Starting phenix.real_space_refine on Mon Aug 25 09:31:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6flp_4274/08_2025/6flp_4274_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6flp_4274/08_2025/6flp_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 { model { file = "/net/cci-nas-00/data/ceres_data/6flp_4274/08_2025/6flp_4274_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6flp_4274/08_2025/6flp_4274_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6flp_4274/08_2025/6flp_4274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6flp_4274/08_2025/6flp_4274.map" } 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-2.0-5787/lib/python3.9/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: 5.77, per 1000 atoms: 0.22 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: 2.29 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 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: 2.86 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: 5.99 Time building geometry restraints manager: 2.92 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=" C ASP D1184 " pdb=" N PRO D1185 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.41e+00 bond pdb=" CA THR D 514 " pdb=" CB THR D 514 " ideal model delta sigma weight residual 1.528 1.564 -0.036 2.61e-02 1.47e+03 1.92e+00 bond pdb=" CA VAL D 83 " pdb=" CB VAL D 83 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.05e-02 9.07e+03 1.44e+00 bond pdb=" N ILE C 445 " pdb=" CA ILE C 445 " ideal model delta sigma weight residual 1.474 1.456 0.018 1.57e-02 4.06e+03 1.39e+00 bond pdb=" CA ASP D1184 " pdb=" C ASP D1184 " ideal model delta sigma weight residual 1.524 1.537 -0.013 1.26e-02 6.30e+03 1.06e+00 ... (remaining 27065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 36192 1.71 - 3.42: 629 3.42 - 5.13: 75 5.13 - 6.84: 10 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=" 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=" N ILE D1253 " pdb=" CA ILE D1253 " pdb=" C ILE D1253 " ideal model delta sigma weight residual 111.81 108.46 3.35 8.60e-01 1.35e+00 1.52e+01 angle pdb=" C VAL C 727 " pdb=" N ASP C 728 " pdb=" CA ASP C 728 " ideal model delta sigma weight residual 122.44 117.90 4.54 1.19e+00 7.06e-01 1.45e+01 angle pdb=" C TYR D 46 " pdb=" N ARG D 47 " pdb=" CA ARG D 47 " ideal model delta sigma weight residual 121.54 128.51 -6.97 1.91e+00 2.74e-01 1.33e+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: 2938 0.035 - 0.071: 890 0.071 - 0.106: 292 0.106 - 0.141: 95 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 28.450 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.256 27074 Z= 0.149 Angle : 0.571 8.550 36910 Z= 0.340 Chirality : 0.041 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 aren 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 covalent geometry : bond 0.00222 (27070) covalent geometry : angle 0.57086 (36910) hydrogen bonds : bond 0.18063 ( 1025) hydrogen bonds : angle 6.33904 ( 2843) metal coordination : bond 0.21324 ( 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 : 0.893 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 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: 0.8654 (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: 0.1996 time to fit residues: 153.6952 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 : 0.963 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 HIS A 132 HIS B 66 HIS ** 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 C1209 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.062332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.045041 restraints weight = 144924.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.046365 restraints weight = 80862.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.047279 restraints weight = 54603.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.047858 restraints weight = 41723.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.048284 restraints weight = 35003.569| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 27074 Z= 0.211 Angle : 0.643 8.108 36910 Z= 0.337 Chirality : 0.043 0.217 4224 Planarity : 0.005 0.076 4556 Dihedral : 16.319 154.835 4407 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.40 % Favored : 91.54 % Rotamer: Outliers : 0.04 % Allowed : 3.15 % Favored : 96.81 % 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 aren not related in a simple way. whole: -2.24 (0.14), residues: 3166 helix: 0.32 (0.16), residues: 1118 sheet: -2.26 (0.24), residues: 392 loop : -2.68 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1149 TYR 0.021 0.002 TYR A 177 PHE 0.027 0.002 PHE D 892 TRP 0.014 0.002 TRP D 409 HIS 0.005 0.001 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00458 (27070) covalent geometry : angle 0.64324 (36910) hydrogen bonds : bond 0.04689 ( 1025) hydrogen bonds : angle 4.80602 ( 2843) metal coordination : bond 0.00543 ( 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 260 