Starting phenix.real_space_refine on Mon Sep 14 00:46:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6flp_4274/09_2026/6flp_4274_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6flp_4274/09_2026/6flp_4274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6flp_4274/09_2026/6flp_4274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6flp_4274/09_2026/6flp_4274.map" model { file = "/net/cci-nas-00/data/ceres_data/6flp_4274/09_2026/6flp_4274_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6flp_4274/09_2026/6flp_4274_neut.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.058 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 80 5.49 5 Mg 1 5.21 5 S 105 5.16 5 C 16357 2.51 5 N 4696 2.21 5 O 5271 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26512 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1767 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 219} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1667 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 10363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1314, 10363 Classifications: {'peptide': 1314} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 54, 'TRANS': 1258} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 10357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10357 Classifications: {'peptide': 1334} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 55, 'TRANS': 1278} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 709 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "N" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 647 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain breaks: 1 Chain: "R" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'RNA': 10} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 785 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} 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 14260 SG CYS D 72 111.636 59.038 75.832 1.00211.78 S ATOM 20080 SG CYS D 814 88.557 126.912 76.974 1.00152.41 S ATOM 20645 SG CYS D 888 87.250 123.598 76.448 1.00144.53 S ATOM 20696 SG CYS D 895 88.413 124.558 79.651 1.00144.06 S Time building chain proxies: 5.44, per 1000 atoms: 0.21 Number of scatterers: 26512 At special positions: 0 Unit cell: (155.1, 163.9, 169.4, 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 105 16.00 P 80 15.00 Mg 1 11.99 O 5271 8.00 N 4696 7.00 C 16357 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: 2.36 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " 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 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5880 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 43 sheets defined 38.0% alpha, 13.1% beta 36 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.666A pdb=" N SER A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.630A pdb=" N ILE A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.739A pdb=" N ASP A 114 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 161 removed outlier: 3.718A pdb=" N ILE A 159 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 161 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 removed outlier: 3.521A pdb=" N ALA A 216 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.876A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.738A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 116 removed outlier: 4.075A pdb=" N ASP B 114 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR B 116 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 227 Processing helix chain 'C' and resid 30 through 40 Processing helix chain 'C' and resid 49 through 57 removed outlier: 4.331A pdb=" N SER C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 Processing helix chain 'C' and resid 206 through 212 removed outlier: 4.003A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 223 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.893A pdb=" N GLU C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 389 removed outlier: 4.607A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 408 Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 481 removed outlier: 4.127A pdb=" N ARG C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.774A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 removed outlier: 3.598A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.934A pdb=" N LYS C 527 " --> pdb=" O GLU C 523 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.836A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 612 removed outlier: 3.632A pdb=" N GLU C 611 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 607 through 612' Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 656 through 660 removed outlier: 3.937A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 removed outlier: 3.987A 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: 4.332A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 710 removed outlier: 4.592A pdb=" N ALA C 709 " --> pdb=" O GLU C 705 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL C 710 " --> pdb=" O ARG C 706 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 705 through 710' Processing helix chain 'C' and resid 820 through 826 Processing helix chain 'C' and resid 860 through 864 removed outlier: 3.783A pdb=" N SER C 863 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 860 through 864' Processing helix chain 'C' and resid 942 through 981 removed outlier: 3.696A pdb=" N LEU C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY C 970 " --> pdb=" O ILE C 966 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 971 " --> pdb=" O LEU C 967 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1000 Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.561A pdb=" N ILE C1036 " --> pdb=" O LYS C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1102 through 1107 Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 4.175A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C1114 " --> pdb=" O GLY C1110 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1149 Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.515A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE C1164 " --> pdb=" O LEU C1161 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1160 through 1164' Processing helix chain 'C' and resid 1166 through 1176 removed outlier: 3.689A pdb=" N MET C1170 " --> pdb=" O ASP C1166 " (cutoff:3.500A) Processing helix chain 'C' and resid 1177 through 1179 No H-bonds generated for 'chain 'C' and resid 1177 through 1179' Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1262 through 1266 removed outlier: 4.002A pdb=" N PHE C1265 " --> pdb=" O LYS C1262 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.729A pdb=" N VAL C1275 " --> pdb=" O GLY C1271 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1292 Processing helix chain 'C' and resid 1299 through 1309 removed outlier: 3.973A pdb=" N LYS C1303 " --> pdb=" O ASN C1299 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1334 removed outlier: 3.614A pdb=" N GLY C1334 " --> pdb=" O ILE C1330 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 95 through 101 Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.549A pdb=" N SER D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 263 through 285 removed outlier: 4.296A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 369 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 406 through 417 removed outlier: 3.869A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (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 453 through 458 removed outlier: 3.734A pdb=" N TYR D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 removed outlier: 3.849A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 581 through 583 No H-bonds generated for 'chain 'D' and resid 581 through 