Starting phenix.real_space_refine on Mon Sep 14 19:47:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6jnx_9852/09_2026/6jnx_9852.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jnx_9852/09_2026/6jnx_9852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6jnx_9852/09_2026/6jnx_9852.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6jnx_9852/09_2026/6jnx_9852.cif" model { file = "/net/cci-nas-00/data/ceres_data/6jnx_9852/09_2026/6jnx_9852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jnx_9852/09_2026/6jnx_9852.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6jnx_9852/09_2026/6jnx_9852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jnx_9852/09_2026/6jnx_9852.map" } resolution = 4.08 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= 0.007 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 144 5.49 5 Mg 1 5.21 5 S 140 5.16 5 C 20038 2.51 5 N 5784 2.21 5 O 6530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32639 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1686 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1681 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1282} Chain: "D" Number of atoms: 10388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10388 Classifications: {'peptide': 1335} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1279} Chain breaks: 2 Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2513 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 6, 'TRANS': 300} Chain breaks: 2 Chain: "N" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1303 Classifications: {'DNA': 63} Link IDs: {'rna3p': 62} Chain: "R" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 394 Classifications: {'RNAv2': 18} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 10, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 14} Chain: "T" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1281 Classifications: {'DNA': 63} Link IDs: {'rna3p': 62} Chain: "P" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1179 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 141} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1017 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain breaks: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14383 SG CYS D 70 111.878 74.258 65.292 1.00223.00 S ATOM 14397 SG CYS D 72 112.736 73.289 61.949 1.00232.47 S ATOM 14505 SG CYS D 85 115.346 73.984 65.124 1.00231.39 S ATOM 20217 SG CYS D 814 88.075 90.596 127.947 1.00146.96 S ATOM 20782 SG CYS D 888 87.842 90.725 123.283 1.00139.40 S ATOM 20833 SG CYS D 895 86.868 88.075 125.508 1.00144.50 S ATOM 20854 SG CYS D 898 85.112 91.115 126.069 1.00145.73 S Time building chain proxies: 6.31, per 1000 atoms: 0.19 Number of scatterers: 32639 At special positions: 0 Unit cell: (172.524, 184.287, 164.682, 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 140 16.00 P 144 15.00 Mg 1 11.99 O 6530 8.00 N 5784 7.00 C 20038 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " Number of angles added : 6 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6988 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 54 sheets defined 43.2% alpha, 13.1% beta 57 base pairs and 110 stacking pairs defined. Time for finding SS restraints: 3.50 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.787A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.902A pdb=" N ASP A 114 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A 115 " --> pdb=" O ALA A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 115' Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.700A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.709A pdb=" N LEU B 82 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.869A pdb=" N ALA B 216 " --> pdb=" O ASP B 212 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 232 removed outlier: 3.567A pdb=" N VAL B 232 " --> pdb=" O GLU B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 28 through 39 removed outlier: 3.503A pdb=" N ILE C 39 " --> pdb=" O PHE C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.511A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.610A pdb=" N CYS C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.581A pdb=" N ALA C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 289 through 294' Processing helix chain 'C' and resid 318 through 327 Processing helix chain 'C' and resid 345 through 354 removed outlier: 4.203A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR C 350 " --> pdb=" O TYR C 346 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP C 354 " --> pdb=" O THR C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.996A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.789A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.829A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.387A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.640A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.678A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 removed outlier: 3.716A pdb=" N LEU C 667 " --> pdb=" O VAL C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 688 removed outlier: 3.754A pdb=" N GLN C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 826 Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.905A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 942 through 977 Processing helix chain 'C' and resid 993 through 998 removed outlier: 3.583A pdb=" N ARG C 996 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP C 997 " --> pdb=" O ARG C 994 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 993 through 998' Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.504A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN C1038 " --> pdb=" O ARG C1034 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1084 removed outlier: 3.597A pdb=" N ASP C1084 " --> pdb=" O PRO C1081 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1081 through 1084' Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.415A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.729A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.875A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C1151 " --> pdb=" O ARG C1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 1167 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1242 removed outlier: 3.735A pdb=" N ASP C1241 " --> pdb=" O LEU C1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 Processing helix chain 'C' and resid 1283 through 1293 removed outlier: 4.426A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN C1288 " --> pdb=" O ALA C1284 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1309 Processing helix chain 'C' and resid 1320 through 1333 Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.546A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU D 100 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 163 through 172 Processing helix chain 'D' and resid 180 through 191 Processing helix chain 'D' and resid 194 through 208 Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.593A pdb=" N GLN D 229 " --> pdb=" O GLU D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 removed outlier: 3.693A pdb=" N TRP D 236 " --> pdb=" O LYS D 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 233 through 236' Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 286 removed outlier: 3.566A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.571A pdb=" N LEU D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 removed outlier: 3.514A pdb=" N ALA D 397 " --> pdb=" O THR D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 416 removed outlier: 4.251A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 452 through 458 removed outlier: 4.416A pdb=" N ALA D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.569A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.970A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.595A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 702 Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 769 through 805 removed outlier: 3.706A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP D 802 " --> pdb=" O ARG D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 840 Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 897 through 899 No H-bonds generated for 'chain 'D' and resid 897 through 899' Processing helix chain 'D' and resid 914 through 925 removed outlier: 4.119A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 928 No H-bonds generated for 'chain 'D' and resid 926 through 928' Processing helix chain 'D' and resid 1137 through 1147 removed outlier: 3.677A pdb=" N VAL D1141 " --> pdb=" O GLY D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1225 removed outlier: 3.608A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1245 removed outlier: 3.555A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 Processing helix chain 'D' and resid 1282 through 1293 Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1318 through 1325 removed outlier: 3.588A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1349 through 1354 Processing helix chain 'D' and resid 1360 through 1373 removed outlier: 3.987A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG D1373 " --> pdb=" O ARG D1369 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.884A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 78 removed