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 259 time to evaluate : 0.881 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: 0.9053 (tm-30) cc_final: 0.8820 (tm-30) REVERT: A 142 MET cc_start: 0.8663 (ptp) cc_final: 0.8457 (ptp) REVERT: B 8 PHE cc_start: 0.8106 (p90) cc_final: 0.7061 (p90) REVERT: B 25 LYS cc_start: 0.9335 (ptmm) cc_final: 0.9003 (ptmm) REVERT: C 124 MET cc_start: 0.8840 (pmm) cc_final: 0.8535 (pmm) REVERT: C 239 MET cc_start: 0.8988 (ppp) cc_final: 0.8644 (tpt) REVERT: C 484 LEU cc_start: 0.8789 (mt) cc_final: 0.8193 (tp) REVERT: C 519 ASN cc_start: 0.8794 (t0) cc_final: 0.8342 (t0) REVERT: C 696 ASP cc_start: 0.9005 (t70) cc_final: 0.8624 (t0) REVERT: C 996 ARG cc_start: 0.8739 (tmt-80) cc_final: 0.8470 (tpt90) REVERT: C 1080 ASN cc_start: 0.9073 (m110) cc_final: 0.8816 (m-40) REVERT: C 1119 MET cc_start: 0.9373 (tpp) cc_final: 0.9060 (tpp) REVERT: C 1243 MET cc_start: 0.9072 (tmm) cc_final: 0.8857 (tmm) REVERT: D 29 MET cc_start: 0.8988 (ttm) cc_final: 0.8730 (ttp) REVERT: D 183 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8950 (pm20) REVERT: D 321 LYS cc_start: 0.8599 (mptt) cc_final: 0.8106 (mmtt) REVERT: D 375 GLU cc_start: 0.9191 (tp30) cc_final: 0.8718 (tm-30) REVERT: D 466 MET cc_start: 0.8728 (mtp) cc_final: 0.8515 (mtp) REVERT: D 513 MET cc_start: 0.9134 (ttp) cc_final: 0.8749 (tmm) REVERT: D 698 MET cc_start: 0.9419 (mmt) cc_final: 0.9187 (tpp) REVERT: D 725 MET cc_start: 0.8938 (mtp) cc_final: 0.8644 (tmm) REVERT: D 1186 TYR cc_start: 0.8728 (m-10) cc_final: 0.8436 (m-10) REVERT: D 1189 MET cc_start: 0.8678 (ppp) cc_final: 0.8352 (ppp) REVERT: D 1236 GLU cc_start: 0.8943 (tp30) cc_final: 0.8604 (tp30) REVERT: D 1254 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8440 (mt-10) REVERT: E 62 GLN cc_start: 0.9612 (mp10) cc_final: 0.9391 (mp10) outliers start: 1 outliers final: 1 residues processed: 259 average time/residue: 0.1613 time to fit residues: 66.1094 Evaluate side-chains 186 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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: 9.9990 chunk 249 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 267 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS ** C 65 ASN ** 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 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.061746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.044223 restraints weight = 146780.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.045581 restraints weight = 81171.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.046492 restraints weight = 54555.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.047114 restraints weight = 41763.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.047467 restraints weight = 34962.413| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27074 Z= 0.193 Angle : 0.607 8.371 36910 Z= 0.318 Chirality : 0.042 0.209 4224 Planarity : 0.004 0.078 4556 Dihedral : 16.465 159.446 4407 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.86 % Favored : 92.07 % Rotamer: Outliers : 0.04 % Allowed : 2.97 % Favored : 97.00 % 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 aren not related in a simple way. whole: -1.82 (0.15), residues: 3166 helix: 0.66 (0.16), residues: 1120 sheet: -1.91 (0.27), residues: 345 loop : -2.47 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 69 TYR 0.017 0.001 TYR D1241 PHE 0.021 0.002 PHE C 57 TRP 0.010 0.001 TRP D 409 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00417 (27070) covalent geometry : angle 0.60690 (36910) hydrogen bonds : bond 0.04348 ( 1025) hydrogen bonds : angle 4.62376 ( 2843) metal coordination : bond 0.00265 ( 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 230 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 0.661 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: 0.8130 (p90) cc_final: 0.7166 (p90) REVERT: B 227 GLN cc_start: 0.8827 (tt0) cc_final: 0.8559 (tt0) REVERT: C 124 MET cc_start: 0.8863 (pmm) cc_final: 0.8622 (pmm) REVERT: C 239 MET cc_start: 0.8951 (ppp) cc_final: 0.8546 (tpt) REVERT: C 319 LEU cc_start: 0.9108 (mt) cc_final: 0.8884 (tp) REVERT: C 519 ASN cc_start: 0.8800 (t0) cc_final: 0.8390 (t0) REVERT: C 696 ASP cc_start: 0.9039 (t70) cc_final: 0.8620 (t0) REVERT: C 800 MET cc_start: 0.9273 (pmm) cc_final: 0.9035 (pmm) REVERT: C 930 ASP cc_start: 0.8754 (t70) cc_final: 0.8341 (t0) REVERT: C 1064 ASP cc_start: 0.8102 (m-30) cc_final: 0.7554 (m-30) REVERT: C 1119 MET cc_start: 0.9456 (tpp) cc_final: 0.8982 (tpp) REVERT: C 1131 MET cc_start: 0.8947 (mtt) cc_final: 0.8680 (mmm) REVERT: C 1170 MET cc_start: 0.8921 (tmm) cc_final: 0.8666 (tmm) REVERT: C 1304 MET cc_start: 0.9157 (tpp) cc_final: 0.8878 (tpp) REVERT: D 29 MET cc_start: 0.9012 (ttm) cc_final: 0.8758 (ttp) REVERT: D 321 LYS cc_start: 0.8665 (mptt) cc_final: 0.8184 (mmtt) REVERT: D 372 MET cc_start: 0.8951 (mtm) cc_final: 0.8596 (ptm) REVERT: D 375 GLU cc_start: 0.9209 (tp30) cc_final: 0.8708 (tm-30) REVERT: D 466 MET