (mtmt) cc_final: 0.8816 (mtmm) REVERT: I 1034 ARG cc_start: 0.9121 (ttm-80) cc_final: 0.8841 (mmm160) REVERT: K 8 ASP cc_start: 0.8495 (m-30) cc_final: 0.8192 (m-30) REVERT: K 11 GLU cc_start: 0.8622 (pp20) cc_final: 0.8381 (pp20) REVERT: K 70 GLN cc_start: 0.8384 (tm-30) cc_final: 0.8060 (tm-30) REVERT: H 66 HIS cc_start: 0.8936 (t-90) cc_final: 0.8573 (t-90) REVERT: J 216 LYS cc_start: 0.9024 (mtpm) cc_final: 0.8802 (mmpt) REVERT: J 818 GLU cc_start: 0.8705 (mp0) cc_final: 0.8201 (mp0) REVERT: J 1040 MET cc_start: -0.0181 (mtt) cc_final: -0.2527 (ptp) REVERT: J 1152 GLU cc_start: 0.8084 (pp20) cc_final: 0.7849 (tm-30) REVERT: J 1196 LEU cc_start: 0.9370 (mm) cc_final: 0.8897 (tp) REVERT: L 144 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9027 (pp) REVERT: L 273 MET cc_start: 0.9146 (tmm) cc_final: 0.8810 (mmt) REVERT: L 277 MET cc_start: 0.9033 (tpt) cc_final: 0.8700 (tpp) REVERT: L 288 MET cc_start: 0.8921 (tmm) cc_final: 0.8432 (pp-130) REVERT: L 297 MET cc_start: 0.1966 (OUTLIER) cc_final: 0.1102 (ppp) REVERT: L 458 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.8862 (mt-10) outliers start: 43 outliers final: 23 residues processed: 263 average time/residue: 0.7818 time to fit residues: 239.4458 Evaluate side-chains 254 residues out of total 3135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 425 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 610 GLU Chi-restraints excluded: chain I residue 914 LYS Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 749 LYS Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain L residue 132 CYS Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 267 ASP Chi-restraints excluded: chain L residue 297 MET Chi-restraints excluded: chain L residue 458 GLU Chi-restraints excluded: chain L residue 464 ASN Chi-restraints excluded: chain L residue 552 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 233 optimal weight: 0.1980 chunk 208 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 315 optimal weight: 5.9990 chunk 184 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 171 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 65 ASN I 165 HIS H 186 ASN J 430 HIS J 651 HIS J 777 HIS ** L 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.110650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.066215 restraints weight = 63039.012| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.49 r_work: 0.2722 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31969 Z= 0.160 Angle : 0.523 11.531 43665 Z= 0.284 Chirality : 0.042 0.247 4977 Planarity : 0.004 0.056 5281 Dihedral : 16.541 179.474 5377 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.53 % Allowed : 13.33 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.14), residues: 3638 helix: 2.02 (0.14), residues: 1475 sheet: 1.00 (0.26), residues: 422 loop : -0.22 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 247 TYR 0.013 0.001 TYR J 631 PHE 0.011 0.001 PHE I 35 TRP 0.043 0.001 TRP J1193 HIS 0.006 0.001 HIS J 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (31960) covalent geometry : angle 0.52211 / 0.28 (43653) hydrogen bonds : bond 0.04400 / 2.83 ( 1455) hydrogen bonds : angle 4.02654 / 2.78 ( 3995) metal coordination : bond 0.00644 / 0.31 ( 8) metal coordination : angle 2.02400 / 1.05 ( 12) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 237 time to evaluate : 1.296 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: I 425 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8534 (mp) REVERT: I 542 ARG cc_start: 0.7627 (mmm-85) cc_final: 0.7054 (mtp180) REVERT: I 546 GLU cc_start: 0.8481 (pm20) cc_final: 0.8114 (pm20) REVERT: I 643 SER cc_start: 0.8546 (t) cc_final: 0.8304 (m) REVERT: I 914 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8444 (ttpp) REVERT: I 1028 LYS cc_start: 0.9102 (mtmt) cc_final: 0.8822 (mtmm) REVERT: I 1034 ARG cc_start: 0.9167 (ttm-80) cc_final: 0.8857 (mmm160) REVERT: I 1163 THR