outlier: 3.722A pdb=" N LEU E 64 " --> pdb=" O ASN E 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.801A pdb=" N MET F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 136 removed outlier: 3.578A pdb=" N GLU F 116 " --> pdb=" O THR F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 3.657A pdb=" N ILE F 141 " --> pdb=" O TYR F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 234 removed outlier: 4.073A pdb=" N THR F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 258 removed outlier: 3.957A pdb=" N GLN F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 292 removed outlier: 3.744A pdb=" N PHE F 266 " --> pdb=" O VAL F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 306 removed outlier: 3.934A pdb=" N LEU F 305 " --> pdb=" O ASN F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 321 Processing helix chain 'F' and resid 324 through 330 Processing helix chain 'F' and resid 333 through 352 removed outlier: 4.107A pdb=" N LYS F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 392 removed outlier: 5.963A pdb=" N ARG F 385 " --> pdb=" O GLU F 381 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU F 386 " --> pdb=" O ALA F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 418 removed outlier: 3.554A pdb=" N LEU F 404 " --> pdb=" O GLN F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 446 removed outlier: 4.085A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 29 Processing helix chain 'P' and resid 39 through 46 removed outlier: 4.366A pdb=" N SER P 46 " --> pdb=" O LYS P 42 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 75 Processing helix chain 'P' and resid 77 through 89 Processing helix chain 'P' and resid 93 through 104 removed outlier: 3.738A pdb=" N VAL P 104 " --> pdb=" O TYR P 100 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 153 removed outlier: 3.527A pdb=" N ARG P 127 " --> pdb=" O LEU P 123 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ARG P 128 " --> pdb=" O ALA P 124 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE P 133 " --> pdb=" O GLU P 129 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU P 134 " --> pdb=" O VAL P 130 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE P 139 " --> pdb=" O ASN P 135 " (cutoff:3.500A) Proline residue: P 143 - end of helix removed outlier: 3.708A pdb=" N LYS P 150 " --> pdb=" O ASP P 146 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 29 removed outlier: 3.897A pdb=" N SER Q 29 " --> pdb=" O ALA Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 45 Processing helix chain 'Q' and resid 61 through 74 Processing helix chain 'Q' and resid 78 through 88 Processing helix chain 'Q' and resid 93 through 104 Processing helix chain 'Q' and resid 122 through 142 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 17 removed outlier: 5.256A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 61 removed outlier: 5.560A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A 142 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 removed outlier: 3.782A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 16 through 18 removed outlier: 3.502A pdb=" N GLU B 17 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 101 removed outlier: 3.585A pdb=" N VAL B 98 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA9, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AB1, first strand: chain 'B' and resid 108 through 111 Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.786A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.786A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 453 Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 158 removed outlier: 3.759A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 227 through 231 Processing sheet with id=AB8, first strand: chain 'C' and resid 239 through 240 Processing sheet with id=AB9, first strand: chain 'C' and resid 255 through 257 removed outlier: 7.219A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.863A pdb=" N TYR C 301 " --> pdb=" O CYS C 311 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.397A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.528A pdb=" N ILE C 616 " --> pdb=" O ARG C 637 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG C 637 " --> pdb=" O ILE C 616 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 718 removed outlier: 6.508A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP C 781 " --> pdb=" O ALA C 718 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 749 through 752 removed outlier: 6.881A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.536A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 5.150A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1066 through 1067 Processing sheet with id=AD1, first strand: chain 'C' and resid 830 through 838 removed outlier: 6.805A pdb=" N ILE C1049 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL C 933 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.791A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1086 through 1087 Processing sheet with id=AD4, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.786A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD6, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 3.584A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS D 345 " --> pdb=" O PHE C1270 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD8, first strand: chain 'D' and resid 34 through 37 removed outlier: 4.374A pdb=" N SER D 34 " --> pdb=" O MET D 102 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N HIS D 104 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLY D 36 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU D 106 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.510A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.298A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 144 through 145 Processing sheet with id=AE1, first strand: chain 'D' and resid 253 through 254 removed outlier: 3.893A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 366 through 369 removed outlier: 6.366A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.561A pdb=" N LEU D 527 " --> pdb=" O LYS D 549 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 552 through 554 removed outlier: 3.628A pdb=" N ILE D 552 " --> pdb=" O SER D 568 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AE6, first strand: chain 'D' and resid 809 through 811 removed outlier: 6.174A pdb=" N VAL D 894 " --> pdb=" O VAL D 809 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU D 811 " --> pdb=" O VAL D 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE8, first strand: chain 'D' and resid 825 through 826 removed outlier: 3.810A pdb=" N GLU D 833 " --> pdb=" O VAL D 825 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 848 through 849 removed outlier: 6.409A pdb=" N VAL D 848 " --> pdb=" O LEU D 857 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 957 through 961 removed outlier: 4.369A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AF3, first strand: chain 'D' and resid 1025 through 1026 Processing sheet with id=AF4, first strand: chain 'D' and resid 1077 through 1081 removed outlier: 4.206A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY D1033 " --> pdb=" O ILE D1115 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 1046 through 1049 removed outlier: 3.531A pdb=" N SER D1058 " --> pdb=" O GLN D1049 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 1162 through 1165 Processing sheet with id=AF7, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.332A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 162 through 165 removed outlier: 6.013A pdb=" N ARG F 260 " --> pdb=" O THR F 163 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 108 through 109 1311 hydrogen bonds defined for protein. 3732 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 138 hydrogen bonds 272 hydrogen bond angles 0 basepair planarities 57 basepair parallelities 110 stacking parallelities Total time for adding SS restraints: 8.08 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7115 1.32 - 1.45: 7632 1.45 - 1.57: 18173 1.57 - 1.69: 285 1.69 - 1.81: 244 Bond restraints: 33449 Sorted by residual: bond pdb=" C SER A 178 " pdb=" N PRO A 179 " ideal model delta sigma weight residual 1.337 1.269 0.068 1.24e-02 6.50e+03 3.02e+01 bond pdb=" N9 DA T 7 " pdb=" C4 DA T 7 " ideal model delta sigma weight residual 1.374 1.344 0.030 6.00e-03 2.78e+04 2.47e+01 bond pdb=" N9 DG N 52 " pdb=" C4 DG N 52 " ideal model delta sigma weight residual 1.375 1.337 0.038 8.00e-03 1.56e+04 2.26e+01 bond pdb=" N9 DA N 57 " pdb=" C4 DA N 57 " ideal model delta sigma weight residual 1.374 1.346 0.028 6.00e-03 2.78e+04 2.17e+01 bond pdb=" N9 DA T 53 " pdb=" C4 DA T 53 " ideal model delta sigma weight residual 1.374 1.346 0.028 6.00e-03 2.78e+04 2.14e+01 ... (remaining 33444 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 43189 2.46 - 4.92: 2270 4.92 - 7.38: 260 7.38 - 9.84: 60 9.84 - 12.29: 7 Bond angle restraints: 45786 Sorted by residual: angle pdb=" N ARG Q 113 " pdb=" CA ARG Q 113 " pdb=" C ARG Q 113 " ideal model delta sigma weight residual 111.36 101.38 9.98 1.09e+00 8.42e-01 8.38e+01 angle pdb=" N ASP D 710 " pdb=" CA ASP D 710 " pdb=" C ASP D 710 " ideal model delta sigma weight residual 113.38 104.26 9.12 1.17e+00 7.31e-01 6.07e+01 