583' Processing helix chain 'D' and resid 597 through 612 removed outlier: 3.598A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 636 removed outlier: 3.806A pdb=" N THR D 617 " --> pdb=" O GLY D 613 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.680A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 669 removed outlier: 4.491A pdb=" N GLU D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.830A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.528A pdb=" N TYR D 772 " --> pdb=" O ASN D 768 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 840 Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 895 through 900 removed outlier: 3.539A pdb=" N TYR D 899 " --> pdb=" O CYS D 895 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 895 through 900' Processing helix chain 'D' and resid 915 through 925 Processing helix chain 'D' and resid 1138 through 1147 Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.708A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1243 Processing helix chain 'D' and resid 1250 through 1260 removed outlier: 4.200A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1293 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1327 through 1337 Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.658A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1361 through 1373 removed outlier: 4.344A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 16 through 32 removed outlier: 4.326A pdb=" N VAL E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 91 removed outlier: 3.505A pdb=" N ARG E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 19 removed outlier: 5.254A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU A 17 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 24 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A 205 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU A 201 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU A 188 " --> pdb=" O LYS A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 104 removed outlier: 3.522A pdb=" N LEU A 102 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 149 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.604A pdb=" N ARG A 91 " --> pdb=" O GLU A 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 removed outlier: 3.702A 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 removed outlier: 3.706A pdb=" N VAL A 153 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 14 through 18 removed outlier: 3.624A pdb=" N LEU B 201 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS B 200 " --> pdb=" O GLU B 188 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA B 184 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU B 206 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 4.100A 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 104 removed outlier: 3.592A pdb=" N MET B 142 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS B 104 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 140 " --> pdb=" O LYS B 104 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 110 removed outlier: 3.900A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 67 through 75 removed outlier: 3.688A pdb=" N GLU C 67 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL C 71 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA C 94 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLY C 125 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU C 96 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TYR C 123 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL C 98 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU C 121 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU C 100 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS C 115 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB2, first strand: chain 'C' and resid 154 through 159 removed outlier: 3.612A pdb=" N PHE C 156 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG C 175 " --> pdb=" O PHE C 156 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 238 through 239 removed outlier: 4.159A pdb=" N GLN C 238 " --> pdb=" O GLU C 231 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU C 231 " --> pdb=" O GLN C 238 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 296 through 297 removed outlier: 3.910A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 301 through 302 removed outlier: 6.868A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 558 through 559 removed outlier: 4.648A pdb=" N SER C 574 " --> pdb=" O CYS C 559 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.532A pdb=" N THR C 589 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR C 591 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AB9, first strand: chain 'C' and resid 633 through 636 Processing sheet with id=AC1, first strand: chain 'C' and resid 700 through 701 Processing sheet with id=AC2, first strand: chain 'C' and resid 748 through 752 removed outlier: 7.105A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC4, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC5, first strand: chain 'C' and resid 1097 through 1098 removed outlier: 7.338A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N MET C 800 " --> pdb=" O MET C1230 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY C1228 " --> pdb=" O VAL C 802 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE C 804 " --> pdb=" O THR C1226 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 816 through 819 removed outlier: 7.717A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.535A pdb=" N THR C 830 " --> pdb=" O ARG C1058 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG C1058 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY C 926 " --> pdb=" O VAL C 877 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 882 through 885 removed outlier: 7.275A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.796A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY D 351 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER D 353 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.796A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AD3, first strand: chain 'C' and resid 1336 through 1339 Processing sheet with id=AD4, first strand: chain 'D' and resid 104 through 105 Processing sheet with id=AD5, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AD6, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.581A pdb=" N THR D 572 " --> pdb=" O VAL D 548 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 550 " --> pdb=" O LYS D 570 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE D 552 " --> pdb=" O SER D 568 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS D 566 " --> pdb=" O GLU D 554 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU D 562 " --> pdb=" O ASP D 558 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 706 through 708 Processing sheet with id=AD8, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AD9, first strand: chain 'D' and resid 951 through 952 Processing sheet with id=AE1, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.602A pdb=" N LYS D 959 " --> pdb=" O LYS D 983 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 965 through 967 removed outlier: 3.626A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1025 through 1028 removed outlier: 6.524A pdb=" N MET D1025 " --> pdb=" O ARG D1123 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ARG D1123 " --> pdb=" O MET D1025 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL D1027 " --> pdb=" O LEU D1121 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1079 through 1081 removed outlier: 3.970A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1046 through 1050 removed outlier: 3.619A pdb=" N VAL D1060 " --> pdb=" O THR D1047 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1187 through 1190 removed outlier: 3.863A pdb=" N GLU D1188 " --> pdb=" O LEU D1175 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU D1175 " --> pdb=" O GLU D1188 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG D1173 " --> pdb=" O ILE D1190 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1277 through 1279 removed outlier: 6.466A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) 940 hydrogen bonds defined for protein. 