cc_start: 0.9289 (m) cc_final: 0.9078 (p) REVERT: K 11 GLU cc_start: 0.8601 (pp20) cc_final: 0.8386 (pp20) REVERT: H 66 HIS cc_start: 0.8966 (t-90) cc_final: 0.8547 (t-90) REVERT: H 95 LYS cc_start: 0.8922 (mtmm) cc_final: 0.8495 (mtmm) REVERT: J 206 ASN cc_start: 0.9207 (p0) cc_final: 0.8934 (p0) REVERT: J 216 LYS cc_start: 0.9024 (mtpm) cc_final: 0.8798 (mmpt) REVERT: J 818 GLU cc_start: 0.8717 (mp0) cc_final: 0.8174 (mp0) REVERT: J 1040 MET cc_start: 0.0132 (mtt) cc_final: -0.2378 (ptp) REVERT: J 1152 GLU cc_start: 0.8089 (pp20) cc_final: 0.7843 (tm-30) REVERT: J 1196 LEU cc_start: 0.9365 (mm) cc_final: 0.8878 (tp) REVERT: L 144 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9021 (pp) REVERT: L 273 MET cc_start: 0.9151 (tmm) cc_final: 0.8783 (mmt) REVERT: L 277 MET cc_start: 0.9044 (tpt) cc_final: 0.8707 (tpp) REVERT: L 288 MET cc_start: 0.8842 (tmm) cc_final: 0.8479 (tmm) REVERT: L 297 MET cc_start: 0.1863 (OUTLIER) cc_final: 0.1085 (ppp) REVERT: L 458 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.8856 (mt-10) outliers start: 48 outliers final: 28 residues processed: 273 average time/residue: 0.8549 time to fit residues: 271.1903 Evaluate side-chains 268 residues out of total 3135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 235 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 279 LYS Chi-restraints excluded: chain I residue 425 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 610 GLU Chi-restraints excluded: chain I residue 914 LYS Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 749 LYS Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1231 ARG Chi-restraints excluded: chain L residue 132 CYS Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 267 ASP Chi-restraints excluded: chain L residue 297 MET Chi-restraints excluded: chain L residue 458 GLU Chi-restraints excluded: chain L residue 552 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 9.9990 chunk 348 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 363 optimal weight: 8.9990 chunk 314 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 249 optimal weight: 0.7980 chunk 273 optimal weight: 6.9990 chunk 272 optimal weight: 5.9990 chunk 284 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 65 ASN I 165 HIS H 186 ASN J 430 HIS J 651 HIS J 777 HIS ** L 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.109305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.064818 restraints weight = 63042.461| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.48 r_work: 0.2690 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 31969 Z= 0.248 Angle : 0.575 13.046 43665 Z= 0.310 Chirality : 0.044 0.247 4977 Planarity : 0.004 0.063 5281 Dihedral : 16.640 178.673 5377 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.47 % Allowed : 13.52 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.14), residues: 3638 helix: 1.93 (0.14), residues: 1475 sheet: 0.91 (0.26), residues: 423 loop : -0.29 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 77 TYR 0.016 0.001 TYR H 152 PHE 0.013 0.001 PHE I 405 TRP 0.041 0.002 TRP J1193 HIS 0.006 0.001 HIS J 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.25 (31960) covalent geometry : angle 0.57348 / 0.31 (43653) hydrogen bonds : bond 0.05191 / 3.36 ( 1455) hydrogen bonds : angle 4.13747 / 2.86 ( 3995) metal coordination : bond 0.00958 / 0.46 ( 8) metal coordination : angle 2.33875 / 1.24 ( 12) Misc. bond : bond 0.00039 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 230 time to evaluate : 1.521 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: I 425 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8596 (mp) REVERT: I 546 GLU cc_start: 0.8460 (pm20) cc_final: 0.8172 (pm20) REVERT: I 643 SER cc_start: 0.8584 (t) cc_final: 0.8331 (m) REVERT: I 894 GLN cc_start: 0.8772 (tp40) cc_final: 0.8282 (tp40) REVERT: I 914 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8450 (ttpp) REVERT: I 1019 ASP cc_start: -0.2989 (OUTLIER) cc_final: -0.3383 (m-30) REVERT: I 1028 LYS cc_start: 0.9105 (mtmt) cc_final: 0.8815 (mtmm) REVERT: I 1032 LYS cc_start: 0.9217 (mmmm) cc_final: 0.8902 (mmmt) REVERT: I 1034 ARG cc_start: 0.9169 (ttm-80) cc_final: 0.8892 (mmm160) REVERT: K 11 GLU cc_start: 0.8641 (pp20) cc_final: 0.8421 (pp20) REVERT: K 35 LYS cc_start: 0.8357 (mptt) cc_final: 0.8051 (mptm) REVERT: K 74 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8716 (tm-30) REVERT: H 95 LYS cc_start: 0.8963 (mtmm) cc_final: 0.8531 (mtmm) REVERT: J 206 ASN cc_start: 0.9221 (p0) cc_final: 0.8941 (p0) REVERT: J 216 LYS cc_start: 0.9033 (mtpm) cc_final: 0.8800 (mmpt) REVERT: J 818 GLU cc_start: 0.8752 (mp0) cc_final: 0.8183 (mp0) REVERT: J 1040 MET cc_start: 0.0170 (mtt) cc_final: -0.2350 (ptp) REVERT: J 1196 LEU cc_start: 0.9363 (mm) cc_final: 0.8883 (tp) REVERT: L 144 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9042 (pp) REVERT: L 273 MET cc_start: 0.9180 (tmm) cc_final: 0.8834 (mmt) REVERT: L 277 MET cc_start: 0.9061 (tpt) cc_final: 0.8721 (tpp) REVERT: L 297 MET cc_start: 0.1733 (OUTLIER) cc_final: 0.1033 (ppp) REVERT: L 458 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8874 (mt-10) outliers start: 46 outliers final: 23 residues processed: 263 average time/residue: 0.8353 time to fit residues: 255.1930 Evaluate side-chains 255 residues out of total 3135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 226 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 279 LYS Chi-restraints excluded: chain I residue 425 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 610 GLU Chi-restraints excluded: chain I residue 914 LYS Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1019 ASP Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 319 SER Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 749 LYS Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain L residue 132 CYS Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 267 ASP Chi-restraints excluded: chain L residue 297 MET Chi-restraints excluded: chain L residue 458 GLU Chi-restraints excluded: chain L residue 552 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 321 optimal weight: 5.9990 chunk 237 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 279 optimal weight: 0.9990 chunk 358 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 202 optimal weight: 0.0870 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 65 ASN H 186 ASN J 153 ASN J 430 HIS J 651 HIS ** L 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.110801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.066082 restraints weight = 62700.694| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.52 r_work: 0.2817 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 31969 Z= 0.114 Angle : 0.530 13.218 43665 Z= 0.286 Chirality : 0.041 0.252 4977 Planarity : 0.004 0.126 5281 Dihedral : 16.573 179.396 5377 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.08 % Allowed : 14.07 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.14), residues: 3638 helix: 2.10 (0.14), residues: 1469 sheet: 1.04 (0.26), residues: 422 loop : -0.18 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.000 ARG J 77 TYR 0.014 0.001 TYR J 631 PHE 0.012 0.001 PHE J1319 TRP 0.045 0.001 TRP J1193 HIS 0.006 0.001 HIS J 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (31960) covalent geometry : angle 0.52952 / 0.29 (43653) hydrogen bonds : bond 0.03917 / 2.51 ( 1455) hydrogen bonds : angle 3.97198 / 2.74 ( 3995) metal coordination : bond 0.00365 / 0.19 ( 8) metal coordination : angle 1.96429 / 1.03 ( 12) Misc. bond : bond 0.00060 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 237 time to evaluate : 1.272 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: I 165 HIS cc_start: 0.8422 (t-90) cc_final: 0.8144 (t70) REVERT: I 425 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8579 (mp) REVERT: I 542 ARG cc_start: 0.7649 (mmm-85) cc_final: 0.7125 (mtp180) REVERT: I 546 GLU cc_start: 0.8461 (pm20) cc_final: 0.8173 (pm20) REVERT: I 643 SER cc_start: 0.8569 (t) cc_final: 0.8332 (m) REVERT: I 894 GLN cc_start: 0.8494 (tp40) cc_final: 0.8290 (mt0) REVERT: I 1028 LYS cc_start: 0.9103 (mtmt) cc_final: 0.8824 (mtmm) REVERT: I 1034 ARG cc_start: 0.9154 (ttm-80) cc_final: 0.8858 (mmm160) REVERT: K 11 GLU cc_start: 0.8681 (pp20) cc_final: 0.8448 (pp20) REVERT: H 29 GLU cc_start: 0.8807 (pt0) cc_final: 0.8501 (pt0) REVERT: H 66 HIS cc_start: 0.8961 (t-90) cc_final: 0.8584 (t-90) REVERT: H 95 LYS cc_start: 0.8980 (mtmm) cc_final: 0.8526 (mtmm) REVERT: J 77 ARG cc_start: 0.8129 (mmm160) cc_final: 0.7559 (mmm-85) REVERT: J 206 ASN cc_start: 0.9208 (p0) cc_final: 0.8942 (p0) REVERT: J 216 LYS cc_start: 0.9035 (mtpm) cc_final: 0.8809 (mmpt) REVERT: J 818 GLU cc_start: 0.8749 (mp0) cc_final: 0.8191 (mp0) REVERT: J 1040 MET cc_start: -0.0043 (mtt) cc_final: -0.2505 (ptp) REVERT: L 144 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9026 (pp) REVERT: L 273 MET cc_start: 0.9171 (tmm) cc_final: 0.8805 (mmt) REVERT: L 277 MET cc_start: 0.9038 (tpt) cc_final: 0.8672 (tpp) REVERT: L 288 MET cc_start: 0.8847 (tmm) cc_final: 0.8459 (pp-130) REVERT: L 297 MET cc_start: 0.1635 (OUTLIER) cc_final: 0.0909 (ppp) REVERT: L 458 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.8856 (mt-10) outliers start: 34 outliers final: 24 residues processed: 263 average time/residue: 0.8350 time to fit residues: 255.1177 Evaluate side-chains 255 residues out of total 3135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 227 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 279 LYS Chi-restraints excluded: chain I residue 425 ILE Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 610 GLU Chi-restraints excluded: chain I residue 905 ILE Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 749 LYS Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain L residue 132 CYS Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 267 ASP Chi-restraints excluded: chain L residue 297 MET Chi-restraints excluded: chain L residue 458 GLU Chi-restraints excluded: chain L residue 552 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 9 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 338 optimal weight: 0.9990 chunk 263 optimal weight: 1.9990 chunk 350 optimal weight: 0.9980 chunk 312 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 65 ASN ** I 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN J 229 GLN J 651 HIS J 777 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.110989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.066619 restraints weight = 63263.912| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.51 r_work: 0.2813 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31969 Z= 0.129 Angle : 0.539 13.171 43665 Z= 0.290 Chirality : 0.041 0.252 4977 Planarity : 0.004 0.077 5281 Dihedral : 16.556 178.494 5377 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.02 % Allowed : 14.13 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.14), residues: 3638 helix: 2.10 (0.14), residues: 1469 sheet: 1.08 (0.26), residues: 422 loop : -0.16 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG J 77 TYR 0.015 0.001 TYR H 152 PHE 0.027 0.001 PHE I 906 TRP 0.047 0.001 TRP J1193 HIS 0.006 0.001 HIS J 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (31960) covalent geometry : angle 0.53810 / 0.29 (43653) hydrogen bonds : bond 0.04000 / 2.56 ( 1455) hydrogen bonds : angle 3.96365 / 2.74 ( 3995) metal coordination : bond 0.00451 / 0.23 ( 8) metal coordination : angle 1.97172 / 1.01 ( 12) Misc. bond : bond 0.00037 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 231 time to evaluate : 1.199 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: I 165 HIS cc_start: 0.8415 (t-90) cc_final: 0.8199 (t70) REVERT: I 425 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8615 (mp) REVERT: I 546 GLU cc_start: 0.8476 (pm20) cc_final: 