angle pdb=" N ILE D1210 " pdb=" CA ILE D1210 " pdb=" C ILE D1210 " ideal model delta sigma weight residual 112.12 106.72 5.40 8.40e-01 1.42e+00 4.14e+01 angle pdb=" N GLY D1171 " pdb=" CA GLY D1171 " pdb=" C GLY D1171 " ideal model delta sigma weight residual 115.08 107.97 7.11 1.19e+00 7.06e-01 3.57e+01 angle pdb=" C THR D 853 " pdb=" N ALA D 854 " pdb=" CA ALA D 854 " ideal model delta sigma weight residual 123.93 115.13 8.80 1.54e+00 4.22e-01 3.27e+01 ... (remaining 45781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.26: 19220 35.26 - 70.51: 918 70.51 - 105.77: 24 105.77 - 141.03: 2 141.03 - 176.28: 2 Dihedral angle restraints: 20166 sinusoidal: 9313 harmonic: 10853 Sorted by residual: dihedral pdb=" C4' A R 7 " pdb=" C3' A R 7 " pdb=" C2' A R 7 " pdb=" C1' A R 7 " ideal model delta sinusoidal sigma weight residual 36.34 -40.34 76.68 1 3.10e+00 1.04e-01 7.69e+02 dihedral pdb=" C4' G R 9 " pdb=" C3' G R 9 " pdb=" C2' G R 9 " pdb=" C1' G R 9 " ideal model delta sinusoidal sigma weight residual 36.34 -38.97 75.31 1 3.10e+00 1.04e-01 7.46e+02 dihedral pdb=" C4' G R 21 " pdb=" C3' G R 21 " pdb=" C2' G R 21 " pdb=" C1' G R 21 " ideal model delta sinusoidal sigma weight residual 36.34 -38.25 74.60 1 3.10e+00 1.04e-01 7.34e+02 ... (remaining 20163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 4084 0.078 - 0.155: 965 0.155 - 0.233: 125 0.233 - 0.311: 21 0.311 - 0.388: 6 Chirality restraints: 5201 Sorted by residual: chirality pdb=" C3' G R 9 " pdb=" C4' G R 9 " pdb=" O3' G R 9 " pdb=" C2' G R 9 " both_signs ideal model delta sigma weight residual False -2.50 -2.89 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" C3' U R 16 " pdb=" C4' U R 16 " pdb=" O3' U R 16 " pdb=" C2' U R 16 " both_signs ideal model delta sigma weight residual False -2.50 -2.12 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CB ILE C 765 " pdb=" CA ILE C 765 " pdb=" CG1 ILE C 765 " pdb=" CG2 ILE C 765 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 5198 not shown) Planarity restraints: 5447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 357 " 0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C ASN C 357 " -0.073 2.00e-02 2.50e+03 pdb=" O ASN C 357 " 0.028 2.00e-02 2.50e+03 pdb=" N ASP C 358 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 43 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C THR D 43 " 0.064 2.00e-02 2.50e+03 pdb=" O THR D 43 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE D 44 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 29 " 0.054 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO B 30 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 30 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 30 " 0.041 5.00e-02 4.00e+02 ... (remaining 5444 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 202 2.47 - 3.08: 22308 3.08 - 3.68: 53379 3.68 - 4.29: 73715 4.29 - 4.90: 115170 Nonbonded interactions: 264774 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 1.858 2.170 nonbonded pdb=" OP1 G R 19 " pdb="MG MG D1501 " model vdw 1.882 2.170 nonbonded pdb=" OD2 ASP D 462 " pdb="MG MG D1501 " model vdw 1.970 2.170 nonbonded pdb=" O GLY D1171 " pdb=" CD LYS D1172 " model vdw 2.014 3.440 nonbonded pdb=" N GLU P 33 " pdb=" OE1 GLU P 33 " model vdw 2.212 3.120 ... (remaining 264769 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 'A' and (resid 8 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 158 or resid 170 through 232)) selection = (chain 'B' and (resid 8 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 232)) } ncs_group { reference = (chain 'P' and (resid 7 through 47 or resid 60 through 144)) selection = chain 'Q' } 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 group one per residue 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 35.260 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 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 : 0.012 0.163 33456 Z= 0.690 Angle : 1.276 43.432 45792 Z= 0.761 Chirality : 0.067 0.388 5201 Planarity : 0.008 0.082 5447 Dihedral : 16.556 176.282 13178 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.67 % Favored : 92.01 % Rotamer: Outliers : 0.90 % Allowed : 6.18 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % 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: -3.99 (0.11), residues: 3741 helix: -2.81 (0.10), residues: 1448 sheet: -2.00 (0.25), residues: 386 loop : -2.65 (0.12), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 312 TYR 0.043 0.004 TYR C1251 PHE 0.032 0.004 PHE C 224 TRP 0.039 0.005 TRP C 183 HIS 0.019 0.003 HIS D1252 Details of bonding type rmsd/Z covalent geometry : bond 0.01169 / 0.69 (33449) covalent geometry : angle 1.25256 / 0.76 (45786) hydrogen bonds : bond 0.18089 / 12.17 ( 1434) hydrogen bonds : angle 9.98308 / 6.86 ( 4004) metal coordination : bond 0.12592 / 6.18 ( 7) metal coordination : angle 21.31159 / 12.91 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 974 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 945 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.6167 (mt) cc_final: 0.5877 (mm) REVERT: A 10 LYS cc_start: 0.8434 (mttp) cc_final: 0.8231 (mmtp) REVERT: A 29 GLU cc_start: 0.7019 (tt0) cc_final: 0.6763 (pm20) REVERT: A 41 ASN cc_start: 0.8731 (t0) cc_final: 0.8485 (t0) REVERT: A 97 GLU cc_start: 0.8034 (pp20) cc_final: 0.7669 (pm20) REVERT: A 206 GLU cc_start: 0.7535 (tp30) cc_final: 0.6554 (tm-30) REVERT: A 212 ASP cc_start: 0.8641 (m-30) cc_final: 0.7931 (p0) REVERT: B 18 GLN cc_start: 0.7531 (pt0) cc_final: 0.7318 (pm20) REVERT: B 59 VAL cc_start: 0.9323 (t) cc_final: 0.8872 (p) REVERT: B 77 ASP cc_start: 0.6194 (m-30) cc_final: 0.5449 (m-30) REVERT: B 79 LEU cc_start: 0.8041 (tp) cc_final: 0.7715 (pp) REVERT: B 81 ILE cc_start: 0.7982 (tt) cc_final: 0.7485 (tt) REVERT: B 205 MET cc_start: 0.7480 (ppp) cc_final: 0.7061 (ppp) REVERT: B 226 GLU cc_start: 0.8443 (mm-30) cc_final: 0.7899 (tt0) REVERT: B 227 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7743 (mm-40) REVERT: C 8 LYS cc_start: 0.8569 (mttt) cc_final: 0.8148 (mttp) REVERT: C 83 GLN cc_start: 0.5719 (pm20) cc_final: 0.5135 (tp40) REVERT: C 84 GLU cc_start: 0.8418 (tt0) cc_final: 0.8086 (tt0) REVERT: C 132 ASP cc_start: 0.8704 (m-30) cc_final: 0.8450 (t0) REVERT: C 214 ASN cc_start: 0.8517 (t0) cc_final: 0.8304 (p0) REVERT: C 256 GLU cc_start: 0.5352 (pt0) cc_final: 0.4931 (tt0) REVERT: C 265 LYS cc_start: 0.1851 (mtmp) cc_final: 0.0738 (tttt) REVERT: C 423 ASP cc_start: 0.6727 (m-30) cc_final: 0.6366 (t0) REVERT: C 549 ASP cc_start: 0.8680 (t0) cc_final: 0.8011 (m-30) REVERT: C 563 THR cc_start: 0.9221 (t) cc_final: 0.8876 (m) REVERT: C 645 PHE cc_start: 0.8218 (m-10) cc_final: 0.7487 (m-10) REVERT: C 694 ARG cc_start: 0.7748 (tpp80) cc_final: 0.6783 (mtm110) REVERT: C 706 ARG cc_start: 0.8092 (mmm-85) cc_final: 0.7026 (mmt180) REVERT: C 741 MET cc_start: 0.8057 (ttp) cc_final: 0.7557 (ttt) REVERT: C 768 MET cc_start: 0.6804 (mtp) cc_final: 0.6237 (mtm) REVERT: C 778 GLU cc_start: 0.7686 (tp30) cc_final: 0.7345 (mm-30) REVERT: C 779 ARG cc_start: 0.7298 (ttt-90) cc_final: 0.7064 (ttp80) REVERT: C 800 MET cc_start: 0.7977 (mtm) cc_final: 0.7748 (mtp) REVERT: C 835 GLU cc_start: 0.8902 (tt0) cc_final: 0.8094 (tm-30) REVERT: C 909 LYS cc_start: 0.8300 (pmmt) cc_final: 0.7664 (tmtt) REVERT: C 937 ASP cc_start: 0.8539 (t0) cc_final: 0.8267 (t0) REVERT: C 949 GLU cc_start: 0.9069 (tt0) cc_final: 0.8467 (mt-10) REVERT: C 1073 LYS cc_start: 0.8587 (mttt) cc_final: 0.8203 (mmtt) REVERT: C 1080 ASN cc_start: 0.8144 (t0) cc_final: 0.7920 (t0) REVERT: C 1089 GLU cc_start: 0.7781 (pp20) cc_final: 0.7426 (pt0) REVERT: C 1107 MET cc_start: 0.7067 (mtm) cc_final: 0.6775 (mtt) REVERT: C 1122 LYS cc_start: 0.8154 (tptp) cc_final: 0.7311 (tptt) REVERT: C 1126 ASP cc_start: 0.8680 (t70) cc_final: 0.8186 (t70) REVERT: C 1207 SER cc_start: 0.9198 (m) cc_final: 0.8869 (t) REVERT: C 1211 ARG cc_start: 0.8095 (ptp-170) cc_final: 0.7530 (ptp-170) REVERT: C 1296 ASP cc_start: 0.8557 (t0) cc_final: 0.7986 (t0) REVERT: C 1322 SER cc_start: 0.8417 (p) cc_final: 0.8117 (t) REVERT: D 155 GLU cc_start: 0.7566 (mm-30) cc_final: 0.6758 (mp0) REVERT: D 160 LEU cc_start: 0.7507 (mt) cc_final: 0.7306 (mt) REVERT: D 180 MET cc_start: 0.7935 (ptm) cc_final: 0.7575 (ttp) REVERT: D 190 LYS cc_start: 0.8661 (ttmt) cc_final: 0.8393 (tppt) REVERT: D 193 ASP cc_start: 0.7443 (t0) cc_final: 0.6687 (p0) REVERT: D 214 ARG cc_start: 0.6475 (ttm-80) cc_final: 0.6265 (mtp180) REVERT: D 308 ASP cc_start: 0.7652 (t0) cc_final: 0.7409 (t0) REVERT: D 314 ARG cc_start: 0.7812 (mtp180) cc_final: 0.7194 (tpp-160) REVERT: D 321 LYS cc_start: 0.7784 (mmpt) cc_final: 0.7202 (mttm) REVERT: D 322 ARG cc_start: 0.6147 (ttp-110) cc_final: 0.5664 (mmm160) REVERT: D 339 ARG cc_start: 0.8292 (mtm110) cc_final: 0.8025 (mtm110) REVERT: D 413 ASP cc_start: 0.8618 (t0) cc_final: 0.8365 (t0) REVERT: D 414 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7605 (tt0) REVERT: D 579 LEU cc_start: 0.7368 (pt) cc_final: 0.7063 (pt) REVERT: D 642 ASP cc_start: 0.8753 (m-30) cc_final: 0.8345 (t70) REVERT: D 660 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7122 (mm-30) REVERT: D 684 ASP cc_start: 0.7895 (m-30) cc_final: 0.7620 (m-30) REVERT: D 723 TYR cc_start: 0.7842 (t80) cc_final: 0.7606 (t80) REVERT: D 805 GLN cc_start: 0.8104 (tp40) cc_final: 