cc_start: 0.8743 (mtp) cc_final: 0.8490 (mtp) REVERT: D 513 MET cc_start: 0.9196 (ttp) cc_final: 0.8734 (tmm) REVERT: D 644 MET cc_start: 0.9289 (mpp) cc_final: 0.8985 (mpp) REVERT: D 698 MET cc_start: 0.9426 (mmt) cc_final: 0.9167 (tpp) REVERT: D 724 MET cc_start: 0.9287 (mtt) cc_final: 0.8935 (mtt) REVERT: D 1186 TYR cc_start: 0.8706 (m-10) cc_final: 0.8367 (m-10) REVERT: D 1189 MET cc_start: 0.8721 (ppp) cc_final: 0.8390 (ppp) REVERT: D 1236 GLU cc_start: 0.8914 (tp30) cc_final: 0.8522 (tp30) REVERT: D 1254 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8255 (mt-10) REVERT: D 1327 GLU cc_start: 0.7295 (tp30) cc_final: 0.7026 (tp30) REVERT: E 7 GLN cc_start: 0.9412 (mm110) cc_final: 0.8920 (mm-40) REVERT: E 62 GLN cc_start: 0.9631 (mp10) cc_final: 0.9413 (mp10) outliers start: 1 outliers final: 0 residues processed: 230 average time/residue: 0.1422 time to fit residues: 53.3862 Evaluate side-chains 172 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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: 1.9990 chunk 38 optimal weight: 7.9990 chunk 167 optimal weight: 4.9990 chunk 314 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 214 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 235 optimal weight: 3.9990 chunk 295 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.062203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.045036 restraints weight = 142799.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.046347 restraints weight = 79102.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.047263 restraints weight = 53075.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.047888 restraints weight = 40474.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.048240 restraints weight = 33700.710| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27074 Z= 0.146 Angle : 0.565 9.593 36910 Z= 0.295 Chirality : 0.041 0.206 4224 Planarity : 0.004 0.077 4556 Dihedral : 16.476 159.592 4407 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.26 % Favored : 92.67 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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 aren not related in a simple way. whole: -1.54 (0.15), residues: 3166 helix: 0.94 (0.16), residues: 1115 sheet: -1.82 (0.27), residues: 362 loop : -2.31 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 45 TYR 0.012 0.001 TYR C1229 PHE 0.018 0.001 PHE C 57 TRP 0.008 0.001 TRP D 409 HIS 0.004 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00317 (27070) covalent geometry : angle 0.56523 (36910) hydrogen bonds : bond 0.03887 ( 1025) hydrogen bonds : angle 4.39601 ( 2843) metal coordination : bond 0.00196 ( 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 220 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.975 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: 0.8062 (p90) cc_final: 0.7144 (p90) REVERT: B 227 GLN cc_start: 0.8939 (tt0) cc_final: 0.8712 (tt0) REVERT: C 124 MET cc_start: 0.8835 (pmm) cc_final: 0.8585 (pmm) REVERT: C 239 MET cc_start: 0.8891 (ppp) cc_final: 0.8579 (tpt) REVERT: C 370 MET cc_start: 0.9138 (tmm) cc_final: 0.8832 (tmm) REVERT: C 484 LEU cc_start: 0.8595 (mp) cc_final: 0.7804 (tp) REVERT: C 488 MET cc_start: 0.8418 (tpt) cc_final: 0.8038 (tpp) REVERT: C 519 ASN cc_start: 0.8816 (t0) cc_final: 0.8449 (t0) REVERT: C 696 ASP cc_start: 0.8962 (t70) cc_final: 0.8545 (t0) REVERT: C 930 ASP cc_start: 0.8736 (t70) cc_final: 0.8309 (t0) REVERT: C 1064 ASP cc_start: 0.8059 (m-30) cc_final: 0.7551 (m-30) REVERT: C 1131 MET cc_start: 0.8935 (mtt) cc_final: 0.8675 (mmm) REVERT: C 1170 MET cc_start: 0.8943 (tmm) cc_final: 0.8691 (tmm) REVERT: C 1304 MET cc_start: 0.9103 (tpp) cc_final: 0.8786 (tpp) REVERT: D 29 MET cc_start: 0.9000 (ttm) cc_final: 0.8727 (ttp) REVERT: D 102 MET cc_start: 0.8504 (pmm) cc_final: 0.8262 (pmm) REVERT: D 321 LYS cc_start: 0.8708 (mptt) cc_final: 0.8158 (mmtt) REVERT: D 375 GLU cc_start: 0.9164 (tp30) cc_final: 0.8696 (tm-30) REVERT: D 466 MET cc_start: 0.8702 (mtp) cc_final: 0.8461 (mtp) REVERT: D 513 MET cc_start: 0.9195 (ttp) cc_final: 0.8733 (tmm) REVERT: D 644 MET cc_start: 0.9189 (mpp) cc_final: 0.8840 (mpp) REVERT: D 698 MET cc_start: 0.9407 (mmt) cc_final: 0.9192 (tpp) REVERT: D 724 MET cc_start: 0.9220 (mtt) cc_final: 0.8830 (mtt) REVERT: D 1186 TYR cc_start: 0.8515 (m-10) cc_final: 0.8263 (m-10) REVERT: D 1189 MET cc_start: 0.8748 (ppp) cc_final: 0.8414 (ppp) REVERT: D 1236 GLU cc_start: 0.8843 (tp30) cc_final: 0.8418 (tp30) REVERT: D 1254 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8192 (mt-10) REVERT: E 7 GLN cc_start: 0.9409 (mm110) cc_final: 0.9052 (pp30) REVERT: E 62 GLN cc_start: 0.9607 (mp10) cc_final: 0.9398 (mp10) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.1578 time to fit residues: 57.2113 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 : 1.035 ------------------------------------------------------------------------------- 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: 3.9990 chunk 242 optimal weight: 9.9990 chunk 70 optimal weight: 0.0470 chunk 169 optimal weight: 7.9990 chunk 188 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 224 optimal weight: 6.9990 chunk 260 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 174 optimal weight: 6.