2667 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 90 hydrogen bonds 176 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 7.06 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8510 1.34 - 1.46: 3657 1.46 - 1.57: 14565 1.57 - 1.69: 156 1.69 - 1.81: 182 Bond restraints: 27070 Sorted by residual: bond pdb=" C3' DA N 38 " pdb=" C2' DA N 38 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.64e+00 bond pdb=" C1' DC T 1 " pdb=" N1 DC T 1 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.34e+00 bond pdb=" C3' DA T 23 " pdb=" C2' DA T 23 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.53e+00 bond pdb=" C3' DC N 9 " pdb=" C2' DC N 9 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.74e+00 bond pdb=" C3' DC T 1 " pdb=" C2' DC T 1 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.15e+00 ... (remaining 27065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 36036 1.71 - 3.42: 778 3.42 - 5.13: 81 5.13 - 6.84: 11 6.84 - 8.55: 4 Bond angle restraints: 36910 Sorted by residual: angle pdb=" N VAL C 630 " pdb=" CA VAL C 630 " pdb=" C VAL C 630 " ideal model delta sigma weight residual 111.91 106.82 5.09 8.90e-01 1.26e+00 3.27e+01 angle pdb=" O4' DG N 11 " pdb=" C4' DG N 11 " pdb=" C3' DG N 11 " ideal model delta sigma weight residual 106.00 103.07 2.93 6.00e-01 2.78e+00 2.38e+01 angle pdb=" N ILE D1210 " pdb=" CA ILE D1210 " pdb=" C ILE D1210 " ideal model delta sigma weight residual 111.48 107.36 4.12 9.40e-01 1.13e+00 1.92e+01 angle pdb=" C3' DT N 33 " pdb=" C2' DT N 33 " pdb=" C1' DT N 33 " ideal model delta sigma weight residual 102.50 97.28 5.22 1.20e+00 6.94e-01 1.89e+01 angle pdb=" N3 DT N 7 " pdb=" C4 DT N 7 " pdb=" O4 DT N 7 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 ... (remaining 36905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.32: 15911 30.32 - 60.63: 522 60.63 - 90.95: 40 90.95 - 121.27: 3 121.27 - 151.59: 3 Dihedral angle restraints: 16479 sinusoidal: 7339 harmonic: 9140 Sorted by residual: dihedral pdb=" CA PHE C 57 " pdb=" C PHE C 57 " pdb=" N PRO C 58 " pdb=" CA PRO C 58 " ideal model delta harmonic sigma weight residual -180.00 -118.71 -61.29 0 5.00e+00 4.00e-02 1.50e+02 dihedral pdb=" CA SER A 20 " pdb=" C SER A 20 " pdb=" N SER A 21 " pdb=" CA SER A 21 " ideal model delta harmonic sigma weight residual 180.00 156.14 23.86 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA VAL B 19 " pdb=" C VAL B 19 " pdb=" N SER B 20 " pdb=" CA SER B 20 " ideal model delta harmonic sigma weight residual -180.00 -157.02 -22.98 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 16476 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2873 0.035 - 0.071: 925 0.071 - 0.106: 314 0.106 - 0.141: 103 0.141 - 0.176: 9 Chirality restraints: 4224 Sorted by residual: chirality pdb=" C3' G R 20 " pdb=" C4' G R 20 " pdb=" O3' G R 20 " pdb=" C2' G R 20 " both_signs ideal model delta sigma weight residual False -2.48 -2.30 -0.18 2.00e-01 2.50e+01 7.78e-01 chirality pdb=" CA ILE C 59 " pdb=" N ILE C 59 " pdb=" C ILE C 59 " pdb=" CB ILE C 59 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.77e-01 chirality pdb=" CA ASP D1184 " pdb=" N ASP D1184 " pdb=" C ASP D1184 " pdb=" CB ASP D1184 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.59e-01 ... (remaining 4221 not shown) Planarity restraints: 4556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 57 " -0.054 5.00e-02 4.00e+02 8.21e-02 1.08e+01 pdb=" N PRO C 58 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO C 58 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 58 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 109 " 0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO C 110 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 110 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 110 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 559 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO C 560 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 560 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 560 " -0.023 5.00e-02 4.00e+02 ... (remaining 4553 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 287 2.63 - 3.20: 23404 3.20 - 3.76: 38985 3.76 - 4.33: 51882 4.33 - 4.90: 83587 Nonbonded interactions: 198145 Sorted by model distance: nonbonded pdb=" N2 DG N 29 " pdb=" O2 DC T 11 " model vdw 2.062 2.496 nonbonded pdb=" NH2 ARG C 200 " pdb=" OP2 DC N 24 " model vdw 2.108 3.120 nonbonded pdb=" OE1 GLU C 562 " pdb=" OG SER C 662 " model vdw 2.195 3.040 nonbonded pdb=" N CYS D 72 " pdb="ZN ZN D1502 " model vdw 2.233 2.310 nonbonded pdb=" OD2 ASP D 129 " pdb=" NH1 ARG D 220 " model vdw 2.235 3.120 ... (remaining 198140 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 6 through 158 or resid 171 through 234)) selection = chain 'B' } 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 31.870 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 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 : 0.004 0.256 27074 Z= 0.219 Angle : 0.598 8.550 36910 Z= 0.406 Chirality : 0.042 0.176 4224 Planarity : 0.004 0.082 4556 Dihedral : 13.142 151.585 10599 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.29 % Favored : 93.65 % Rotamer: Outliers : 0.04 % Allowed : 1.74 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.78 % 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: -3.10 (0.13), residues: 3166 helix: -0.56 (0.14), residues: 1085 sheet: -2.53 (0.24), residues: 355 loop : -3.08 (0.13), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1301 TYR 0.018 0.001 TYR D1241 PHE 0.022 0.001 PHE D 49 TRP 0.020 0.002 TRP C1276 HIS 0.004 0.001 HIS D 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.20 (27070) covalent geometry : angle 0.59809 / 0.41 (36910) hydrogen bonds : bond 0.18063 / 12.31 ( 1025) hydrogen bonds : angle 6.33904 / 4.38 ( 2843) metal coordination : bond 0.21324 / 10.15 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 507 time to evaluate : 0.919 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 183 ILE cc_start: 0.9395 (mt) cc_final: 0.9094 (mm) REVERT: B 28 LEU cc_start: 0.9461 (tp) cc_final: 0.9253 (tt) REVERT: C 96 LEU cc_start: 0.9084 (tp) cc_final: 0.8832 (tp) REVERT: C 336 LEU cc_start: 0.9143 (mt) cc_final: 0.8842 (mp) REVERT: C 484 LEU cc_start: 0.8928 (mt) cc_final: 0.8353 (tp) REVERT: C 510 GLN cc_start: 0.8343 (tt0) cc_final: 0.8138 (tm-30) REVERT: C 515 MET cc_start: 0.6482 (ptm) cc_final: 0.4818 (ptm) REVERT: C 519 ASN cc_start: 0.8595 (t0) cc_final: 0.8015 (t0) REVERT: C 653 MET cc_start: 0.8367 (ttp) cc_final: 0.8038 (ttp) REVERT: C 696 ASP cc_start: 0.8887 (t70) cc_final: 0.8525 (t0) REVERT: C 930 ASP cc_start: 0.8490 (t70) cc_final: 0.8197 (t0) REVERT: C 1094 VAL cc_start: 0.9475 (t) cc_final: 0.9271 (p) REVERT: C 1107 MET cc_start: 0.8899 (mtp) cc_final: 0.8649 (mtt) REVERT: C 1292 THR cc_start: 0.9201 (m) cc_final: 0.8909 (m) REVERT: D 183 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8846 (pm20) REVERT: D 189 LEU cc_start: 0.9637 (mp) cc_final: 0.9352 (mt) REVERT: D 375 GLU cc_start: 0.9161 (tp30) cc_final: 0.8741 (tm-30) REVERT: D 466 MET cc_start: 0.8575 (mtp) cc_final: 0.8280 (mtp) REVERT: D 513 MET cc_start: 0.9104 (ttp) cc_final: 0.8527 (tmm) REVERT: D 654 ILE cc_start: 0.8991 (mt) cc_final: 0.8620 (pt) REVERT: D 724 MET cc_start: 0.9311 (mtm) cc_final: 0.8830 (mtt) REVERT: D 756 GLU cc_start: 0.8849 (pt0) cc_final: 0.8490 (pp20) REVERT: D 1236 GLU cc_start: 0.8955 (tp30) cc_final: 0.8699 (tp30) REVERT: D 1254 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8351 (mt-10) REVERT: E 38 LEU cc_start: 0.9432 (mp) cc_final: 0.8298 (tt) REVERT: E 52 ARG cc_start: 0.9428 (mtp85) cc_final: 0.9207 (ttm110) outliers start: 1 outliers final: 0 residues processed: 507 average time/residue: 0.1904 time to fit residues: 148.1799 Evaluate side-chains 234 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 HIS A 132 HIS B 66 HIS B 84 ASN C 65 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 551 HIS C 604 HIS C 628 HIS C 686 GLN C1080 ASN C1134 GLN C1136 GLN C1146 GLN ** C1237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1257 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS D 157 GLN D 232 ASN D 341 ASN D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 488 ASN D 489 ASN D 665 GLN D1218 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.063426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.046035 restraints weight = 146283.