0.7859 (tp40) REVERT: D 822 MET cc_start: 0.7911 (mmt) cc_final: 0.6964 (mmm) REVERT: D 853 THR cc_start: 0.6779 (m) cc_final: 0.6381 (p) REVERT: D 860 ARG cc_start: 0.6933 (ptt-90) cc_final: 0.6672 (ptm160) REVERT: D 874 GLU cc_start: 0.8529 (mm-30) cc_final: 0.7939 (pt0) REVERT: D 929 GLN cc_start: 0.7507 (mt0) cc_final: 0.6898 (tm-30) REVERT: D 979 ASN cc_start: 0.7395 (m-40) cc_final: 0.6933 (p0) REVERT: D 1146 GLU cc_start: 0.7970 (tp30) cc_final: 0.7597 (tp30) REVERT: D 1151 LYS cc_start: 0.8507 (tptp) cc_final: 0.7730 (ttmt) REVERT: D 1189 MET cc_start: 0.7013 (mtt) cc_final: 0.6806 (mtm) REVERT: D 1205 GLU cc_start: 0.6227 (tp30) cc_final: 0.5957 (pm20) REVERT: D 1244 GLN cc_start: 0.8354 (mm-40) cc_final: 0.7992 (mm110) REVERT: E 8 ASP cc_start: 0.8389 (m-30) cc_final: 0.7196 (t0) REVERT: E 15 ASN cc_start: 0.7821 (t0) cc_final: 0.7419 (t0) REVERT: E 26 ARG cc_start: 0.8086 (tpt170) cc_final: 0.7028 (tpt-90) REVERT: E 30 MET cc_start: 0.7150 (mtm) cc_final: 0.6888 (mtp) REVERT: E 35 LYS cc_start: 0.7980 (mtmp) cc_final: 0.7596 (ttmt) REVERT: E 53 GLU cc_start: 0.8560 (mt-10) cc_final: 0.7963 (mt-10) REVERT: F 347 ILE cc_start: 0.5917 (mt) cc_final: 0.5709 (mt) REVERT: F 374 ARG cc_start: 0.7100 (mtt90) cc_final: 0.6716 (mtp-110) REVERT: F 379 MET cc_start: 0.7570 (tpp) cc_final: 0.7186 (tpt) REVERT: F 405 ILE cc_start: 0.8439 (pt) cc_final: 0.8236 (pt) REVERT: P 44 MET cc_start: 0.6697 (tpt) cc_final: 0.6195 (ttp) REVERT: P 45 GLU cc_start: 0.6521 (pp20) cc_final: 0.6083 (mt-10) REVERT: P 48 GLU cc_start: 0.6279 (tp30) cc_final: 0.5587 (tm-30) REVERT: P 53 MET cc_start: 0.2573 (mmm) cc_final: 0.1973 (tpt) REVERT: P 129 GLU cc_start: 0.8638 (mt-10) cc_final: 0.7961 (tp30) REVERT: Q 16 LEU cc_start: 0.8672 (tp) cc_final: 0.8407 (tt) REVERT: Q 19 TRP cc_start: 0.3422 (m100) cc_final: 0.2919 (m100) REVERT: Q 23 TRP cc_start: 0.7463 (t60) cc_final: 0.7162 (t60) REVERT: Q 60 ASP cc_start: 0.6524 (m-30) cc_final: 0.6077 (m-30) REVERT: Q 75 TYR cc_start: 0.6714 (t80) cc_final: 0.6417 (t80) outliers start: 29 outliers final: 4 residues processed: 965 average time/residue: 0.2476 time to fit residues: 367.6083 Evaluate side-chains 502 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 498 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 HIS B 117 HIS ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS C 767 GLN C 808 ASN C 824 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1268 GLN C1313 HIS D 45 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 ASN D 320 ASN D 365 GLN D 489 ASN ** D 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 GLN D1295 ASN E 15 ASN P 68 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.153528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.124477 restraints weight = 61359.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.124347 restraints weight = 68727.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.124716 restraints weight = 64198.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.124776 restraints weight = 43781.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.125087 restraints weight = 39042.473| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 33456 Z= 0.196 Angle : 0.822 14.687 45792 Z= 0.431 Chirality : 0.053 0.963 5201 Planarity : 0.006 0.072 5447 Dihedral : 19.674 164.511 5756 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.96 % Favored : 93.96 % Rotamer: Outliers : 0.22 % Allowed : 4.07 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.80 (0.12), residues: 3741 helix: -1.31 (0.12), residues: 1494 sheet: -1.75 (0.24), residues: 396 loop : -2.34 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 994 TYR 0.029 0.002 TYR P 142 PHE 0.026 0.002 PHE C1187 TRP 0.018 0.002 TRP D 409 HIS 0.008 0.001 HIS Q 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.20 (33449) covalent geometry : angle 0.82068 / 0.43 (45786) hydrogen bonds : bond 0.06120 / 4.22 ( 1434) hydrogen bonds : angle 6.51560 / 4.47 ( 4004) metal coordination : bond 0.01170 / 0.60 ( 7) metal coordination : angle 4.67655 / 3.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 706 time to evaluate : 1.026 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: A 120 ASP cc_start: 0.8970 (p0) cc_final: 0.8560 (p0) REVERT: A 131 CYS cc_start: 0.7691 (p) cc_final: 0.7020 (p) REVERT: B 79 LEU cc_start: 0.8490 (tp) cc_final: 0.8172 (pp) REVERT: B 110 VAL cc_start: 0.8648 (t) cc_final: 0.8244 (t) REVERT: C 34 SER cc_start: 0.8555 (t) cc_final: 0.8238 (m) REVERT: C 363 LEU cc_start: 0.8987 (mt) cc_final: 0.8707 (mp) REVERT: C 515 MET cc_start: 0.8336 (ttp) cc_final: 0.7848 (ttm) REVERT: C 741 MET cc_start: 0.8233 (ttp) cc_final: 0.7996 (ttt) REVERT: C 972 PHE cc_start: 0.5383 (m-80) cc_final: 0.4874 (m-80) REVERT: C 1018 TYR cc_start: 0.6282 (t80) cc_final: 0.6062 (t80) REVERT: C 1078 LYS cc_start: 0.9308 (tttt) cc_final: 0.8919 (tttp) REVERT: C 1126 ASP cc_start: 0.7694 (t70) cc_final: 0.7006 (t70) REVERT: C 1291 LEU cc_start: 0.8380 (tp) cc_final: 0.7984 (tp) REVERT: C 1322 SER cc_start: 0.9191 (p) cc_final: 0.8420 (t) REVERT: C 1329 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8215 (tm-30) REVERT: D 29 MET cc_start: 0.8091 (tpp) cc_final: 0.7659 (tpp) REVERT: D 154 LEU cc_start: 0.7506 (tt) cc_final: 0.7208 (pp) REVERT: D 260 PHE cc_start: 0.7612 (m-80) cc_final: 0.7346 (m-80) REVERT: D 321 LYS cc_start: 0.8063 (mmpt) cc_final: 0.7800 (mttp) REVERT: D 349 TYR cc_start: 0.8905 (m-80) cc_final: 0.8616 (m-80) REVERT: D 412 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8662 (tt) REVERT: D 1040 MET cc_start: 0.2486 (OUTLIER) cc_final: -0.1303 (tpp) REVERT: D 1151 LYS cc_start: 0.8459 (tptp) cc_final: 0.8047 (ttmt) REVERT: D 1370 MET cc_start: 0.6851 (tpp) cc_final: 0.6303 (tpp) REVERT: E 8 ASP cc_start: 0.8348 (m-30) cc_final: 0.7657 (t0) REVERT: E 15 ASN cc_start: 0.8114 (t0) cc_final: 0.7823 (t0) REVERT: E 26 ARG cc_start: 0.8859 (tpt170) cc_final: 0.8037 (tpt-90) REVERT: E 30 MET cc_start: 0.8279 (mtm) cc_final: 0.7891 (mtp) REVERT: E 41 GLU cc_start: 0.7253 (pm20) cc_final: 0.6666 (pt0) REVERT: F 141 ILE cc_start: 0.8332 (mm) cc_final: 0.8038 (tt) REVERT: F 335 GLU cc_start: 0.2692 (tm-30) cc_final: 0.2440 (mp0) REVERT: F 365 MET cc_start: 0.7617 (ttp) cc_final: 0.6954 (tmm) REVERT: F 366 SER cc_start: 0.8402 (m) cc_final: 0.8177 (p) REVERT: F 405 ILE cc_start: 0.8489 (pt) cc_final: 0.8042 (pt) REVERT: P 36 MET cc_start: 0.5559 (ttp) cc_final: 0.4956 (ttp) REVERT: P 48 GLU cc_start: 0.5846 (tp30) cc_final: 0.5632 (tm-30) REVERT: P 53 MET cc_start: 0.1797 (mmm) cc_final: 0.1508 (tpt) REVERT: P 57 MET cc_start: 0.7854 (pmm) cc_final: 0.7317 (pmm) REVERT: P 69 VAL cc_start: 0.8454 (t) cc_final: 0.8006 (p) REVERT: P 106 ARG cc_start: 0.6388 (mtp180) cc_final: 0.5763 (ttm170) REVERT: P 129 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7144 (tp30) REVERT: P 142 TYR cc_start: 0.8051 (t80) cc_final: 0.7822 (t80) REVERT: Q 16 LEU cc_start: 0.7972 (tp) cc_final: 0.7566 (tt) REVERT: Q 130 VAL cc_start: 0.8602 (t) cc_final: 0.8213 (t) outliers start: 7 outliers final: 0 residues processed: 710 average time/residue: 0.2168 time to fit residues: 245.4509 Evaluate side-chains 450 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 448 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 336 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 120 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 306 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 146 optimal weight: 3.9990 chunk 260 optimal weight: 0.6980 chunk 93 optimal weight: 6.9990 chunk 341 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 HIS B 23 HIS ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 ASN C 490 GLN C 808 ASN D 157 GLN D 196 GLN D 365 GLN D 488 ASN ** D 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 GLN D 817 HIS D1197 ASN D1279 GLN F 147 GLN P 13 HIS P 68 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.147314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.117248 restraints weight = 61301.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.115904 restraints weight = 80851.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.116983 restraints weight = 71782.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.117506 restraints weight = 47555.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117688 restraints weight = 43589.550| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 33456 Z= 0.266 Angle : 0.830 12.296 45792 Z= 0.437 Chirality : 0.052 0.445 5201 Planarity : 0.006 0.065 5447 Dihedral : 19.237 162.896 5756 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.95 % Favored : 93.00 % Rotamer: Outliers : 0.12 % Allowed : 5.25 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.30 (0.13), residues: 3741 helix: -0.67 (0.13), residues: 1481 sheet: -1.64 (0.23), residues: 420 loop : -2.23 (0.13), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 52 TYR 0.021 0.002 TYR C1231 PHE 0.031 0.002 PHE D 49 TRP 0.018 0.002 TRP P 15 HIS 0.009 0.002 HIS Q 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.27 (33449) covalent geometry : angle 0.82878 / 0.44 (45786) hydrogen bonds : bond 0.06008 / 4.13 ( 1434) hydrogen bonds : angle 5.87859 / 4.06 ( 4004) metal coordination : bond 0.01393 / 0.86 ( 7) metal coordination : angle 4.43824 / 2.