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 HIS C 618 GLN C 628 HIS C 658 GLN C1080 ASN ** 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** D 593 ASN D 907 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.061683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.044140 restraints weight = 146201.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.045445 restraints weight = 81836.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.046332 restraints weight = 55376.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.046910 restraints weight = 42589.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.047317 restraints weight = 35784.086| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27074 Z= 0.177 Angle : 0.596 10.211 36910 Z= 0.310 Chirality : 0.042 0.208 4224 Planarity : 0.004 0.074 4556 Dihedral : 16.533 159.401 4407 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.31 % Favored : 91.63 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % 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 aren not related in a simple way. whole: -1.43 (0.15), residues: 3166 helix: 0.95 (0.16), residues: 1129 sheet: -1.69 (0.27), residues: 365 loop : -2.22 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 838 TYR 0.013 0.001 TYR C 367 PHE 0.018 0.001 PHE C 57 TRP 0.011 0.001 TRP D 580 HIS 0.004 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00383 (27070) covalent geometry : angle 0.59605 (36910) hydrogen bonds : bond 0.04048 ( 1025) hydrogen bonds : angle 4.44678 ( 2843) metal coordination : bond 0.00289 ( 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 201 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.655 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: 0.8115 (p90) cc_final: 0.7258 (p90) REVERT: C 176 ILE cc_start: 0.9422 (mt) cc_final: 0.9049 (tt) REVERT: C 239 MET cc_start: 0.8924 (ppp) cc_final: 0.8541 (tpt) REVERT: C 484 LEU cc_start: 0.8605 (mp) cc_final: 0.7817 (tp) REVERT: C 696 ASP cc_start: 0.8952 (t70) cc_final: 0.8567 (t0) REVERT: C 800 MET cc_start: 0.9348 (pmm) cc_final: 0.9014 (pmm) REVERT: C 930 ASP cc_start: 0.8778 (t70) cc_final: 0.8372 (t0) REVERT: C 1064 ASP cc_start: 0.8024 (m-30) cc_final: 0.7595 (m-30) REVERT: C 1119 MET cc_start: 0.9402 (tpp) cc_final: 0.8867 (tpp) REVERT: C 1131 MET cc_start: 0.8937 (mtt) cc_final: 0.8636 (mmm) REVERT: C 1170 MET cc_start: 0.8956 (tmm) cc_final: 0.8729 (tmm) REVERT: C 1243 MET cc_start: 0.9017 (tmm) cc_final: 0.8787 (tmm) REVERT: C 1290 MET cc_start: 0.9451 (ttm) cc_final: 0.9110 (ttm) REVERT: D 29 MET cc_start: 0.8963 (ttm) cc_final: 0.8734 (ttp) REVERT: D 102 MET cc_start: 0.8576 (pmm) cc_final: 0.8213 (pmm) REVERT: D 192 MET cc_start: 0.8016 (ppp) cc_final: 0.7810 (ppp) REVERT: D 321 LYS cc_start: 0.8753 (mptt) cc_final: 0.8415 (mmtm) REVERT: D 375 GLU cc_start: 0.9141 (tp30) cc_final: 0.8710 (tm-30) REVERT: D 513 MET cc_start: 0.9165 (ttp) cc_final: 0.8732 (tmm) REVERT: D 644 MET cc_start: 0.9202 (mpp) cc_final: 0.8818 (mpp) REVERT: D 698 MET cc_start: 0.9416 (mmt) cc_final: 0.9200 (tpp) REVERT: D 724 MET cc_start: 0.9120 (mtt) cc_final: 0.8781 (mtt) REVERT: D 1186 TYR cc_start: 0.8557 (m-10) cc_final: 0.8282 (m-10) REVERT: D 1189 MET cc_start: 0.8713 (ppp) cc_final: 0.8386 (ppp) REVERT: D 1219 ASP cc_start: 0.9161 (p0) cc_final: 0.8941 (p0) REVERT: D 1236 GLU cc_start: 0.8823 (tp30) cc_final: 0.8386 (tp30) REVERT: D 1254 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8208 (mt-10) REVERT: D 1327 GLU cc_start: 0.7398 (mm-30) cc_final: 0.6945 (tp30) REVERT: E 7 GLN cc_start: 0.9433 (mm110) cc_final: 0.9081 (pp30) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.1561 time to fit residues: 51.5130 Evaluate side-chains 160 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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: 9.9990 chunk 135 optimal weight: 9.9990 chunk 239 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 269 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN D 897 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.060225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.042693 restraints weight = 148965.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.043938 restraints weight = 84131.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.044807 restraints weight = 57364.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.045381 restraints weight = 44250.