0.8199 (pm20) REVERT: I 643 SER cc_start: 0.8617 (t) cc_final: 0.8384 (m) REVERT: I 894 GLN cc_start: 0.8491 (tp40) cc_final: 0.8284 (mt0) REVERT: I 905 ILE cc_start: 0.8437 (mp) cc_final: 0.8134 (mp) REVERT: I 1028 LYS cc_start: 0.9116 (mtmt) cc_final: 0.8839 (mtmm) REVERT: I 1034 ARG cc_start: 0.9134 (ttm-80) cc_final: 0.8835 (mmm160) REVERT: K 11 GLU cc_start: 0.8708 (pp20) cc_final: 0.8470 (pp20) REVERT: K 74 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8697 (tm-30) REVERT: H 29 GLU cc_start: 0.8815 (pt0) cc_final: 0.8512 (pt0) REVERT: H 66 HIS cc_start: 0.8956 (t-90) cc_final: 0.8586 (t-90) REVERT: H 95 LYS cc_start: 0.8997 (mtmm) cc_final: 0.8594 (mtmm) REVERT: J 77 ARG cc_start: 0.8127 (mmm160) cc_final: 0.7572 (mmm-85) REVERT: J 206 ASN cc_start: 0.9236 (p0) cc_final: 0.8999 (p0) REVERT: J 216 LYS cc_start: 0.9030 (mtpm) cc_final: 0.8811 (mmpt) REVERT: J 818 GLU cc_start: 0.8762 (mp0) cc_final: 0.8214 (mp0) REVERT: J 1025 MET cc_start: 0.8245 (mpm) cc_final: 0.7504 (ppp) REVERT: J 1040 MET cc_start: 0.0118 (mtt) cc_final: -0.2377 (ptp) REVERT: L 144 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9034 (pp) REVERT: L 273 MET cc_start: 0.9171 (tmm) cc_final: 0.8801 (mmt) REVERT: L 277 MET cc_start: 0.9047 (tpt) cc_final: 0.8670 (tpt) REVERT: L 288 MET cc_start: 0.8860 (tmm) cc_final: 0.8460 (pp-130) REVERT: L 297 MET cc_start: 0.1787 (OUTLIER) cc_final: 0.1032 (ppp) REVERT: L 458 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8872 (mt-10) outliers start: 32 outliers final: 22 residues processed: 253 average time/residue: 0.8542 time to fit residues: 250.4645 Evaluate side-chains 256 residues out of total 3135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 230 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 279 LYS Chi-restraints excluded: chain I residue 425 ILE Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 610 GLU Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 749 LYS Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain L residue 132 CYS Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 267 ASP Chi-restraints excluded: chain L residue 297 MET Chi-restraints excluded: chain L residue 458 GLU Chi-restraints excluded: chain L residue 552 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 157 optimal weight: 6.9990 chunk 178 optimal weight: 7.9990 chunk 310 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 357 optimal weight: 0.7980 chunk 201 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 361 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 258 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 65 ASN I 894 GLN H 186 ASN J 651 HIS J 777 HIS ** L 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.110881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.066436 restraints weight = 63127.249| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.48 r_work: 0.2812 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31969 Z= 0.137 Angle : 0.543 15.432 43665 Z= 0.291 Chirality : 0.042 0.252 4977 Planarity : 0.004 0.073 5281 Dihedral : 16.563 178.120 5376 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.93 % Allowed : 14.26 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.14), residues: 3638 helix: 2.09 (0.14), residues: 1469 sheet: 1.07 (0.26), residues: 422 loop : -0.16 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG J 77 TYR 0.014 0.001 TYR J 631 PHE 0.012 0.001 PHE J1319 TRP 0.049 0.001 TRP J1193 HIS 0.006 0.001 HIS J 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (31960) covalent geometry : angle 0.54243 / 0.29 (43653) hydrogen bonds : bond 0.04047 / 2.59 ( 1455) hydrogen bonds : angle 3.96938 / 2.75 ( 3995) metal coordination : bond 0.00504 / 0.26 ( 8) metal coordination : angle 1.96843 / 1.02 ( 12) Misc. bond : bond 0.00027 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16710.14 seconds wall clock time: 283 minutes 30.82 seconds (17010.82 seconds total)