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 567 time to evaluate : 1.315 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: A 120 ASP cc_start: 0.9034 (p0) cc_final: 0.8637 (p0) REVERT: A 131 CYS cc_start: 0.7670 (p) cc_final: 0.7198 (p) REVERT: B 79 LEU cc_start: 0.8567 (tp) cc_final: 0.8365 (pp) REVERT: B 81 ILE cc_start: 0.7617 (tt) cc_final: 0.7408 (tt) REVERT: C 563 THR cc_start: 0.9222 (t) cc_final: 0.8919 (m) REVERT: C 813 GLU cc_start: 0.7611 (tp30) cc_final: 0.7308 (tt0) REVERT: C 881 ASP cc_start: 0.7652 (t70) cc_final: 0.7365 (t70) REVERT: C 900 LYS cc_start: 0.7837 (tptm) cc_final: 0.7166 (tmtt) REVERT: C 1126 ASP cc_start: 0.7584 (t70) cc_final: 0.6946 (t70) REVERT: C 1194 GLU cc_start: 0.6938 (mp0) cc_final: 0.6714 (mp0) REVERT: C 1244 HIS cc_start: 0.8281 (t70) cc_final: 0.7993 (t70) REVERT: C 1273 MET cc_start: 0.8309 (mtp) cc_final: 0.7747 (mtp) REVERT: C 1322 SER cc_start: 0.9277 (p) cc_final: 0.8766 (t) REVERT: C 1329 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8263 (tm-30) REVERT: D 29 MET cc_start: 0.8083 (tpp) cc_final: 0.7563 (tpp) REVERT: D 154 LEU cc_start: 0.7472 (tt) cc_final: 0.7141 (pp) REVERT: D 193 ASP cc_start: 0.7700 (t0) cc_final: 0.7143 (p0) REVERT: D 196 GLN cc_start: 0.6859 (mt0) cc_final: 0.6376 (mt0) REVERT: D 245 LEU cc_start: 0.9575 (tp) cc_final: 0.9348 (mt) REVERT: D 260 PHE cc_start: 0.8049 (m-80) cc_final: 0.7736 (m-80) REVERT: D 321 LYS cc_start: 0.8127 (mmpt) cc_final: 0.7809 (mttp) REVERT: D 995 TYR cc_start: 0.5527 (m-80) cc_final: 0.5157 (m-80) REVERT: D 1151 LYS cc_start: 0.8544 (tptp) cc_final: 0.8094 (mtmt) REVERT: D 1212 ASP cc_start: 0.8500 (p0) cc_final: 0.8293 (p0) REVERT: D 1370 MET cc_start: 0.7061 (tpp) cc_final: 0.6716 (tpp) REVERT: E 8 ASP cc_start: 0.8425 (m-30) cc_final: 0.7813 (t0) REVERT: E 26 ARG cc_start: 0.8675 (tpt170) cc_final: 0.8216 (tpt-90) REVERT: E 67 ARG cc_start: 0.7825 (ttm170) cc_final: 0.7428 (ttm110) REVERT: E 68 GLU cc_start: 0.7893 (pt0) cc_final: 0.7160 (tp30) REVERT: F 141 ILE cc_start: 0.8120 (mm) cc_final: 0.7854 (tt) REVERT: F 365 MET cc_start: 0.7594 (ttp) cc_final: 0.6929 (tmm) REVERT: F 405 ILE cc_start: 0.8630 (pt) cc_final: 0.8332 (pt) REVERT: P 21 GLU cc_start: 0.6860 (pp20) cc_final: 0.6579 (pp20) REVERT: P 57 MET cc_start: 0.8106 (pmm) cc_final: 0.7621 (pmm) REVERT: P 68 GLN cc_start: 0.9234 (mt0) cc_final: 0.8974 (mt0) REVERT: P 69 VAL cc_start: 0.8658 (t) cc_final: 0.8137 (p) REVERT: P 106 ARG cc_start: 0.6465 (mtp180) cc_final: 0.6066 (ttt90) REVERT: P 120 LYS cc_start: 0.6522 (mptt) cc_final: 0.6108 (mmtt) REVERT: P 129 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7141 (tp30) REVERT: Q 62 ASP cc_start: 0.3855 (t0) cc_final: 0.3338 (t70) REVERT: Q 70 VAL cc_start: 0.7657 (t) cc_final: 0.7197 (p) outliers start: 4 outliers final: 0 residues processed: 570 average time/residue: 0.2105 time to fit residues: 196.7150 Evaluate side-chains 415 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 114 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 210 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 94 optimal weight: 0.6980 chunk 197 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 224 optimal weight: 0.0980 chunk 45 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN C 150 HIS ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN C 618 GLN D 805 GLN D 910 ASN D1197 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.150377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.119347 restraints weight = 61301.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.118631 restraints weight = 71853.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.119817 restraints weight = 59611.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.120188 restraints weight = 41309.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.120318 restraints weight = 39140.692| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 33456 Z= 0.160 Angle : 0.715 10.075 45792 Z= 0.376 Chirality : 0.048 0.344 5201 Planarity : 0.005 0.076 5447 Dihedral : 19.024 163.429 5756 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.91 % Favored : 94.04 % Rotamer: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.93 (0.13), residues: 3741 helix: -0.30 (0.13), residues: 1491 sheet: -1.48 (0.23), residues: 429 loop : -2.07 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1058 TYR 0.019 0.001 TYR Q 142 PHE 0.022 0.001 PHE D 49 TRP 0.077 0.003 TRP Q 15 HIS 0.006 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (33449) covalent geometry : angle 0.71190 / 0.38 (45786) hydrogen bonds : bond 0.05188 / 3.55 ( 1434) hydrogen bonds : angle 5.50465 / 3.78 ( 4004) metal coordination : bond 0.01001 / 0.45 ( 7) metal coordination : angle 5.82229 / 3.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 573 time to evaluate : 1.265 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: A 57 THR cc_start: 0.8357 (m) cc_final: 0.8136 (m) REVERT: A 120 ASP cc_start: 0.8988 (p0) cc_final: 0.8391 (p0) REVERT: B 75 GLN cc_start: 0.5458 (mp-120) cc_final: 0.4670 (mp10) REVERT: B 79 LEU cc_start: 0.8599 (tp) cc_final: 0.8209 (tt) REVERT: B 199 ASP cc_start: 0.7787 (m-30) cc_final: 0.7464 (m-30) REVERT: C 488 MET cc_start: 0.6565 (ptp) cc_final: 0.6311 (ptt) REVERT: C 704 MET cc_start: 0.8901 (mmp) cc_final: 0.8660 (tpp) REVERT: C 862 LEU cc_start: 0.7777 (mm) cc_final: 0.7269 (pp) REVERT: C 900 LYS cc_start: 0.8332 (tptt) cc_final: 0.7723 (tptp) REVERT: C 1126 ASP cc_start: 0.7502 (t70) cc_final: 0.6898 (t70) REVERT: C 1194 GLU cc_start: 0.6970 (mp0) cc_final: 0.6750 (mp0) REVERT: C 1244 HIS cc_start: 0.8219 (t70) cc_final: 0.8000 (t70) REVERT: C 1329 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8083 (tm-30) REVERT: D 193 ASP cc_start: 0.7722 (t0) cc_final: 0.6992 (p0) REVERT: D 196 GLN cc_start: 0.6748 (mt0) cc_final: 0.6093 (mt0) REVERT: D 197 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7525 (mm-30) REVERT: D 245 LEU cc_start: 0.9558 (tp) cc_final: 0.9285 (mt) REVERT: D 260 PHE cc_start: 0.7924 (m-80) cc_final: 0.7594 (m-80) REVERT: D 321 LYS cc_start: 0.8138 (mmpt) cc_final: 0.7783 (mttm) REVERT: D 349 TYR cc_start: 0.8811 (m-80) cc_final: 0.8585 (m-80) REVERT: D 822 MET cc_start: 0.8599 (mmt) cc_final: 0.7763 (mmm) REVERT: D 995 TYR cc_start: 0.5415 (m-80) cc_final: 0.4992 (m-80) REVERT: D 1095 MET cc_start: 0.1820 (ttp) cc_final: 0.1296 (ttp) REVERT: D 1151 LYS cc_start: 0.8477 (tptp) cc_final: 0.8027 (mtmt) REVERT: D 1370 MET cc_start: 0.6912 (tpp) cc_final: 0.6426 (tpp) REVERT: E 8 ASP cc_start: 0.8389 (m-30) cc_final: 0.7767 (t0) REVERT: E 68 GLU cc_start: 0.7920 (pt0) cc_final: 0.7235 (tp30) REVERT: F 141 ILE cc_start: 0.8052 (mm) cc_final: 0.7812 (tt) REVERT: F 322 MET cc_start: 0.1039 (mtt) cc_final: 0.0721 (mtt) REVERT: F 365 MET cc_start: 0.7716 (ttp) cc_final: 0.6836 (tmm) REVERT: P 21 GLU cc_start: 0.6722 (pp20) cc_final: 0.6455 (pp20) REVERT: P 53 MET cc_start: 0.3206 (mmm) cc_final: 0.0891 (tpt) REVERT: P 57 MET cc_start: 0.8046 (pmm) cc_final: 0.7602 (pmm) REVERT: P 68 GLN cc_start: 0.9225 (mt0) cc_final: 0.8930 (mt0) REVERT: P 69 VAL cc_start: 0.8666 (t) cc_final: 0.8150 (p) REVERT: P 106 ARG cc_start: 0.6720 (mtp180) cc_final: 0.6171 (ttt90) REVERT: P 120 LYS cc_start: 0.6519 (mptt) cc_final: 0.6045 (mmtt) REVERT: P 129 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7243 (tp30) REVERT: P 142 TYR cc_start: 0.8140 (t80) cc_final: 0.7758 (t80) outliers start: 2 outliers final: 2 residues processed: 574 average time/residue: 0.2173 time to fit residues: 203.8753 Evaluate side-chains 419 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 417 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 205 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 191 optimal weight: 20.0000 chunk 3 optimal weight: 0.9980 chunk 134 optimal weight: 0.5980 chunk 339 optimal weight: 0.9980 chunk 46 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.0139 > 50:) chunk 333 optimal weight: 30.0000 chunk 11 optimal weight: 9.9990 chunk 291 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN D 805 GLN D1197 ASN F 383 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.150604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.119023 restraints weight = 61387.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.118413 restraints weight = 68184.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.120109 restraints weight = 56946.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.119853 restraints weight = 39960.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.120187 restraints weight = 38064.062| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 33456 Z= 0.154 Angle : 0.683 10.318 45792 Z= 0.359 Chirality : 0.047 0.316 5201 Planarity : 0.005 0.065 5447 Dihedral : 18.846 164.051 5756 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.77 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.67 (0.13), residues: 3741 helix: -0.03 (0.13), residues: 1506 sheet: -1.28 (0.24), residues: 418 loop : -2.01 (0.14), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 744 TYR 0.018 0.001 TYR Q 100 PHE 0.021 0.001 PHE D 49 TRP 0.039 0.001 TRP Q 15 HIS 0.005 0.001 HIS C 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (33449) covalent geometry : angle 0.68169 / 0.36 (45786) hydrogen bonds : bond 0.04915 / 3.38 ( 1434) hydrogen bonds : angle 5.24283 / 3.61 ( 4004) metal coordination : bond 0.00650 / 0.30 ( 7) metal coordination : angle 4.28136 / 2.