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.045720 restraints weight = 37363.448| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 27074 Z= 0.255 Angle : 0.682 9.667 36910 Z= 0.354 Chirality : 0.043 0.229 4224 Planarity : 0.005 0.078 4556 Dihedral : 16.773 160.948 4407 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.70 % Favored : 90.24 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % 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 aren not related in a simple way. whole: -1.55 (0.15), residues: 3166 helix: 0.70 (0.16), residues: 1133 sheet: -1.65 (0.26), residues: 373 loop : -2.20 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 838 TYR 0.022 0.002 TYR C 367 PHE 0.022 0.002 PHE C 57 TRP 0.013 0.002 TRP D 580 HIS 0.005 0.001 HIS C 832 Details of bonding type rmsd covalent geometry : bond 0.00546 (27070) covalent geometry : angle 0.68225 (36910) hydrogen bonds : bond 0.04664 ( 1025) hydrogen bonds : angle 4.74654 ( 2843) metal coordination : bond 0.00500 ( 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 192 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.720 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: 0.8257 (p90) cc_final: 0.7376 (p90) REVERT: C 124 MET cc_start: 0.8985 (pmm) cc_final: 0.8496 (pmm) REVERT: C 176 ILE cc_start: 0.9350 (mt) cc_final: 0.8959 (tt) REVERT: C 696 ASP cc_start: 0.9014 (t70) cc_final: 0.8674 (t0) REVERT: C 800 MET cc_start: 0.9352 (pmm) cc_final: 0.8967 (pmm) REVERT: C 1064 ASP cc_start: 0.8075 (m-30) cc_final: 0.7576 (m-30) REVERT: C 1119 MET cc_start: 0.9470 (tpp) cc_final: 0.9119 (tpp) REVERT: C 1131 MET cc_start: 0.8923 (mtt) cc_final: 0.8466 (mmp) REVERT: C 1170 MET cc_start: 0.8973 (tmm) cc_final: 0.8767 (tmm) REVERT: C 1290 MET cc_start: 0.9418 (ttm) cc_final: 0.9053 (ttm) REVERT: C 1304 MET cc_start: 0.9154 (tpp) cc_final: 0.8899 (tpp) REVERT: D 29 MET cc_start: 0.8962 (ttm) cc_final: 0.8655 (ttp) REVERT: D 102 MET cc_start: 0.8648 (pmm) cc_final: 0.8102 (pmm) REVERT: D 321 LYS cc_start: 0.8852 (mptt) cc_final: 0.8490 (mmtm) REVERT: D 375 GLU cc_start: 0.9167 (tp30) cc_final: 0.8771 (tm-30) REVERT: D 644 MET cc_start: 0.9250 (mpp) cc_final: 0.8811 (mpp) REVERT: D 698 MET cc_start: 0.9438 (mmt) cc_final: 0.9106 (tpp) REVERT: D 724 MET cc_start: 0.9183 (mtt) cc_final: 0.8817 (mtt) REVERT: D 1040 MET cc_start: 0.4157 (ttp) cc_final: 0.3685 (ppp) REVERT: D 1186 TYR cc_start: 0.8661 (m-10) cc_final: 0.8305 (m-10) REVERT: D 1189 MET cc_start: 0.8768 (ppp) cc_final: 0.8455 (tmm) REVERT: D 1219 ASP cc_start: 0.9260 (p0) cc_final: 0.9034 (p0) REVERT: D 1236 GLU cc_start: 0.8765 (tp30) cc_final: 0.8313 (tp30) REVERT: D 1254 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8260 (mt-10) REVERT: D 1327 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7072 (mm-30) REVERT: E 7 GLN cc_start: 0.9429 (mm110) cc_final: 0.9000 (mm-40) REVERT: E 43 ASN cc_start: 0.9563 (t0) cc_final: 0.9328 (t0) REVERT: E 62 GLN cc_start: 0.9626 (mp10) cc_final: 0.9414 (mp10) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.1731 time to fit residues: 54.4174 Evaluate side-chains 150 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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: 0.0170 chunk 176 optimal weight: 6.9990 chunk 214 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 23 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 195 optimal weight: 5.9990 chunk 208 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 200 optimal weight: 5.9990 overall best weight: 0.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 979 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.062575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.045234 restraints weight = 141701.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.046591 restraints weight = 77906.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.047512 restraints weight = 52078.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.048073 restraints weight = 39676.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.048529 restraints weight = 33193.896| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27074 Z= 0.110 Angle : 0.564 11.659 36910 Z= 0.292 Chirality : 0.042 0.204 4224 Planarity : 0.004 0.075 4556 Dihedral : 16.595 162.656 4407 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.38 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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 aren not related in a simple way. whole: -1.16 (0.15), residues: 3166 helix: 1.15 (0.16), residues: 1113 sheet: -1.43 (0.27), residues: 388 loop : -2.04 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 54 TYR 0.013 0.001 TYR C1229 PHE 0.031 0.001 PHE C 253 TRP 0.014 0.001 TRP D 236 HIS 0.003 0.001 HIS D 450 Details of bonding type rmsd covalent geometry : bond 0.00233 (27070) covalent geometry : angle 0.56444 (36910) hydrogen bonds : bond 0.03586 ( 1025) hydrogen bonds : angle 4.21472 ( 2843) metal coordination : bond 0.00054 ( 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 224 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.901 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: B 8 PHE cc_start: 0.7936 (p90) cc_final: 0.7171 (p90) REVERT: C 176 ILE cc_start: 0.9340 (mt) cc_final: 