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.047393 restraints weight = 80891.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.048330 restraints weight = 54226.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.048935 restraints weight = 41358.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.049355 restraints weight = 34538.231| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 27074 Z= 0.215 Angle : 0.661 8.115 36910 Z= 0.349 Chirality : 0.044 0.262 4224 Planarity : 0.005 0.080 4556 Dihedral : 16.322 156.769 4407 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.96 % Favored : 92.01 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.78 % 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: -2.29 (0.14), residues: 3166 helix: 0.28 (0.15), residues: 1102 sheet: -2.29 (0.24), residues: 385 loop : -2.68 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 407 TYR 0.019 0.001 TYR D1241 PHE 0.035 0.002 PHE D 892 TRP 0.010 0.002 TRP D 409 HIS 0.005 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.22 (27070) covalent geometry : angle 0.66055 / 0.35 (36910) hydrogen bonds : bond 0.04935 / 3.56 ( 1025) hydrogen bonds : angle 5.10542 / 3.54 ( 2843) metal coordination : bond 0.00633 / 0.30 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.828 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: A 54 CYS cc_start: 0.8096 (m) cc_final: 0.7867 (m) REVERT: A 75 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8555 (tm-30) REVERT: A 142 MET cc_start: 0.8694 (ptp) cc_final: 0.8481 (ptp) REVERT: A 174 ASP cc_start: 0.8718 (p0) cc_final: 0.8398 (p0) REVERT: A 183 ILE cc_start: 0.9505 (mt) cc_final: 0.9158 (mm) REVERT: C 124 MET cc_start: 0.8728 (pmm) cc_final: 0.8308 (pmm) REVERT: C 484 LEU cc_start: 0.8804 (mt) cc_final: 0.8286 (tp) REVERT: C 510 GLN cc_start: 0.8421 (tt0) cc_final: 0.8147 (tm-30) REVERT: C 519 ASN cc_start: 0.8755 (t0) cc_final: 0.8345 (t0) REVERT: C 696 ASP cc_start: 0.8978 (t70) cc_final: 0.8582 (t0) REVERT: C 827 ARG cc_start: 0.8599 (mtp180) cc_final: 0.8269 (mtp-110) REVERT: C 996 ARG cc_start: 0.8739 (tmt-80) cc_final: 0.8418 (tpt90) REVERT: C 1094 VAL cc_start: 0.9490 (t) cc_final: 0.9212 (p) REVERT: C 1107 MET cc_start: 0.8877 (mtp) cc_final: 0.8601 (mtt) REVERT: C 1119 MET cc_start: 0.9320 (tpp) cc_final: 0.8842 (tpp) REVERT: C 1196 LYS cc_start: 0.9386 (mmtt) cc_final: 0.9183 (mmmm) REVERT: C 1243 MET cc_start: 0.9002 (tmm) cc_final: 0.8760 (tmm) REVERT: C 1329 GLU cc_start: 0.8716 (tt0) cc_final: 0.8481 (tt0) REVERT: D 29 MET cc_start: 0.8970 (ttm) cc_final: 0.8726 (ttp) REVERT: D 183 GLU cc_start: 0.9199 (mt-10) cc_final: 0.8985 (pm20) REVERT: D 321 LYS cc_start: 0.8534 (mptt) cc_final: 0.8049 (mmtt) REVERT: D 375 GLU cc_start: 0.9218 (tp30) cc_final: 0.8704 (tm-30) REVERT: D 466 MET cc_start: 0.8723 (mtp) cc_final: 0.8499 (mtp) REVERT: D 513 MET cc_start: 0.9147 (ttp) cc_final: 0.8626 (tmm) REVERT: D 644 MET cc_start: 0.9174 (mpp) cc_final: 0.8823 (mpp) REVERT: D 724 MET cc_start: 0.9324 (mtm) cc_final: 0.8883 (mtt) REVERT: D 725 MET cc_start: 0.8906 (mtp) cc_final: 0.8631 (tmm) REVERT: D 756 GLU cc_start: 0.8757 (pt0) cc_final: 0.8436 (pp20) REVERT: D 1189 MET cc_start: 0.8594 (ppp) cc_final: 0.8279 (ppp) REVERT: D 1236 GLU cc_start: 0.9002 (tp30) cc_final: 0.8757 (tp30) REVERT: D 1254 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8480 (mt-10) REVERT: E 26 ARG cc_start: 0.9384 (tpm170) cc_final: 0.9163 (tpm170) REVERT: E 38 LEU cc_start: 0.9433 (mp) cc_final: 0.8321 (tt) REVERT: E 62 GLN cc_start: 0.9620 (mp10) cc_final: 0.9386 (mp10) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.1685 time to fit residues: 73.4938 Evaluate side-chains 193 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 106 optimal weight: 3.9990 chunk 249 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 267 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 172 optimal weight: 8.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 HIS C 658 GLN ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 GLN C1209 GLN ** C1237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.062886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.045362 restraints weight = 147102.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.046711 restraints weight = 81271.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.047643 restraints weight = 54655.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.048256 restraints weight = 41742.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.048604 restraints weight = 35060.373| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27074 Z= 0.194 Angle : 0.619 8.361 36910 Z= 0.327 Chirality : 0.044 0.259 4224 Planarity : 0.004 0.078 4556 Dihedral : 16.401 157.512 4407 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.83 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.15), residues: 3166 helix: 0.57 (0.16), residues: 1103 sheet: -2.07 (0.24), residues: 385 loop : -2.51 (0.14), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 52 TYR 0.022 0.001 TYR D 626 PHE 0.021 0.002 PHE C 57 TRP 0.014 0.001 TRP C 807 HIS 0.004 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (27070) covalent geometry : angle 0.61927 / 0.33 (36910) hydrogen bonds : bond 0.04678 / 3.37 ( 1025) hydrogen bonds : angle 4.81720 / 3.34 ( 2843) metal coordination : bond 0.00262 / 0.11 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.940 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: A 75 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8629 (tm-30) REVERT: B 8 PHE cc_start: 0.8147 (p90) cc_final: 0.6985 (p90) REVERT: C 124 MET cc_start: 0.8756 (pmm) cc_final: 0.8501 (pmm) REVERT: C 239 MET cc_start: 0.8997 (ppp) cc_final: 0.8611 (tpt) REVERT: C 484 LEU cc_start: 0.8784 (mt) cc_final: 0.8187 (tp) REVERT: C 510 GLN cc_start: 0.8442 (tt0) cc_final: 0.8199 (tm-30) REVERT: C 519 ASN cc_start: 0.8768 (t0) cc_final: 0.8357 (t0) REVERT: C 696 ASP cc_start: 0.8999 (t70) cc_final: 0.8595 (t0) REVERT: C 800 MET cc_start: 0.9185 (pmm) cc_final: 0.8963 (pmm) REVERT: C 930 ASP cc_start: 0.8714 (t70) cc_final: 0.8341 (t0) REVERT: C 1094 VAL cc_start: 0.9497 (t) cc_final: 0.9243 (p) REVERT: C 1131 MET cc_start: 0.8916 (mtt) cc_final: 0.8625 (mmm) REVERT: C 1170 MET cc_start: 0.8755 (tmm) cc_final: 0.8552 (tmm) REVERT: C 1243 MET cc_start: 0.9059 (tmm) cc_final: 0.8772 (tmm) REVERT: C 1329 GLU cc_start: 0.8786 (tt0) cc_final: 0.8438 (tt0) REVERT: D 29 MET cc_start: 0.8972 (ttm) cc_final: 0.8710 (ttp) REVERT: D 321 LYS cc_start: 0.8582 (mptt) cc_final: 0.8070 (mmtt) REVERT: D 330 MET cc_start: 0.8617 (ttt) cc_final: 0.8338 (ttm) REVERT: D 375 GLU cc_start: 0.9192 (tp30) cc_final: 0.8735 (tm-30) REVERT: D 466 MET cc_start: 0.8777 (mtp) cc_final: 0.8540 (mtp) REVERT: D 479 GLU cc_start: 0.8641 (tt0) cc_final: 0.8394 (tt0) REVERT: D 484 MET cc_start: 0.8440 (mtm) cc_final: 0.8234 (mtm) REVERT: D 513 MET cc_start: 0.9124 (ttp) cc_final: 0.8576 (tmm) REVERT: D 604 MET cc_start: 0.9224 (tmm) cc_final: 0.9022 (tmm) REVERT: D 644 MET cc_start: 0.9199 (mpp) cc_final: 0.8836 (mpp) REVERT: D 698 MET cc_start: 0.9436 (mmt) cc_final: 0.9181 (tpp) REVERT: D 724 MET cc_start: 0.9341 (mtm) cc_final: 0.8917 (mtt) REVERT: D 725 MET cc_start: 0.8983 (mtp) cc_final: 0.8628 (tmm) REVERT: D 1186 TYR cc_start: 0.8872 (m-80) cc_final: 0.8378 (m-10) REVERT: D 1189 MET cc_start: 0.8685 (ppp) cc_final: 0.8370 (ppp) REVERT: D 1236 GLU cc_start: 0.8957 (tp30) cc_final: 0.8682 (tp30) REVERT: D 1254 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8437 (mt-10) REVERT: E 26 ARG cc_start: 0.9464 (tpm170) cc_final: 0.9059 (tpm170) REVERT: E 62 GLN cc_start: 0.9603 (mp10) cc_final: 0.9366 (mp10) REVERT: E 67 ARG cc_start: 0.9533 (ttm110) cc_final: 0.9326 (tpp80) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.1607 time to fit residues: 62.1619 Evaluate side-chains 185 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 247 optimal weight: 0.9990 chunk 38 optimal weight: 0.0050 chunk 167 optimal weight: 4.9990 chunk 314 optimal weight: 2.9990 chunk 165 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 214 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 235 optimal weight: 5.9990 chunk 295 optimal weight: 6.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.064092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.046804 restraints weight = 142582.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.048183 restraints weight = 78628.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.049093 restraints weight = 52659.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.049755 restraints weight = 40184.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.050112 restraints weight = 33469.179| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 27074 Z= 0.109 Angle : 0.566 9.540 36910 Z= 0.296 Chirality : 0.043 0.265 4224 Planarity : 0.004 0.074 4556 Dihedral : 16.396 158.287 4407 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.79 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.15), residues: 3166 helix: 0.81 (0.16), residues: 1109 sheet: -1.97 (0.25), residues: 372 loop : -2.34 (0.14), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 314 TYR 0.020 0.001 TYR D 626 PHE 0.021 0.001 PHE C 57 TRP 0.011 0.001 TRP D1193 HIS 0.004 0.001 HIS D 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (27070) covalent geometry : angle 0.56608 / 0.30 (36910) hydrogen bonds : bond 0.04064 / 2.94 ( 1025) hydrogen bonds : angle 4.47369 / 3.11 ( 2843) metal coordination : bond 0.00087 / 0.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.861 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: A 25 LYS cc_start: 0.8952 (mmmt) cc_final: 0.8646 (mmmt) REVERT: A 75 GLN cc_start: 0.9028 (tm-30) cc_final: 0.8556 (tm-30) REVERT: B 8 PHE cc_start: 0.7939 (p90) cc_final: 0.6850 (p90) REVERT: B 25 LYS cc_start: 0.9372 (ptmm) cc_final: 0.9025 (ptmm) REVERT: B 227 GLN cc_start: 0.8860 (tt0) cc_final: 0.8632 (tt0) REVERT: C 124 MET cc_start: 0.8835 (pmm) cc_final: 0.8560 (pmm) REVERT: C 239 MET cc_start: 0.8935 (ppp) cc_final: 0.8608 (tpt) REVERT: C 484 LEU cc_start: 0.8616 (mt) cc_final: 0.8047 (tp) REVERT: C 510 GLN cc_start: 0.8424 (tt0) cc_final: 0.8198 (tm-30) REVERT: C 519 ASN cc_start: 0.8658 (t0) cc_final: 0.8321 (t0) REVERT: C 696 ASP cc_start: 0.8904 (t70) cc_final: 0.8478 (t0) REVERT: C 800 MET cc_start: 0.9198 (pmm) cc_final: 0.8979 (pmm) REVERT: C 827 ARG cc_start: 0.8617 (mtp180) cc_final: 0.8411 (mtp-110) REVERT: C 930 ASP cc_start: 0.8689 (t70) cc_final: 0.8295 (t0) REVERT: C 1094 VAL cc_start: 0.9512 (t) cc_final: 0.9252 (p) REVERT: C 1098 LEU cc_start: 0.9587 (mp) cc_final: 0.9344 (mp) REVERT: C 1119 MET cc_start: 0.9269 (tpp) cc_final: 0.8944 (tpp) REVERT: C 1131 MET cc_start: 0.8875 (mtt) cc_final: 0.8579 (mmm) REVERT: C 1170 MET cc_start: 0.8738 (tmm) cc_final: 0.8499 (tmm) REVERT: C 1196 LYS cc_start: 0.9422 (mmtt) cc_final: 0.9216 (mmmm) REVERT: D 29 MET cc_start: 0.8927 (ttm) cc_final: 0.8667 (ttp) REVERT: D 321 LYS cc_start: 0.8582 (mptt) cc_final: 0.8062 (mmtt) REVERT: D 372 MET cc_start: 0.8815 (mtm) cc_final: 0.8550 (ptm) REVERT: D 375 GLU cc_start: 0.9132 (tp30) cc_final: 0.8685 (tm-30) REVERT: D 466 MET cc_start: 0.8725 (mtp) cc_final: 0.8435 (mtp) REVERT: D 484 MET cc_start: 0.8390 (mtm) cc_final: 0.8135 (mtm) REVERT: D 513 MET cc_start: 0.9107 (ttp) cc_final: 0.8626 (tmm) REVERT: D 544 LEU cc_start: 0.9284 (tp) cc_final: 0.9045 (tp) REVERT: D 644 MET cc_start: 0.9172 (mpp) cc_final: 0.8795 (mpp) REVERT: D 724 MET cc_start: 0.9333 (mtm) cc_final: 0.8890 (mtt) REVERT: D 725 MET cc_start: 0.8938 (mtp) cc_final: 0.8639 (tmm) REVERT: D 1186 TYR cc_start: 0.8792 (m-80) cc_final: 0.8265 (m-10) REVERT: D 1189 MET cc_start: 0.8657 (ppp) cc_final: 0.8368 (ppp) REVERT: D 1236 GLU cc_start: 0.8907 (tp30) cc_final: 0.8596 (tp30) REVERT: D 1254 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8233 (mt-10) REVERT: E 26 ARG cc_start: 0.9478 (tpm170) cc_final: 0.9022 (tpm170) REVERT: E 38 LEU cc_start: 0.9463 (mp) cc_final: 0.8367 (tt) REVERT: E 62 GLN cc_start: 0.9588 (mp10) cc_final: 0.9353 (mp10) REVERT: E 72 GLN cc_start: 0.9370 (mm-40) cc_final: 0.8685 (mm-40) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.1605 time to fit residues: 61.8771 Evaluate side-chains 188 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 295 optimal weight: 4.9990 chunk 242 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 169 optimal weight: 9.9990 chunk 188 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 224 optimal weight: 10.0000 chunk 260 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 174 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN C 658 GLN ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.061659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.044356 restraints weight = 146399.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.045667 restraints weight = 81080.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.046563 restraints weight = 54619.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.047167 restraints weight = 41841.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.047562 restraints weight = 35065.528| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 27074 Z= 0.279 Angle : 0.697 8.643 36910 Z= 0.361 Chirality : 0.045 0.268 4224 Planarity : 0.005 0.079 4556 Dihedral : 16.527 160.289 4407 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.13 % Favored : 90.84 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.78 % 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: -1.70 (0.15), residues: 3166 helix: 0.70 (0.16), residues: 1125 sheet: -1.88 (0.26), residues: 354 loop : -2.34 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 107 TYR 0.024 0.002 TYR D1241 PHE 0.023 0.002 PHE C 57 TRP 0.012 0.002 TRP D 409 HIS 0.007 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.28 (27070) covalent geometry : angle 0.69667 / 0.36 (36910) hydrogen bonds : bond 0.04783 / 3.46 ( 1025) hydrogen bonds : angle 4.77897 / 3.32 ( 2843) metal coordination : bond 0.00535 / 0.21 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.985 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: A 75 GLN cc_start: 0.9094 (tm-30) cc_final: 0.8600 (tm-30) REVERT: B 8 PHE cc_start: 0.8262 (p90) cc_final: 0.7226 (p90) REVERT: C 124 MET cc_start: 0.8817 (pmm) cc_final: 0.8567 (pmm) REVERT: C 239 MET cc_start: 0.8927 (ppp) cc_final: 0.8579 (tpt) REVERT: C 319 LEU cc_start: 0.9112 (mt) cc_final: 0.8905 (tp) REVERT: C 484 LEU cc_start: 0.8874 (mt) cc_final: 0.8194 (tp) REVERT: C 488 MET cc_start: 0.8374 (tpt) cc_final: 0.7981 (tpp) REVERT: C 510 GLN cc_start: 0.8511 (tt0) cc_final: 0.8302 (tm-30) REVERT: C 519 ASN cc_start: 0.8844 (t0) cc_final: 0.8420 (t0) REVERT: C 588 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7626 (mp0) REVERT: C 696 ASP cc_start: 0.9003 (t70) cc_final: 0.8631 (t0) REVERT: C 800 MET cc_start: 0.9305 (pmm) cc_final: 0.8917 (pmm) REVERT: C 930 ASP cc_start: 0.8753 (t70) cc_final: 0.8353 (t0) REVERT: C 1119 MET cc_start: 0.9436 (tpp) cc_final: 0.8974 (tpp) REVERT: C 1131 MET cc_start: 0.8938 (mtt) cc_final: 0.8661 (mmm) REVERT: C 1170 MET cc_start: 0.8890 (tmm) cc_final: 0.8648 (tmm) REVERT: D 29 MET cc_start: 0.9012 (ttm) cc_final: 0.8761 (ttp) REVERT: D 102 MET cc_start: 0.8450 (pmm) cc_final: 0.8205 (pmm) REVERT: D 321 LYS cc_start: 0.8673 (mptt) cc_final: 0.8329 (mmtm) REVERT: D 375 GLU cc_start: 0.9207 (tp30) cc_final: 0.8682 (tm-30) REVERT: D 513 MET cc_start: 0.9165 (ttp) cc_final: 0.8688 (tmm) REVERT: D 644 MET cc_start: 0.9144 (mpp) cc_final: 0.8718 (mpp) REVERT: D 724 MET cc_start: 0.9346 (mtm) cc_final: 0.9020 (mtt) REVERT: D 725 MET cc_start: 0.9011 (mtp) cc_final: 0.8654 (tmm) REVERT: D 1186 TYR cc_start: 0.8833 (m-80) cc_final: 0.8275 (m-10) REVERT: D 1189 MET cc_start: 0.8738 (ppp) cc_final: 0.8437 (ppp) REVERT: D 1219 ASP cc_start: 0.9175 (p0) cc_final: 0.8943 (p0) REVERT: D 1236 GLU cc_start: 0.8929 (tp30) cc_final: 0.8568 (tp30) REVERT: D 1254 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8431 (mt-10) REVERT: E 43 ASN cc_start: 0.9622 (t0) cc_final: 0.9388 (t0) REVERT: E 62 GLN cc_start: 0.9611 (mp10) cc_final: 0.9385 (mp10) REVERT: E 72 GLN cc_start: 0.9387 (mm-40) cc_final: 0.8876 (mm-40) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1551 time to fit residues: 55.6439 Evaluate side-chains 175 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 86 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 239 optimal weight: 0.0870 chunk 55 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 269 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS C 658 GLN ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.062023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.044679 restraints weight = 144134.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.046009 restraints weight = 79335.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.046883 restraints weight = 53185.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.047536 restraints weight = 40665.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.047917 restraints weight = 33946.187| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 27074 Z= 0.188 Angle : 0.619 9.602 36910 Z= 0.324 Chirality : 0.044 0.262 4224 Planarity : 0.004 0.075 4556 Dihedral : 16.592 160.027 4407 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.96 % Favored : 91.98 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.15), residues: 3166 helix: 0.80 (0.16), residues: 1128 sheet: -1.83 (0.27), residues: 347 loop : -2.24 (0.14), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 47 TYR 0.023 0.001 TYR D 144 PHE 0.021 0.002 PHE C 57 TRP 0.010 0.001 TRP D 580 HIS 0.004 0.001 HIS C 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.19 (27070) covalent geometry : angle 0.61917 / 0.32 (36910) hydrogen bonds : bond 0.04290 / 3.09 ( 1025) hydrogen bonds : angle 4.61965 / 3.21 ( 2843) metal coordination : bond 0.00314 / 0.13 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.977 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: A 75 GLN cc_start: 0.9139 (tm-30) cc_final: 0.8643 (tm-30) REVERT: A 183 ILE cc_start: 0.9452 (mt) cc_final: 0.9088 (mm) REVERT: B 8 PHE cc_start: 0.8113 (p90) cc_final: 0.7120 (p90) REVERT: C 239 MET cc_start: 0.8921 (ppp) cc_final: 0.8537 (tpt) REVERT: C 319 LEU cc_start: 0.9103 (mt) cc_final: 0.8886 (tp) REVERT: C 429 MET cc_start: 0.9242 (mmm) cc_final: 0.9001 (mmm) REVERT: C 484 LEU cc_start: 0.8799 (mt) cc_final: 0.8084 (tp) REVERT: C 510 GLN cc_start: 0.8492 (tt0) cc_final: 0.8257 (tm-30) REVERT: C 519 ASN cc_start: 0.8827 (t0) cc_final: 0.8426 (t0) REVERT: C 636 CYS cc_start: 0.7339 (m) cc_final: 0.7025 (m) REVERT: C 696 ASP cc_start: 0.8990 (t70) cc_final: 0.8599 (t0) REVERT: C 800 MET cc_start: 0.9370 (pmm) cc_final: 0.8930 (pmm) REVERT: C 930 ASP cc_start: 0.8769 (t70) cc_final: 0.8397 (t0) REVERT: C 1119 MET cc_start: 0.9437 (tpp) cc_final: 0.8887 (tpp) REVERT: C 1131 MET cc_start: 0.8942 (mtt) cc_final: 0.8673 (mmm) REVERT: C 1170 MET cc_start: 0.8920 (tmm) cc_final: 0.8654 (tmm) REVERT: D 29 MET cc_start: 0.9005 (ttm) cc_final: 0.8752 (ttp) REVERT: D 102 MET cc_start: 0.8602 (pmm) cc_final: 0.8317 (pmm) REVERT: D 321 LYS cc_start: 0.8663 (mptt) cc_final: 0.8321 (mmtm) REVERT: D 372 MET cc_start: 0.8917 (mtp) cc_final: 0.8709 (mtp) REVERT: D 375 GLU cc_start: 0.9161 (tp30) cc_final: 0.8669 (tm-30) REVERT: D 644 MET cc_start: 0.9149 (mpp) cc_final: 0.8714 (mpp) REVERT: D 724 MET cc_start: 0.9368 (mtm) cc_final: 0.9042 (mtt) REVERT: D 725 MET cc_start: 0.8971 (mtp) cc_final: 0.8655 (tmm) REVERT: D 1186 TYR cc_start: 0.8799 (m-80) cc_final: 0.8252 (m-10) REVERT: D 1189 MET cc_start: 0.8737 (ppp) cc_final: 0.8446 (ppp) REVERT: D 1219 ASP cc_start: 0.9120 (p0) cc_final: 0.8889 (p0) REVERT: D 1236 GLU cc_start: 0.8876 (tp30) cc_final: 0.8485 (tp30) REVERT: D 1254 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8260 (mt-10) REVERT: E 43 ASN cc_start: 0.9628 (t0) cc_final: 0.9409 (t0) REVERT: E 62 GLN cc_start: 0.9611 (mp10) cc_final: 0.9411 (mp10) REVERT: E 67 ARG cc_start: 0.9431 (ttm-80) cc_final: 0.9186 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1637 time to fit residues: 58.7462 Evaluate side-chains 175 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 181 optimal weight: 7.9990 chunk 176 optimal weight: 10.0000 chunk 214 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.061154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.043675 restraints weight = 147707.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.044955 restraints weight = 82940.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.045829 restraints weight = 56246.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.046408 restraints weight = 43334.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.046763 restraints weight = 36521.476| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 27074 Z= 0.250 Angle : 0.679 10.541 36910 Z= 0.352 Chirality : 0.044 0.258 4224 Planarity : 0.004 0.075 4556 Dihedral : 16.683 161.598 4407 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.51 % Favored : 90.43 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.78 % 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: -1.66 (0.15), residues: 3166 helix: 0.62 (0.15), residues: 1142 sheet: -1.88 (0.26), residues: 364 loop : -2.25 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 67 TYR 0.019 0.002 TYR D1241 PHE 0.026 0.002 PHE C1270 TRP 0.011 0.002 TRP D 580 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.25 (27070) covalent geometry : angle 0.67897 / 0.35 (36910) hydrogen bonds : bond 0.04576 / 3.29 ( 1025) hydrogen bonds : angle 4.78194 / 3.33 ( 2843) metal coordination : bond 0.00470 / 0.19 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.992 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: A 75 GLN cc_start: 0.9174 (tm-30) cc_final: 0.8681 (tm-30) REVERT: A 183 ILE cc_start: 0.9436 (mt) cc_final: 0.9083 (mm) REVERT: B 8 PHE cc_start: 0.8183 (p90) cc_final: 0.7221 (p90) REVERT: C 124 MET cc_start: 0.8904 (pmm) cc_final: 0.8329 (pmm) REVERT: C 239 MET cc_start: 0.8951 (ppp) cc_final: 0.8481 (tpt) REVERT: C 488 MET cc_start: 0.8176 (tpt) cc_final: 0.7882 (tpt) REVERT: C 510 GLN cc_start: 0.8512 (tt0) cc_final: 0.8284 (tm-30) REVERT: C 588 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7651 (mp0) REVERT: C 636 CYS cc_start: 0.7396 (m) cc_final: 0.7071 (m) REVERT: C 696 ASP cc_start: 0.9008 (t70) cc_final: 0.8664 (t0) REVERT: C 800 MET cc_start: 0.9304 (pmm) cc_final: 0.8957 (pmm) REVERT: C 930 ASP cc_start: 0.8803 (t70) cc_final: 0.8446 (t0) REVERT: C 1119 MET cc_start: 0.9453 (tpp) cc_final: 0.8897 (tpp) REVERT: C 1131 MET cc_start: 0.8925 (mtt) cc_final: 0.8670 (mmm) REVERT: C 1170 MET cc_start: 0.8947 (tmm) cc_final: 0.8685 (tmm) REVERT: C 1243 MET cc_start: 0.9000 (tmm) cc_final: 0.8781 (tmm) REVERT: D 29 MET cc_start: 0.9003 (ttm) cc_final: 0.8732 (ttp) REVERT: D 102 MET cc_start: 0.8670 (pmm) cc_final: 0.8328 (pmm) REVERT: D 237 MET cc_start: 0.8881 (ttm) cc_final: 0.8524 (tpp) REVERT: D 321 LYS cc_start: 0.8731 (mptt) cc_final: 0.8377 (mmtm) REVERT: D 375 GLU cc_start: 0.9150 (tp30) cc_final: 0.8689 (tm-30) REVERT: D 513 MET cc_start: 0.9064 (ttp) cc_final: 0.8725 (tmm) REVERT: D 644 MET cc_start: 0.9161 (mpp) cc_final: 0.8727 (mpp) REVERT: D 724 MET cc_start: 0.9350 (mtm) cc_final: 0.9024 (mtt) REVERT: D 725 MET cc_start: 0.8964 (mtp) cc_final: 0.8726 (tmm) REVERT: D 822 MET cc_start: 0.9120 (mmp) cc_final: 0.8676 (mmp) REVERT: D 1186 TYR cc_start: 0.8819 (m-80) cc_final: 0.8280 (m-10) REVERT: D 1189 MET cc_start: 0.8701 (ppp) cc_final: 0.8412 (ppp) REVERT: D 1236 GLU cc_start: 0.8820 (tp30) cc_final: 0.8429 (tp30) REVERT: D 1254 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8245 (mt-10) REVERT: E 7 GLN cc_start: 0.9350 (mm-40) cc_final: 0.8865 (mm-40) REVERT: E 43 ASN cc_start: 0.9637 (t0) cc_final: 0.9414 (t0) REVERT: E 62 GLN cc_start: 0.9591 (mp10) cc_final: 0.9387 (mp10) REVERT: E 72 GLN cc_start: 0.9407 (mm-40) cc_final: 0.8960 (mm-40) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.1649 time to fit residues: 57.5638 Evaluate side-chains 162 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 154 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 274 optimal weight: 30.0000 chunk 175 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 285 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.062137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.044643 restraints weight = 144830.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.045936 restraints weight = 80682.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.046847 restraints weight = 54574.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.047412 restraints weight = 41788.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.047846 restraints weight = 35135.280| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27074 Z= 0.138 Angle : 0.601 9.944 36910 Z= 0.313 Chirality : 0.044 0.265 4224 Planarity : 0.004 0.074 4556 Dihedral : 16.665 161.536 4407 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.71 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.15), residues: 3166 helix: 0.90 (0.16), residues: 1121 sheet: -1.75 (0.26), residues: 358 loop : -2.15 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 69 TYR 0.012 0.001 TYR C 5 PHE 0.022 0.001 PHE C 57 TRP 0.010 0.001 TRP D 580 HIS 0.003 0.001 HIS C 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (27070) covalent geometry : angle 0.60055 / 0.31 (36910) hydrogen bonds : bond 0.04139 / 2.97 ( 1025) hydrogen bonds : angle 4.52365 / 3.16 ( 2843) metal coordination : bond 0.00156 / 0.07 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 1.013 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 75 GLN cc_start: 0.9136 (tm-30) cc_final: 0.8668 (tm-30) REVERT: B 8 PHE cc_start: 0.8108 (p90) cc_final: 0.7183 (p90) REVERT: B 25 LYS cc_start: 0.9376 (ptmm) cc_final: 0.9044 (ptmm) REVERT: C 130 MET cc_start: 0.8542 (tpp) cc_final: 0.8342 (tpp) REVERT: C 239 MET cc_start: 0.8923 (ppp) cc_final: 0.8487 (tpt) REVERT: C 429 MET cc_start: 0.9240 (mmm) cc_final: 0.9028 (mmm) REVERT: C 484 LEU cc_start: 0.8563 (mp) cc_final: 0.7774 (tp) REVERT: C 510 GLN cc_start: 0.8509 (tt0) cc_final: 0.8263 (tm-30) REVERT: C 519 ASN cc_start: 0.8846 (t0) cc_final: 0.8413 (t0) REVERT: C 588 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7590 (mp0) REVERT: C 696 ASP cc_start: 0.8985 (t70) cc_final: 0.8590 (t0) REVERT: C 800 MET cc_start: 0.9312 (pmm) cc_final: 0.8835 (pmm) REVERT: C 930 ASP cc_start: 0.8773 (t70) cc_final: 0.8400 (t0) REVERT: C 1131 MET cc_start: 0.8899 (mtt) cc_final: 0.8562 (mmm) REVERT: C 1170 MET cc_start: 0.8950 (tmm) cc_final: 0.8711 (tmm) REVERT: C 1329 GLU cc_start: 0.9079 (tt0) cc_final: 0.8822 (tt0) REVERT: D 29 MET cc_start: 0.9012 (ttm) cc_final: 0.8734 (ttp) REVERT: D 102 MET cc_start: 0.8609 (pmm) cc_final: 0.8175 (pmm) REVERT: D 192 MET cc_start: 0.7996 (ppp) cc_final: 0.7794 (ppp) REVERT: D 321 LYS cc_start: 0.8747 (mptt) cc_final: 0.8391 (mmtm) REVERT: D 375 GLU cc_start: 0.9118 (tp30) cc_final: 0.8649 (tm-30) REVERT: D 513 MET cc_start: 0.9076 (ttp) cc_final: 0.8689 (tmm) REVERT: D 644 MET cc_start: 0.9155 (mpp) cc_final: 0.8676 (mpp) REVERT: D 724 MET cc_start: 0.9367 (mtm) cc_final: 0.9008 (mtt) REVERT: D 725 MET cc_start: 0.8939 (mtp) cc_final: 0.8666 (tmm) REVERT: D 822 MET cc_start: 0.9142 (mmp) cc_final: 0.8798 (mmp) REVERT: D 1186 TYR cc_start: 0.8810 (m-80) cc_final: 0.8254 (m-10) REVERT: D 1189 MET cc_start: 0.8716 (ppp) cc_final: 0.8418 (ppp) REVERT: D 1236 GLU cc_start: 0.8830 (tp30) cc_final: 0.8397 (tp30) REVERT: D 1254 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8221 (mt-10) REVERT: E 7 GLN cc_start: 0.9352 (mm-40) cc_final: 0.8995 (pp30) REVERT: E 43 ASN cc_start: 0.9639 (t0) cc_final: 0.9421 (t0) REVERT: E 62 GLN cc_start: 0.9587 (mp10) cc_final: 0.9386 (mp10) REVERT: E 72 GLN cc_start: 0.9401 (mm-40) cc_final: 0.9106 (mm-40) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.1688 time to fit residues: 59.8759 Evaluate side-chains 167 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 147 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 276 optimal weight: 0.3980 chunk 216 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 239 optimal weight: 8.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 979 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.062348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.044804 restraints weight = 144261.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.046124 restraints weight = 80431.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.047032 restraints weight = 54320.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.047637 restraints weight = 41579.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.047984 restraints weight = 34902.370| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27074 Z= 0.130 Angle : 0.597 10.156 36910 Z= 0.310 Chirality : 0.043 0.269 4224 Planarity : 0.004 0.074 4556 Dihedral : 16.638 161.950 4407 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.80 % Favored : 92.14 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.15), residues: 3166 helix: 0.97 (0.16), residues: 1127 sheet: -1.60 (0.27), residues: 351 loop : -2.09 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 67 TYR 0.015 0.001 TYR D 626 PHE 0.031 0.001 PHE C 253 TRP 0.009 0.001 TRP D 580 HIS 0.003 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (27070) covalent geometry : angle 0.59680 / 0.31 (36910) hydrogen bonds : bond 0.03917 / 2.81 ( 1025) hydrogen bonds : angle 4.42499 / 3.09 ( 2843) metal coordination : bond 0.00150 / 0.06 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.966 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: B 8 PHE cc_start: 0.8155 (p90) cc_final: 0.7313 (p90) REVERT: C 429 MET cc_start: 0.9245 (mmm) cc_final: 0.9034 (mmm) REVERT: C 484 LEU cc_start: 0.8577 (mp) cc_final: 0.7827 (tp) REVERT: C 510 GLN cc_start: 0.8492 (tt0) cc_final: 0.8267 (tm-30) REVERT: C 519 ASN cc_start: 0.8846 (t0) cc_final: 0.8413 (t0) REVERT: C 588 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7584 (mp0) REVERT: C 636 CYS cc_start: 0.7263 (m) cc_final: 0.6984 (m) REVERT: C 696 ASP cc_start: 0.8973 (t70) cc_final: 0.8593 (t0) REVERT: C 930 ASP cc_start: 0.8761 (t70) cc_final: 0.8361 (t0) REVERT: C 1085 MET cc_start: 0.9300 (mmt) cc_final: 0.8966 (mmt) REVERT: C 1131 MET cc_start: 0.8896 (mtt) cc_final: 0.8574 (mmm) REVERT: C 1170 MET cc_start: 0.8927 (tmm) cc_final: 0.8694 (tmm) REVERT: C 1243 MET cc_start: 0.9109 (tmm) cc_final: 0.8748 (tmm) REVERT: C 1279 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8686 (mt-10) REVERT: C 1315 MET cc_start: 0.8020 (tmm) cc_final: 0.7763 (tmm) REVERT: D 29 MET cc_start: 0.9025 (ttm) cc_final: 0.8791 (ttp) REVERT: D 102 MET cc_start: 0.8644 (pmm) cc_final: 0.8208 (pmm) REVERT: D 192 MET cc_start: 0.7988 (ppp) cc_final: 0.7778 (ppp) REVERT: D 321 LYS cc_start: 0.8731 (mptt) cc_final: 0.8376 (mmtm) REVERT: D 375 GLU cc_start: 0.9090 (tp30) cc_final: 0.8634 (tm-30) REVERT: D 513 MET cc_start: 0.9113 (ttp) cc_final: 0.8761 (tmm) REVERT: D 644 MET cc_start: 0.9191 (mpp) cc_final: 0.8689 (mpp) REVERT: D 724 MET cc_start: 0.9343 (mtm) cc_final: 0.9009 (mtt) REVERT: D 725 MET cc_start: 0.8994 (mtp) cc_final: 0.8664 (tmm) REVERT: D 822 MET cc_start: 0.9129 (mmp) cc_final: 0.8753 (mmp) REVERT: D 1186 TYR cc_start: 0.8757 (m-80) cc_final: 0.8203 (m-10) REVERT: D 1189 MET cc_start: 0.8672 (ppp) cc_final: 0.8387 (ppp) REVERT: D 1236 GLU cc_start: 0.8759 (tp30) cc_final: 0.8343 (tp30) REVERT: D 1254 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8193 (mt-10) REVERT: E 7 GLN cc_start: 0.9352 (mm-40) cc_final: 0.8956 (pp30) REVERT: E 43 ASN cc_start: 0.9649 (t0) cc_final: 0.9430 (t0) REVERT: E 72 GLN cc_start: 0.9381 (mm-40) cc_final: 0.9071 (mm-40) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.1600 time to fit residues: 58.0525 Evaluate side-chains 168 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 314 optimal weight: 4.9990 chunk 302 optimal weight: 0.9980 chunk 131 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 192 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 229 optimal weight: 0.9990 chunk 225 optimal weight: 0.9990 chunk 268 optimal weight: 20.0000 chunk 160 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.062534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.045465 restraints weight = 141396.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.046757 restraints weight = 79780.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.047642 restraints weight = 54079.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.048230 restraints weight = 41513.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.048588 restraints weight = 34815.090| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 27074 Z= 0.115 Angle : 0.589 10.886 36910 Z= 0.304 Chirality : 0.043 0.273 4224 Planarity : 0.004 0.073 4556 Dihedral : 16.603 161.800 4407 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.08 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.15), residues: 3166 helix: 1.12 (0.16), residues: 1114 sheet: -1.57 (0.26), residues: 371 loop : -2.01 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 67 TYR 0.015 0.001 TYR D 626 PHE 0.029 0.001 PHE C 253 TRP 0.009 0.001 TRP D 580 HIS 0.003 0.001 HIS D 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (27070) covalent geometry : angle 0.58947 / 0.30 (36910) hydrogen bonds : bond 0.03742 / 2.68 ( 1025) hydrogen bonds : angle 4.32598 / 3.02 ( 2843) metal coordination : bond 0.00096 / 0.04 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.814 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: B 8 PHE cc_start: 0.8038 (p90) cc_final: 0.7244 (p90) REVERT: C 124 MET cc_start: 0.8931 (pmm) cc_final: 0.8483 (pmm) REVERT: C 429 MET cc_start: 0.9248 (mmm) cc_final: 0.9030 (mmm) REVERT: C 484 LEU cc_start: 0.8540 (mp) cc_final: 0.7794 (tp) REVERT: C 510 GLN cc_start: 0.8540 (tt0) cc_final: 0.8231 (tm-30) REVERT: C 519 ASN cc_start: 0.8801 (t0) cc_final: 0.8406 (t0) REVERT: C 588 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7573 (mp0) REVERT: C 653 MET cc_start: 0.8498 (tpt) cc_final: 0.8210 (tpp) REVERT: C 696 ASP cc_start: 0.8904 (t70) cc_final: 0.8500 (t0) REVERT: C 800 MET cc_start: 0.9433 (pmm) cc_final: 0.9115 (pmm) REVERT: C 930 ASP cc_start: 0.8746 (t70) cc_final: 0.8346 (t0) REVERT: C 1085 MET cc_start: 0.9246 (mmt) cc_final: 0.8943 (mmt) REVERT: C 1131 MET cc_start: 0.8925 (mtt) cc_final: 0.8687 (mmm) REVERT: C 1170 MET cc_start: 0.8917 (tmm) cc_final: 0.8684 (tmm) REVERT: C 1243 MET cc_start: 0.9107 (tmm) cc_final: 0.8737 (tmm) REVERT: C 1279 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8666 (mt-10) REVERT: C 1329 GLU cc_start: 0.9078 (tt0) cc_final: 0.8789 (tt0) REVERT: D 29 MET cc_start: 0.8965 (ttm) cc_final: 0.8732 (ttp) REVERT: D 102 MET cc_start: 0.8549 (pmm) cc_final: 0.8094 (pmm) REVERT: D 192 MET cc_start: 0.7955 (ppp) cc_final: 0.7739 (ppp) REVERT: D 321 LYS cc_start: 0.8714 (mptt) cc_final: 0.8356 (mmtm) REVERT: D 375 GLU cc_start: 0.9075 (tp30) cc_final: 0.8679 (tm-30) REVERT: D 513 MET cc_start: 0.9098 (ttp) cc_final: 0.8783 (tmm) REVERT: D 644 MET cc_start: 0.9159 (mpp) cc_final: 0.8674 (mpp) REVERT: D 724 MET cc_start: 0.9332 (mtm) cc_final: 0.8976 (mtt) REVERT: D 725 MET cc_start: 0.8940 (mtp) cc_final: 0.8638 (tmm) REVERT: D 822 MET cc_start: 0.9115 (mmp) cc_final: 0.8724 (mmp) REVERT: D 1186 TYR cc_start: 0.8695 (m-80) cc_final: 0.8123 (m-10) REVERT: D 1189 MET cc_start: 0.8668 (ppp) cc_final: 0.8398 (ppp) REVERT: D 1236 GLU cc_start: 0.8733 (tp30) cc_final: 0.8317 (tp30) REVERT: D 1254 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8176 (mt-10) REVERT: E 7 GLN cc_start: 0.9344 (mm-40) cc_final: 0.8867 (mm-40) REVERT: E 43 ASN cc_start: 0.9647 (t0) cc_final: 0.9421 (t0) REVERT: E 72 GLN cc_start: 0.9384 (mm-40) cc_final: 0.9065 (mm-40) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.1562 time to fit residues: 57.0075 Evaluate side-chains 170 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 196 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 264 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 237 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 263 optimal weight: 10.0000 chunk 321 optimal weight: 30.0000 chunk 86 optimal weight: 4.9990 chunk 115 optimal weight: 0.3980 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.062294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.045035 restraints weight = 142148.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.046342 restraints weight = 79141.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.047209 restraints weight = 53485.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.047851 restraints weight = 41044.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.048229 restraints weight = 34359.207| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27074 Z= 0.129 Angle : 0.592 10.905 36910 Z= 0.306 Chirality : 0.043 0.273 4224 Planarity : 0.004 0.073 4556 Dihedral : 16.598 162.042 4407 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.49 % Favored : 92.45 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.15), residues: 3166 helix: 1.13 (0.16), residues: 1114 sheet: -1.59 (0.26), residues: 378 loop : -2.01 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1330 TYR 0.018 0.001 TYR C1229 PHE 0.028 0.001 PHE C 253 TRP 0.009 0.001 TRP D 580 HIS 0.003 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (27070) covalent geometry : angle 0.59168 / 0.31 (36910) hydrogen bonds : bond 0.03784 / 2.70 ( 1025) hydrogen bonds : angle 4.30896 / 3.01 ( 2843) metal coordination : bond 0.00166 / 0.07 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4385.03 seconds wall clock time: 76 minutes 38.83 seconds (4598.83 seconds total)