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 547 time to evaluate : 1.217 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: A 19 VAL cc_start: 0.6985 (p) cc_final: 0.6782 (p) REVERT: A 120 ASP cc_start: 0.8921 (p0) cc_final: 0.8332 (p0) REVERT: B 75 GLN cc_start: 0.5746 (mp-120) cc_final: 0.5432 (mp10) REVERT: B 77 ASP cc_start: 0.6364 (p0) cc_final: 0.5637 (p0) REVERT: B 79 LEU cc_start: 0.8563 (tp) cc_final: 0.8259 (pp) REVERT: B 80 GLU cc_start: 0.6946 (tp30) cc_final: 0.6506 (tp30) REVERT: B 199 ASP cc_start: 0.7836 (m-30) cc_final: 0.7530 (m-30) REVERT: C 34 SER cc_start: 0.8640 (t) cc_final: 0.8367 (t) REVERT: C 653 MET cc_start: 0.7275 (tpp) cc_final: 0.6965 (ttm) REVERT: C 862 LEU cc_start: 0.7783 (mm) cc_final: 0.7342 (pp) REVERT: C 900 LYS cc_start: 0.7962 (tptt) cc_final: 0.7512 (tptp) REVERT: C 939 VAL cc_start: 0.8141 (t) cc_final: 0.7890 (p) REVERT: C 1126 ASP cc_start: 0.7476 (t70) cc_final: 0.6898 (t70) REVERT: C 1244 HIS cc_start: 0.8182 (t70) cc_final: 0.7936 (t70) REVERT: D 91 GLU cc_start: 0.8571 (tp30) cc_final: 0.8042 (tp30) REVERT: D 193 ASP cc_start: 0.7747 (t0) cc_final: 0.6963 (p0) REVERT: D 196 GLN cc_start: 0.6835 (mt0) cc_final: 0.6452 (mt0) REVERT: D 197 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7552 (mm-30) REVERT: D 260 PHE cc_start: 0.8031 (m-80) cc_final: 0.7694 (m-80) REVERT: D 321 LYS cc_start: 0.8109 (mmpt) cc_final: 0.7771 (mttm) REVERT: D 349 TYR cc_start: 0.8827 (m-80) cc_final: 0.8605 (m-80) REVERT: D 458 ASN cc_start: 0.9049 (t0) cc_final: 0.8832 (t0) REVERT: D 506 VAL cc_start: 0.9014 (m) cc_final: 0.8638 (p) REVERT: D 995 TYR cc_start: 0.5496 (m-80) cc_final: 0.5053 (m-80) REVERT: D 1095 MET cc_start: 0.1547 (ttp) cc_final: 0.0937 (ttp) REVERT: D 1151 LYS cc_start: 0.8474 (tptp) cc_final: 0.8100 (mtmt) REVERT: D 1189 MET cc_start: 0.7198 (mtm) cc_final: 0.6806 (ptt) REVERT: D 1370 MET cc_start: 0.6818 (tpp) cc_final: 0.6418 (tpp) REVERT: E 8 ASP cc_start: 0.8130 (m-30) cc_final: 0.7607 (t0) REVERT: E 30 MET cc_start: 0.7281 (mtt) cc_final: 0.7056 (mtt) REVERT: E 53 GLU cc_start: 0.6728 (mt-10) cc_final: 0.6280 (mt-10) REVERT: E 56 GLU cc_start: 0.7449 (mp0) cc_final: 0.6858 (mp0) REVERT: E 67 ARG cc_start: 0.7717 (ttm-80) cc_final: 0.7454 (ttm110) REVERT: E 68 GLU cc_start: 0.7926 (pt0) cc_final: 0.7235 (tp30) REVERT: F 322 MET cc_start: 0.0947 (mtt) cc_final: 0.0703 (mtt) REVERT: F 365 MET cc_start: 0.7495 (ttp) cc_final: 0.6908 (tmm) REVERT: P 53 MET cc_start: 0.3497 (mmm) cc_final: 0.1082 (tpt) REVERT: P 54 THR cc_start: 0.6130 (t) cc_final: 0.5880 (t) REVERT: P 57 MET cc_start: 0.8110 (pmm) cc_final: 0.7635 (pmm) REVERT: P 69 VAL cc_start: 0.8632 (t) cc_final: 0.8162 (p) REVERT: P 120 LYS cc_start: 0.6543 (mptt) cc_final: 0.6061 (mmtt) REVERT: P 129 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7189 (tp30) outliers start: 0 outliers final: 0 residues processed: 547 average time/residue: 0.1928 time to fit residues: 174.4542 Evaluate side-chains 398 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 398 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 363 optimal weight: 9.9990 chunk 274 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 293 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 339 optimal weight: 6.9990 chunk 219 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 GLN D 907 HIS D1197 ASN F 227 GLN Q 90 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.145661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.114384 restraints weight = 61327.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.113519 restraints weight = 72384.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.114968 restraints weight = 64290.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.114774 restraints weight = 45521.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.115667 restraints weight = 39767.298| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 33456 Z= 0.261 Angle : 0.795 11.784 45792 Z= 0.414 Chirality : 0.050 0.318 5201 Planarity : 0.006 0.069 5447 Dihedral : 18.777 163.932 5756 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.75 % Favored : 92.19 % Rotamer: Outliers : 0.03 % Allowed : 3.08 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.80 (0.13), residues: 3741 helix: -0.07 (0.13), residues: 1505 sheet: -1.43 (0.24), residues: 440 loop : -2.14 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1058 TYR 0.022 0.002 TYR C1231 PHE 0.031 0.002 PHE F 221 TRP 0.034 0.002 TRP Q 15 HIS 0.012 0.002 HIS C 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.26 (33449) covalent geometry : angle 0.79213 / 0.41 (45786) hydrogen bonds : bond 0.05532 / 3.82 ( 1434) hydrogen bonds : angle 5.37820 / 3.71 ( 4004) metal coordination : bond 0.01574 / 0.74 ( 7) metal coordination : angle 5.57956 / 3.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 530 time to evaluate : 1.159 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: A 120 ASP cc_start: 0.8957 (p0) cc_final: 0.8454 (p0) REVERT: A 199 ASP cc_start: 0.7780 (m-30) cc_final: 0.6985 (m-30) REVERT: B 75 GLN cc_start: 0.5645 (mp-120) cc_final: 0.4858 (mp10) REVERT: B 79 LEU cc_start: 0.8664 (tp) cc_final: 0.8403 (tt) REVERT: B 80 GLU cc_start: 0.6931 (tp30) cc_final: 0.6344 (tp30) REVERT: C 337 PHE cc_start: 0.5921 (t80) cc_final: 0.5692 (t80) REVERT: C 549 ASP cc_start: 0.8130 (m-30) cc_final: 0.7907 (m-30) REVERT: C 811 ASN cc_start: 0.9081 (p0) cc_final: 0.8709 (p0) REVERT: C 900 LYS cc_start: 0.8015 (tptt) cc_final: 0.7813 (tptp) REVERT: C 1080 ASN cc_start: 0.8885 (t0) cc_final: 0.8575 (t0) REVERT: C 1126 ASP cc_start: 0.7510 (t70) cc_final: 0.6888 (t70) REVERT: C 1244 HIS cc_start: 0.8251 (t70) cc_final: 0.7876 (t70) REVERT: C 1291 LEU cc_start: 0.8419 (tp) cc_final: 0.8198 (tp) REVERT: C 1329 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8180 (tm-30) REVERT: D 193 ASP cc_start: 0.7826 (t0) cc_final: 0.7162 (p0) REVERT: D 196 GLN cc_start: 0.7179 (mt0) cc_final: 0.6609 (mt0) REVERT: D 197 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7490 (mm-30) REVERT: D 321 LYS cc_start: 0.8334 (mmpt) cc_final: 0.7872 (mttm) REVERT: D 634 ARG cc_start: 0.7653 (ttm-80) cc_final: 0.7359 (ttm-80) REVERT: D 805 GLN cc_start: 0.8579 (tp40) cc_final: 0.8336 (tp40) REVERT: D 907 HIS cc_start: 0.7937 (p-80) cc_final: 0.7714 (p90) REVERT: D 995 TYR cc_start: 0.5800 (m-80) cc_final: 0.5552 (m-80) REVERT: D 1095 MET cc_start: 0.1852 (ttp) cc_final: 0.1338 (ttp) REVERT: D 1151 LYS cc_start: 0.8503 (tptp) cc_final: 0.8120 (ttmt) REVERT: E 8 ASP cc_start: 0.8250 (m-30) cc_final: 0.7562 (t0) REVERT: E 10 VAL cc_start: 0.8821 (t) cc_final: 0.8449 (p) REVERT: E 30 MET cc_start: 0.7506 (mtt) cc_final: 0.7252 (mtt) REVERT: E 56 GLU cc_start: 0.7507 (mp0) cc_final: 0.7187 (mp0) REVERT: E 67 ARG cc_start: 0.7725 (ttm-80) cc_final: 0.7462 (ttm110) REVERT: E 68 GLU cc_start: 0.8000 (pt0) cc_final: 0.7400 (tp30) REVERT: F 322 MET cc_start: 0.1333 (mtt) cc_final: 0.1061 (mtt) REVERT: F 365 MET cc_start: 0.7883 (ttp) cc_final: 0.7035 (tmm) REVERT: P 53 MET cc_start: 0.4037 (mmm) cc_final: 0.1611 (tpp) REVERT: P 57 MET cc_start: 0.8085 (pmm) cc_final: 0.7697 (pmm) REVERT: P 68 GLN cc_start: 0.9097 (mt0) cc_final: 0.8780 (mt0) REVERT: P 69 VAL cc_start: 0.8779 (t) cc_final: 0.8329 (p) REVERT: P 129 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7131 (tp30) REVERT: Q 19 TRP cc_start: 0.2107 (m-10) cc_final: 0.1792 (m-10) REVERT: Q 128 ARG cc_start: 0.8565 (mtt180) cc_final: 0.8352 (mtt180) outliers start: 1 outliers final: 1 residues processed: 531 average time/residue: 0.1979 time to fit residues: 173.3903 Evaluate side-chains 404 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 403 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 17 optimal weight: 5.9990 chunk 294 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 277 optimal weight: 30.0000 chunk 325 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 178 optimal weight: 4.9990 chunk 290 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 chunk 141 optimal weight: 20.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 314 ASN C 573 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 HIS D1197 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.147073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.115893 restraints weight = 60630.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.114701 restraints weight = 67714.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.116329 restraints weight = 61821.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.116066 restraints weight = 43084.