0.8989 (tt) REVERT: C 260 LYS cc_start: 0.7389 (mptt) cc_final: 0.7012 (mmtp) REVERT: C 429 MET cc_start: 0.9243 (mmm) cc_final: 0.9016 (mmm) REVERT: C 653 MET cc_start: 0.8286 (tpt) cc_final: 0.7965 (tpt) REVERT: C 696 ASP cc_start: 0.8916 (t70) cc_final: 0.8479 (t0) REVERT: C 800 MET cc_start: 0.9428 (pmm) cc_final: 0.9205 (pmm) REVERT: C 930 ASP cc_start: 0.8747 (t70) cc_final: 0.8294 (t0) REVERT: C 996 ARG cc_start: 0.8810 (tmt-80) cc_final: 0.8427 (tpt90) REVERT: C 1064 ASP cc_start: 0.7974 (m-30) cc_final: 0.7494 (m-30) REVERT: C 1119 MET cc_start: 0.9420 (tpp) cc_final: 0.9013 (tpp) REVERT: C 1131 MET cc_start: 0.8952 (mtt) cc_final: 0.8479 (mmp) REVERT: C 1170 MET cc_start: 0.8972 (tmm) cc_final: 0.8714 (tmm) REVERT: C 1232 MET cc_start: 0.8834 (tpp) cc_final: 0.8421 (mmm) REVERT: C 1290 MET cc_start: 0.9397 (ttm) cc_final: 0.8706 (ttm) REVERT: C 1315 MET cc_start: 0.7846 (tmm) cc_final: 0.7634 (tmm) REVERT: C 1329 GLU cc_start: 0.9117 (tt0) cc_final: 0.8752 (tt0) REVERT: D 29 MET cc_start: 0.8962 (ttm) cc_final: 0.8635 (ttp) REVERT: D 102 MET cc_start: 0.8630 (pmm) cc_final: 0.8183 (pmm) REVERT: D 192 MET cc_start: 0.7994 (ppp) cc_final: 0.7769 (ppp) REVERT: D 321 LYS cc_start: 0.8785 (mptt) cc_final: 0.8446 (mmtm) REVERT: D 375 GLU cc_start: 0.9111 (tp30) cc_final: 0.8676 (tm-30) REVERT: D 513 MET cc_start: 0.9221 (ttp) cc_final: 0.8938 (ttp) REVERT: D 622 ASP cc_start: 0.8654 (t0) cc_final: 0.8418 (t0) REVERT: D 644 MET cc_start: 0.9218 (mpp) cc_final: 0.8848 (mpp) REVERT: D 698 MET cc_start: 0.9406 (mmt) cc_final: 0.9077 (tpp) REVERT: D 724 MET cc_start: 0.9068 (mtt) cc_final: 0.8680 (mtt) REVERT: D 1040 MET cc_start: 0.3987 (ttp) cc_final: 0.3770 (ppp) REVERT: D 1186 TYR cc_start: 0.8505 (m-10) cc_final: 0.8233 (m-10) REVERT: D 1189 MET cc_start: 0.8681 (ppp) cc_final: 0.8403 (ppp) REVERT: D 1219 ASP cc_start: 0.9152 (p0) cc_final: 0.8907 (p0) REVERT: D 1236 GLU cc_start: 0.8822 (tp30) cc_final: 0.8349 (tp30) REVERT: D 1254 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8150 (mt-10) REVERT: D 1327 GLU cc_start: 0.7431 (mm-30) cc_final: 0.6971 (tp30) REVERT: E 7 GLN cc_start: 0.9450 (mm110) cc_final: 0.9029 (mm-40) REVERT: E 43 ASN cc_start: 0.9583 (t0) cc_final: 0.9367 (t0) REVERT: E 62 GLN cc_start: 0.9604 (mp10) cc_final: 0.9370 (mp10) REVERT: E 75 GLN cc_start: 0.8892 (pt0) cc_final: 0.8581 (tp40) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1605 time to fit residues: 58.5871 Evaluate side-chains 166 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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: 0.5980 chunk 50 optimal weight: 9.9990 chunk 274 optimal weight: 20.0000 chunk 175 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 285 optimal weight: 30.0000 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN ** C 799 ASN ** 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 489 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.060723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.043541 restraints weight = 145148.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.044835 restraints weight = 81254.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.045716 restraints weight = 55000.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.046306 restraints weight = 42189.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.046671 restraints weight = 35311.183| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27074 Z= 0.204 Angle : 0.636 10.469 36910 Z= 0.329 Chirality : 0.042 0.231 4224 Planarity : 0.004 0.076 4556 Dihedral : 16.688 161.679 4407 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.37 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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 aren not related in a simple way. whole: -1.26 (0.15), residues: 3166 helix: 1.01 (0.16), residues: 1120 sheet: -1.65 (0.26), residues: 382 loop : -2.03 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 838 TYR 0.026 0.001 TYR C1281 PHE 0.021 0.002 PHE C 253 TRP 0.010 0.001 TRP D 580 HIS 0.005 0.001 HIS D 450 Details of bonding type rmsd covalent geometry : bond 0.00439 (27070) covalent geometry : angle 0.63647 (36910) hydrogen bonds : bond 0.04151 ( 1025) hydrogen bonds : angle 4.45146 ( 2843) metal coordination : bond 0.00373 ( 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 200 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.114 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: B 8 PHE cc_start: 0.8058 (p90) cc_final: 0.7184 (p90) REVERT: C 176 ILE cc_start: 0.9318 (mt) cc_final: 0.9009 (tp) REVERT: C 260 LYS cc_start: 0.7342 (mptt) cc_final: 0.7004 (mmtp) REVERT: C 653 MET cc_start: 0.8325 (tpt) cc_final: 0.8117 (tpt) REVERT: C 696 ASP cc_start: 0.8972 (t70) cc_final: 0.8596 (t0) REVERT: C 800 MET cc_start: 0.9422 (pmm) cc_final: 0.8984 (pmm) REVERT: C 930 ASP cc_start: 0.8832 (t70) cc_final: 0.8419 (t0) REVERT: C 996 ARG cc_start: 0.8778 (tmt-80) cc_final: 0.8408 (tpt90) REVERT: C 1064 ASP cc_start: 0.8104 (m-30) cc_final: 0.7622 (m-30) REVERT: C 1085 MET cc_start: 0.9332 (mmt) cc_final: 0.9010 (mmt) REVERT: C 1119 MET cc_start: 0.9477 (tpp) cc_final: 0.9061 (tpp) REVERT: C 1131 MET cc_start: 0.8960 (mtt) cc_final: 0.8527 (mmp) REVERT: C 1170 MET cc_start: 0.9017 (tmm) cc_final: 0.8783 (tmm) REVERT: C 1232 MET cc_start: 0.8858 (tpp) cc_final: 0.8523 (mmm) REVERT: C 1290 MET cc_start: 0.9405 (ttm) cc_final: 0.9071 (ttm) REVERT: D 29 MET cc_start: 0.9024 (ttm) cc_final: 0.8693 (ttp) REVERT: D 102 MET cc_start: 0.8690 (pmm) cc_final: 0.8143 (pmm) REVERT: D 151 MET cc_start: 0.5477 (mmp) cc_final: 0.3953 (mmp) REVERT: D 192 MET cc_start: 0.8010 (ppp) cc_final: 0.7790 (ppp) REVERT: D 321 LYS cc_start: 0.8818 (mptt) cc_final: 0.8472 (mmtm) REVERT: D 375 GLU cc_start: 0.9132 (tp30) cc_final: 0.8691 (tm-30) REVERT: D 513 MET cc_start: 0.9240 (ttp) cc_final: 0.8950 (ttp) REVERT: D 622 ASP cc_start: 0.8617 (t0) cc_final: 0.8407 (t0) REVERT: D 644 MET cc_start: 0.9219 (mpp) cc_final: 0.8652 (mpp) REVERT: D 698 MET cc_start: 0.9406 (mmt) cc_final: 0.9061 (tpp) REVERT: D 724 MET cc_start: 0.9082 (mtt) cc_final: 0.8706 (mtt) REVERT: D 1040 MET cc_start: 0.4019 (ttp) cc_final: 0.3660 (ppp) REVERT: D 1186 TYR cc_start: 0.8539 (m-10) cc_final: 0.8225 (m-10) REVERT: D 1189 MET cc_start: 0.8730 (ppp) cc_final: 0.8421 (ppp) REVERT: D 1219 ASP cc_start: 0.9260 (p0) cc_final: 0.9023 (p0) REVERT: D 1236 GLU cc_start: 0.8791 (tp30) cc_final: 0.8334 (tp30) REVERT: D 1254 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8230 (mt-10) REVERT: D 1327 GLU cc_start: 0.7469 (mm-30) cc_final: 0.6899 (tp30) REVERT: E 7 GLN cc_start: 0.9386 (mm110) cc_final: 0.9047 (mm-40) REVERT: E 43 ASN cc_start: 0.9590 (t0) cc_final: 0.9357 (t0) REVERT: E 62 GLN cc_start: 0.9629 (mp10) cc_final: 0.9418 (mp10) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.1638 time to fit residues: 53.4904 Evaluate side-chains 159 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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: 4.9990 chunk 65 optimal weight: 8.9990 chunk 215 optimal weight: 3.9990 chunk 86 optimal weight: 0.1980 chunk 130 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 276 optimal weight: 6.9990 chunk 216 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 164 optimal weight: 8.9990 chunk 239 optimal weight: 8.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.061410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.044184 restraints weight = 144386.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.045482 restraints weight = 80627.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.046336 restraints weight = 54465.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.046962 restraints weight = 41829.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.047304 restraints weight = 35097.367| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27074 Z= 0.153 Angle : 0.605 11.322 36910 Z= 0.312 Chirality : 0.042 0.217 4224 Planarity : 0.004 0.076 4556 Dihedral : 16.692 163.567 4407 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.61 % Favored : 92.32 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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 aren not related in a simple way. whole: -1.18 (0.15), residues: 3166 helix: 1.10 (0.16), residues: 1114 sheet: -1.62 (0.26), residues: 391 loop : -1.98 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 838 TYR 0.020 0.001 TYR C1281 PHE 0.025 0.001 PHE A 35 TRP 0.008 0.001 TRP D 580 HIS 0.006 0.001 HIS D 450 Details of bonding type rmsd covalent geometry : bond 0.00334 (27070) covalent geometry : angle 0.60489 (36910) hydrogen bonds : bond 0.03894 ( 1025) hydrogen bonds : angle 4.33936 ( 2843) metal coordination : bond 0.00364 ( 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 193 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.041 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: B 8 PHE cc_start: 0.8052 (p90) cc_final: 0.7360 (p90) REVERT: C 176 ILE cc_start: 0.9294 (mt) cc_final: 0.8932 (tt) REVERT: C 260 LYS cc_start: 0.7477 (mptt) cc_final: 0.7136 (mmtp) REVERT: C 488 MET cc_start: 0.7796 (tpt) cc_final: 0.7530 (tpp) REVERT: C 653 MET cc_start: 0.8324 (tpt) cc_final: 0.8108 (tpt) REVERT: C 696 ASP cc_start: 0.8959 (t70) cc_final: 0.8555 (t0) REVERT: C 800 MET cc_start: 0.9399 (pmm) cc_final: 0.8958 (pmm) REVERT: C 930 ASP cc_start: 0.8804 (t70) cc_final: 0.8385 (t0) REVERT: C 1064 ASP cc_start: 0.8045 (m-30) cc_final: 0.7588 (m-30) REVERT: C 1085 MET cc_start: 0.9234 (mmt) cc_final: 0.9026 (mmt) REVERT: C 1119 MET cc_start: 0.9472 (tpp) cc_final: 0.9041 (tpp) REVERT: C 1131 MET cc_start: 0.8968 (mtt) cc_final: 0.8530 (mmp) REVERT: C 1170 MET cc_start: 0.9005 (tmm) cc_final: 0.8764 (tmm) REVERT: C 1232 MET cc_start: 0.8843 (tpp) cc_final: 0.8525 (mmm) REVERT: C 1290 MET cc_start: 0.9343 (ttm) cc_final: 0.9001 (ttm) REVERT: C 1329 GLU cc_start: 0.9023 (tt0) cc_final: 0.8688 (tt0) REVERT: D 