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.116608 restraints weight = 40042.511| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 33456 Z= 0.194 Angle : 0.730 10.342 45792 Z= 0.381 Chirality : 0.048 0.320 5201 Planarity : 0.005 0.068 5447 Dihedral : 18.657 165.642 5756 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.66 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.61 (0.13), residues: 3741 helix: 0.12 (0.13), residues: 1498 sheet: -1.29 (0.24), residues: 423 loop : -2.08 (0.13), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 542 TYR 0.020 0.002 TYR C1018 PHE 0.016 0.002 PHE A 35 TRP 0.024 0.002 TRP Q 15 HIS 0.006 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (33449) covalent geometry : angle 0.72806 / 0.38 (45786) hydrogen bonds : bond 0.05102 / 3.52 ( 1434) hydrogen bonds : angle 5.19399 / 3.59 ( 4004) metal coordination : bond 0.01100 / 0.54 ( 7) metal coordination : angle 4.90650 / 2.92 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 525 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8987 (p0) cc_final: 0.8401 (p0) REVERT: B 75 GLN cc_start: 0.5599 (mp-120) cc_final: 0.4831 (mp10) REVERT: B 80 GLU cc_start: 0.6927 (tp30) cc_final: 0.6174 (tp30) REVERT: C 546 GLU cc_start: 0.6690 (pm20) cc_final: 0.6483 (tp30) REVERT: C 704 MET cc_start: 0.8981 (mmp) cc_final: 0.8723 (mmp) REVERT: C 811 ASN cc_start: 0.9068 (p0) cc_final: 0.8720 (p0) REVERT: C 881 ASP cc_start: 0.7791 (t70) cc_final: 0.7542 (t70) REVERT: C 930 ASP cc_start: 0.8420 (t0) cc_final: 0.8104 (m-30) REVERT: C 972 PHE cc_start: 0.7155 (m-10) cc_final: 0.6813 (m-80) REVERT: C 1080 ASN cc_start: 0.8834 (t0) cc_final: 0.8504 (t0) REVERT: C 1126 ASP cc_start: 0.7373 (t70) cc_final: 0.6797 (t70) REVERT: C 1194 GLU cc_start: 0.6851 (mp0) cc_final: 0.6644 (mt-10) REVERT: C 1244 HIS cc_start: 0.8244 (t70) cc_final: 0.7878 (t70) REVERT: C 1329 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8089 (tm-30) REVERT: D 193 ASP cc_start: 0.7812 (t0) cc_final: 0.7339 (p0) REVERT: D 196 GLN cc_start: 0.7107 (mt0) cc_final: 0.6498 (mt0) REVERT: D 321 LYS cc_start: 0.7947 (mmpt) cc_final: 0.7497 (mttm) REVERT: D 458 ASN cc_start: 0.9096 (t0) cc_final: 0.8891 (t0) REVERT: D 506 VAL cc_start: 0.9053 (m) cc_final: 0.8704 (p) REVERT: D 594 GLN cc_start: 0.7685 (pm20) cc_final: 0.7357 (pm20) REVERT: D 634 ARG cc_start: 0.7565 (ttm-80) cc_final: 0.7359 (ttm-80) REVERT: D 768 ASN cc_start: 0.7135 (p0) cc_final: 0.6856 (p0) REVERT: D 995 TYR cc_start: 0.6067 (m-80) cc_final: 0.5363 (m-80) REVERT: D 1040 MET cc_start: 0.1312 (ppp) cc_final: 0.0303 (ttm) REVERT: D 1151 LYS cc_start: 0.8517 (tptp) cc_final: 0.8100 (mtmt) REVERT: E 10 VAL cc_start: 0.8852 (t) cc_final: 0.8504 (p) REVERT: E 30 MET cc_start: 0.7585 (mtt) cc_final: 0.7266 (mtt) REVERT: E 67 ARG cc_start: 0.7732 (ttm-80) cc_final: 0.7180 (ttm110) REVERT: E 68 GLU cc_start: 0.7828 (pt0) cc_final: 0.7447 (tp30) REVERT: F 276 MET cc_start: 0.5575 (mmm) cc_final: 0.4975 (tpp) REVERT: F 322 MET cc_start: 0.1047 (mtt) cc_final: 0.0843 (mtt) REVERT: F 365 MET cc_start: 0.7853 (ttp) cc_final: 0.7018 (tmm) REVERT: P 36 MET cc_start: 0.5861 (ttt) cc_final: 0.4478 (tpp) REVERT: P 53 MET cc_start: 0.4183 (mmm) cc_final: 0.1657 (tpt) REVERT: P 57 MET cc_start: 0.8077 (pmm) cc_final: 0.7757 (pmm) REVERT: P 69 VAL cc_start: 0.8815 (t) cc_final: 0.8316 (p) outliers start: 0 outliers final: 0 residues processed: 525 average time/residue: 0.1989 time to fit residues: 172.8731 Evaluate side-chains 402 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 227 optimal weight: 8.9990 chunk 190 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 323 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 290 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 929 GLN D1197 ASN Q 90 HIS ** Q 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.147839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.116309 restraints weight = 60715.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.115250 restraints weight = 66055.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.116990 restraints weight = 59353.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.116764 restraints weight = 39849.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.117218 restraints weight = 38206.706| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33456 Z= 0.168 Angle : 0.708 11.042 45792 Z= 0.369 Chirality : 0.047 0.311 5201 Planarity : 0.005 0.057 5447 Dihedral : 18.502 167.469 5756 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.60 % Favored : 93.34 % Rotamer: Outliers : 0.03 % Allowed : 0.96 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.47 (0.13), residues: 3741 helix: 0.25 (0.13), residues: 1501 sheet: -1.23 (0.24), residues: 428 loop : -2.01 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 542 TYR 0.021 0.001 TYR C1018 PHE 0.017 0.001 PHE A 35 TRP 0.019 0.002 TRP Q 15 HIS 0.007 0.001 HIS Q 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (33449) covalent geometry : angle 0.70622 / 0.37 (45786) hydrogen bonds : bond 0.04824 / 3.30 ( 1434) hydrogen bonds : angle 5.07849 / 3.52 ( 4004) metal coordination : bond 0.00835 / 0.41 ( 7) metal coordination : angle 4.40969 / 2.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 510 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLN cc_start: 0.5650 (mp-120) cc_final: 0.5446 (mp10) REVERT: B 77 ASP cc_start: 0.6636 (p0) cc_final: 0.6345 (p0) REVERT: B 80 GLU cc_start: 0.7100 (tp30) cc_final: 0.6373 (tp30) REVERT: C 337 PHE cc_start: 0.5808 (t80) cc_final: 0.5607 (t80) REVERT: C 363 LEU cc_start: 0.9071 (mt) cc_final: 0.8819 (mp) REVERT: C 704 MET cc_start: 0.8958 (mmp) cc_final: 0.8705 (mmp) REVERT: C 808 ASN cc_start: 0.9151 (m-40) cc_final: 0.8599 (m-40) REVERT: C 811 ASN cc_start: 0.9083 (p0) cc_final: 0.8745 (p0) REVERT: C 881 ASP cc_start: 0.7613 (t70) cc_final: 0.7315 (t70) REVERT: C 1080 ASN cc_start: 0.8826 (t0) cc_final: 0.8502 (t0) REVERT: C 1126 ASP cc_start: 0.7372 (t70) cc_final: 0.6829 (t70) REVERT: C 1244 HIS cc_start: 0.8240 (t70) cc_final: 0.7904 (t70) REVERT: C 1322 SER cc_start: 0.9172 (p) cc_final: 0.8942 (p) REVERT: C 1329 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7904 (tm-30) REVERT: D 193 ASP cc_start: 0.7809 (t0) cc_final: 0.7365 (p0) REVERT: D 196 GLN cc_start: 0.7085 (mt0) cc_final: 0.6434 (mt0) REVERT: D 197 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7566 (mm-30) REVERT: D 245 LEU cc_start: 0.9469 (mt) cc_final: 0.9128 (mp) REVERT: D 321 LYS cc_start: 0.8487 (mmpt) cc_final: 0.8193 (mttm) REVERT: D 458 ASN cc_start: 0.9197 (t0) cc_final: 0.8981 (t0) REVERT: D 506 VAL cc_start: 0.9035 (m) cc_final: 0.8730 (p) REVERT: D 821 MET cc_start: 0.8537 (ttm) cc_final: 0.8171 (ttp) REVERT: D 995 TYR cc_start: 0.6097 (m-80) cc_final: 0.5385 (m-80) REVERT: D 1040 MET cc_start: 0.1238 (ppp) cc_final: 0.0737 (ttm) REVERT: D 1151 LYS cc_start: 0.8474 (tptp) cc_final: 0.8094 (ttmt) REVERT: D 1186 TYR cc_start: 0.6479 (t80) cc_final: 0.6270 (t80) REVERT: E 10 VAL cc_start: 0.8900 (t) cc_final: 0.8573 (p) REVERT: E 30 MET cc_start: 0.7839 (mtt) cc_final: 0.7516 (mtt) REVERT: E 53 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6531 (mt-10) REVERT: E 67 ARG cc_start: 0.7625 (ttm-80) cc_final: 0.7094 (ttm110) REVERT: E 68 GLU cc_start: 0.8080 (pt0) cc_final: 0.7473 (tp30) REVERT: F 365 MET cc_start: 0.7953 (ttp) cc_final: 0.7082 (tmm) REVERT: P 36 MET cc_start: 0.5854 (ttt) cc_final: 0.4598 (tpp) REVERT: P 53 MET cc_start: 0.4550 (mmm) cc_final: 0.2099 (tpt) REVERT: P 57 MET cc_start: 0.8025 (pmm) cc_final: 0.7758 (pmm) outliers start: 1 outliers final: 1 residues processed: 511 average time/residue: 0.1930 time to fit residues: 163.6279 Evaluate side-chains 398 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 397 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 258 optimal weight: 1.9990 chunk 283 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 176 optimal weight: 6.9990 chunk 44 optimal weight: 0.0980 chunk 289 optimal weight: 20.0000 chunk 366 optimal weight: 8.9990 chunk 369 optimal weight: 7.9990 chunk 353 optimal weight: 50.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 HIS C 604 HIS ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 GLN D1197 ASN P 68 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.150862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.123611 restraints weight = 61633.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.122631 restraints weight = 84461.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.123641 restraints weight = 78524.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.123621 restraints weight = 55898.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.124027 restraints weight = 50848.484| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33456 Z= 0.154 Angle : 0.695 15.785 45792 Z= 0.361 Chirality : 0.046 0.309 5201 Planarity : 0.005 0.071 5447 Dihedral : 18.394 169.106 5756 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.20 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.13), residues: 3741 helix: 0.38 (0.13), residues: 1498 sheet: -1.21 (0.24), residues: 438 loop : -1.95 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C1033 TYR 0.023 0.001 TYR Q 142 PHE 0.040 0.001 PHE F 266 TRP 0.052 0.002 TRP D 115 HIS 0.005 0.001 HIS P 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (33449) covalent geometry : angle 0.69369 / 0.36 (45786) hydrogen bonds : bond 0.04685 / 3.21 ( 1434) hydrogen bonds : angle 5.00508 / 3.46 ( 4004) metal coordination : bond 0.00644 / 0.31 ( 7) metal coordination : angle 4.06119 / 2.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 507 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.9116 (mtmt) cc_final: 0.8876 (mtpp) REVERT: A 57 THR cc_start: 0.8467 (m) cc_final: 0.8265 (m) REVERT: B 75 GLN cc_start: 0.5811 (mp-120) cc_final: 0.5543 (mp10) REVERT: B 77 ASP cc_start: 0.6483 (p0) cc_final: 0.6256 (p0) REVERT: B 80 GLU cc_start: 0.7027 (tp30) cc_final: 0.6282 (tp30) REVERT: C 47 TYR cc_start: 0.4813 (m-80) cc_final: 0.3935 (m-80) REVERT: C 163 LYS cc_start: 0.7195 (ptmt) cc_final: 0.6788 (ptmt) REVERT: C 363 LEU cc_start: 0.9032 (mt) cc_final: 0.8790 (mp) REVERT: C 606 LEU cc_start: 0.9108 (mp) cc_final: 0.8893 (mt) REVERT: C 704 MET cc_start: 0.8993 (mmp) cc_final: 0.8638 (mmp) REVERT: C 808 ASN cc_start: 0.9183 (m-40) cc_final: 0.8858 (m-40) REVERT: C 811 ASN cc_start: 0.9097 (p0) cc_final: 0.8764 (p0) REVERT: C 881 ASP cc_start: 0.7615 (t70) cc_final: 0.7323 (t70) REVERT: C 1080 ASN cc_start: 0.8852 (t0) cc_final: 0.8553 (t0) REVERT: C 1126 ASP cc_start: 0.7331 (t70) cc_final: 0.6839 (t70) REVERT: C 1244 HIS cc_start: 0.8229 (t70) cc_final: 0.7990 (t70) REVERT: C 1329 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7859 (tm-30) REVERT: D 50 LYS cc_start: 0.8484 (tttm) cc_final: 0.8247 (tttm) REVERT: D 193 ASP cc_start: 0.7723 (t0) cc_final: 0.7349 (p0) REVERT: D 196 GLN cc_start: 0.7001 (mt0) cc_final: 0.6387 (mt0) REVERT: D 245 LEU cc_start: 0.9514 (mt) cc_final: 0.9169 (mp) REVERT: D 353 SER cc_start: 0.9331 (t) cc_final: 0.9031 (p) REVERT: D 458 ASN cc_start: 0.9236 (t0) cc_final: 0.9017 (t0) REVERT: D 506 VAL cc_start: 0.8942 (m) cc_final: 0.8644 (p) REVERT: D 724 MET cc_start: 0.9371 (mtm) cc_final: 0.9134 (mtm) REVERT: D 821 MET cc_start: 0.8502 (ttm) cc_final: 0.8140 (ttp) REVERT: D 995 TYR cc_start: 0.5944 (m-80) cc_final: 0.5373 (m-80) REVERT: D 1040 MET cc_start: 0.1401 (ppp) cc_final: 0.0703 (ttm) REVERT: D 1151 LYS cc_start: 0.8463 (tptp) cc_final: 0.8133 (mtmt) REVERT: D 1186 TYR cc_start: 0.6340 (t80) cc_final: 0.6134 (t80) REVERT: E 10 VAL cc_start: 0.8908 (t) cc_final: 0.8626 (p) REVERT: E 30 MET cc_start: 0.7859 (mtt) cc_final: 0.7536 (mtt) REVERT: E 53 GLU cc_start: 0.6774 (mt-10) cc_final: 0.6574 (mt-10) REVERT: E 67 ARG cc_start: 0.7542 (ttm-80) cc_final: 0.7049 (ttm110) REVERT: E 68 GLU cc_start: 0.7937 (pt0) cc_final: 0.7558 (tp30) REVERT: F 365 MET cc_start: 0.7784 (ttp) cc_final: 0.6996 (tmm) REVERT: P 36 MET cc_start: 0.5705 (ttt) cc_final: 0.4474 (tpp) REVERT: P 53 MET cc_start: 0.4651 (mmm) cc_final: 0.2773 (tpt) REVERT: P 57 MET cc_start: 0.7919 (pmm) cc_final: 0.7690 (pmm) REVERT: P 66 ILE cc_start: 0.9047 (pt) cc_final: 0.8814 (mt) REVERT: P 68 GLN cc_start: 0.9180 (mt0) cc_final: 0.8972 (mt0) REVERT: P 120 LYS cc_start: 0.6759 (mppt) cc_final: 0.6452 (mmtt) outliers start: 0 outliers final: 0 residues processed: 507 average time/residue: 0.1959 time to fit residues: 165.1778 Evaluate side-chains 398 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 398 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 297 optimal weight: 0.6980 chunk 253 optimal weight: 9.9990 chunk 367 optimal weight: 8.9990 chunk 223 optimal weight: 6.9990 chunk 293 optimal weight: 10.0000 chunk 259 optimal weight: 0.6980 chunk 187 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 301 optimal weight: 20.0000 chunk 128 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 HIS C 314 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 GLN D1197 ASN Q 90 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.150107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.122756 restraints weight = 61843.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.121725 restraints weight = 89912.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.122869 restraints weight = 83991.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.122996 restraints weight = 58225.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.123312 restraints weight = 52219.330| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33456 Z= 0.178 Angle : 0.719 11.753 45792 Z= 0.372 Chirality : 0.047 0.308 5201 Planarity : 0.005 0.067 5447 Dihedral : 18.327 170.283 5756 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.00 % Favored : 92.94 % Rotamer: Outliers : 0.06 % Allowed : 0.56 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.13), residues: 3741 helix: 0.40 (0.13), residues: 1494 sheet: -1.11 (0.25), residues: 419 loop : -1.95 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 363 TYR 0.019 0.002 TYR Q 100 PHE 0.018 0.002 PHE C 972 TRP 0.051 0.002 TRP D 115 HIS 0.006 0.001 HIS P 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (33449) covalent geometry : angle 0.71720 / 0.37 (45786) hydrogen bonds : bond 0.04787 / 3.27 ( 1434) hydrogen bonds : angle 5.02373 / 3.47 ( 4004) metal coordination : bond 0.00865 / 0.42 ( 7) metal coordination : angle 4.07279 / 2.41 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 514 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LEU cc_start: 0.8546 (tp) cc_final: 0.8238 (tt) REVERT: B 80 GLU cc_start: 0.7022 (tp30) cc_final: 0.6405 (tp30) REVERT: B 86 LYS cc_start: 0.8576 (tttt) cc_final: 0.8314 (ttmm) REVERT: C 47 TYR cc_start: 0.4934 (m-80) cc_final: 0.3980 (m-80) REVERT: C 337 PHE cc_start: 0.5762 (t80) cc_final: 0.5545 (t80) REVERT: C 606 LEU cc_start: 0.9088 (mp) cc_final: 0.8818 (mt) REVERT: C 704 MET cc_start: 0.8892 (mmp) cc_final: 0.8550 (mmp) REVERT: C 811 ASN cc_start: 0.9102 (p0) cc_final: 0.8872 (p0) REVERT: C 881 ASP cc_start: 0.7723 (t70) cc_final: 0.7410 (t70) REVERT: C 1080 ASN cc_start: 0.8846 (t0) cc_final: 0.8515 (t0) REVERT: C 1126 ASP cc_start: 0.7232 (t70) cc_final: 0.6713 (t70) REVERT: C 1244 HIS cc_start: 0.8257 (t70) cc_final: 0.7932 (t70) REVERT: C 1329 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7883 (tm-30) REVERT: D 193 ASP cc_start: 0.7770 (t0) cc_final: 0.7453 (p0) REVERT: D 196 GLN cc_start: 0.7075 (mt0) cc_final: 0.6473 (mt0) REVERT: D 245 LEU cc_start: 0.9420 (mt) cc_final: 0.9112 (mp) REVERT: D 353 SER cc_start: 0.9381 (t) cc_final: 0.9094 (p) REVERT: D 506 VAL cc_start: 0.9047 (m) cc_final: 0.8687 (p) REVERT: D 724 MET cc_start: 0.9368 (mtm) cc_final: 0.9081 (mtm) REVERT: D 821 MET cc_start: 0.8468 (ttm) cc_final: 0.8121 (ttp) REVERT: D 995 TYR cc_start: 0.6029 (m-80) cc_final: 0.5522 (m-80) REVERT: D 1040 MET cc_start: 0.1297 (ppp) cc_final: 0.0520 (ttm) REVERT: D 1151 LYS cc_start: 0.8417 (tptp) cc_final: 0.8143 (mtmt) REVERT: D 1327 GLU cc_start: 0.8458 (pt0) cc_final: 0.8169 (pt0) REVERT: E 10 VAL cc_start: 0.8914 (t) cc_final: 0.8652 (p) REVERT: E 30 MET cc_start: 0.7870 (mtt) cc_final: 0.7530 (mtt) REVERT: E 53 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6816 (mt-10) REVERT: E 67 ARG cc_start: 0.7504 (ttm-80) cc_final: 0.7006 (ttm110) REVERT: E 68 GLU cc_start: 0.7822 (pt0) cc_final: 0.7275 (tp30) REVERT: F 261 LEU cc_start: 0.7586 (pp) cc_final: 0.6758 (tp) REVERT: F 366 SER cc_start: 0.8039 (m) cc_final: 0.7724 (p) REVERT: P 36 MET cc_start: 0.5722 (ttt) cc_final: 0.4452 (tpp) REVERT: P 53 MET cc_start: 0.4860 (mmm) cc_final: 0.3068 (tpt) REVERT: P 57 MET cc_start: 0.7923 (pmm) cc_final: 0.7691 (pmm) REVERT: P 68 GLN cc_start: 0.9179 (mt0) cc_final: 0.8933 (mt0) REVERT: P 120 LYS cc_start: 0.6864 (mppt) cc_final: 0.6509 (mmtt) outliers start: 2 outliers final: 1 residues processed: 515 average time/residue: 0.1893 time to fit residues: 161.6502 Evaluate side-chains 396 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 395 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 53 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 339 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 308 optimal weight: 0.0060 chunk 237 optimal weight: 7.9990 chunk 243 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 239 optimal weight: 4.9990 chunk 336 optimal weight: 5.9990 overall best weight: 2.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN B 117 HIS C 314 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 ASN ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 929 GLN D1197 ASN Q 95 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.150911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.123147 restraints weight = 61673.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.122253 restraints weight = 83478.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.123507 restraints weight = 77110.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.123465 restraints weight = 54855.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.123913 restraints weight = 48570.560| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 33456 Z= 0.154 Angle : 0.709 12.296 45792 Z= 0.368 Chirality : 0.047 0.339 5201 Planarity : 0.005 0.067 5447 Dihedral : 18.267 171.607 5756 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.07 % Favored : 93.88 % Rotamer: Outliers : 0.09 % Allowed : 0.50 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.28 (0.13), residues: 3741 helix: 0.43 (0.13), residues: 1508 sheet: -1.06 (0.24), residues: 429 loop : -1.94 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1033 TYR 0.026 0.001 TYR Q 142 PHE 0.050 0.001 PHE C 514 TRP 0.053 0.002 TRP Q 19 HIS 0.009 0.001 HIS B 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (33449) covalent geometry : angle 0.70763 / 0.37 (45786) hydrogen bonds : bond 0.04660 / 3.18 ( 1434) hydrogen bonds : angle 4.95633 / 3.42 ( 4004) metal coordination : bond 0.00621 / 0.30 ( 7) metal coordination : angle 3.94270 / 2.33 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5293.35 seconds wall clock time: 92 minutes 27.55 seconds (5547.55 seconds total)