29 MET cc_start: 0.8977 (ttm) cc_final: 0.8644 (ttp) REVERT: D 102 MET cc_start: 0.8691 (pmm) cc_final: 0.8137 (pmm) REVERT: D 192 MET cc_start: 0.8007 (ppp) cc_final: 0.7791 (ppp) REVERT: D 321 LYS cc_start: 0.8815 (mptt) cc_final: 0.8458 (mmtm) REVERT: D 375 GLU cc_start: 0.9116 (tp30) cc_final: 0.8656 (tm-30) REVERT: D 513 MET cc_start: 0.9280 (ttp) cc_final: 0.8949 (ttp) REVERT: D 644 MET cc_start: 0.9115 (mpp) cc_final: 0.8621 (mpp) REVERT: D 698 MET cc_start: 0.9395 (mmt) cc_final: 0.9030 (tpp) REVERT: D 724 MET cc_start: 0.9064 (mtt) cc_final: 0.8688 (mtt) REVERT: D 1040 MET cc_start: 0.4246 (ttp) cc_final: 0.3676 (ppp) REVERT: D 1184 ASP cc_start: 0.8357 (p0) cc_final: 0.8094 (m-30) REVERT: D 1186 TYR cc_start: 0.8498 (m-10) cc_final: 0.8193 (m-10) REVERT: D 1189 MET cc_start: 0.8704 (ppp) cc_final: 0.8408 (ppp) REVERT: D 1219 ASP cc_start: 0.9214 (p0) cc_final: 0.8977 (p0) REVERT: D 1236 GLU cc_start: 0.8761 (tp30) cc_final: 0.8292 (tp30) REVERT: D 1254 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8179 (mt-10) REVERT: D 1327 GLU cc_start: 0.7432 (mm-30) cc_final: 0.6865 (tp30) REVERT: E 7 GLN cc_start: 0.9328 (mm110) cc_final: 0.8958 (mm-40) REVERT: E 43 ASN cc_start: 0.9519 (t0) cc_final: 0.9186 (t0) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1734 time to fit residues: 54.7242 Evaluate side-chains 152 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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: 0.9990 chunk 302 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 229 optimal weight: 9.9990 chunk 225 optimal weight: 0.8980 chunk 268 optimal weight: 5.9990 chunk 160 optimal weight: 0.2980 chunk 120 optimal weight: 6.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.062554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.045457 restraints weight = 141667.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.046779 restraints weight = 78606.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.047689 restraints weight = 52784.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.048309 restraints weight = 40180.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.048653 restraints weight = 33512.247| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 27074 Z= 0.112 Angle : 0.582 11.525 36910 Z= 0.295 Chirality : 0.042 0.217 4224 Planarity : 0.004 0.076 4556 Dihedral : 16.603 163.483 4407 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.95 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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 aren not related in a simple way. whole: -0.99 (0.15), residues: 3166 helix: 1.29 (0.16), residues: 1109 sheet: -1.34 (0.26), residues: 398 loop : -1.93 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 175 TYR 0.015 0.001 TYR D 144 PHE 0.030 0.001 PHE A 35 TRP 0.007 0.001 TRP D 580 HIS 0.005 0.001 HIS D 450 Details of bonding type rmsd covalent geometry : bond 0.00245 (27070) covalent geometry : angle 0.58164 (36910) hydrogen bonds : bond 0.03545 ( 1025) hydrogen bonds : angle 4.12796 ( 2843) metal coordination : bond 0.00090 ( 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 209 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 1.087 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: B 8 PHE cc_start: 0.7990 (p90) cc_final: 0.7472 (p90) REVERT: C 124 MET cc_start: 0.8895 (pmm) cc_final: 0.8493 (pmm) REVERT: C 176 ILE cc_start: 0.9339 (mt) cc_final: 0.8975 (tt) REVERT: C 260 LYS cc_start: 0.7554 (mptt) cc_final: 0.7328 (mmtp) REVERT: C 369 MET cc_start: 0.9341 (tmm) cc_final: 0.9136 (tmm) REVERT: C 696 ASP cc_start: 0.8840 (t70) cc_final: 0.8425 (t0) REVERT: C 930 ASP cc_start: 0.8830 (t70) cc_final: 0.8357 (t0) REVERT: C 1064 ASP cc_start: 0.8029 (m-30) cc_final: 0.7604 (m-30) REVERT: C 1084 ASP cc_start: 0.8633 (m-30) cc_final: 0.8428 (m-30) REVERT: C 1098 LEU cc_start: 0.9581 (mp) cc_final: 0.9346 (mp) REVERT: C 1119 MET cc_start: 0.9431 (tpp) cc_final: 0.8948 (tpp) REVERT: C 1126 ASP cc_start: 0.8696 (m-30) cc_final: 0.8441 (m-30) REVERT: C 1131 MET cc_start: 0.8958 (mtt) cc_final: 0.8527 (mmp) REVERT: C 1170 MET cc_start: 0.9015 (tmm) cc_final: 0.8759 (tmm) REVERT: C 1232 MET cc_start: 0.8872 (tpp) cc_final: 0.8462 (mmm) REVERT: C 1290 MET cc_start: 0.9374 (ttm) cc_final: 0.9006 (ttm) REVERT: C 1329 GLU cc_start: 0.9018 (tt0) cc_final: 0.8698 (tt0) REVERT: D 29 MET cc_start: 0.8930 (ttm) cc_final: 0.8608 (ttp) REVERT: D 102 MET cc_start: 0.8686 (pmm) cc_final: 0.8201 (pmm) REVERT: D 192 MET cc_start: 0.7977 (ppp) cc_final: 0.7758 (ppp) REVERT: D 321 LYS cc_start: 0.8800 (mptt) cc_final: 0.8419 (mmtm) REVERT: D 375 GLU cc_start: 0.9123 (tp30) cc_final: 0.8661 (tm-30) REVERT: D 513 MET cc_start: 0.9300 (ttp) cc_final: 0.8913 (ttp) REVERT: D 644 MET cc_start: 0.9148 (mpp) cc_final: 0.8634 (mpp) REVERT: D 698 MET cc_start: 0.9393 (mmt) cc_final: 0.9064 (tpp) REVERT: D 724 MET cc_start: 0.8992 (mtt) cc_final: 0.8589 (mtt) REVERT: D 1040 MET cc_start: 0.4286 (ttp) cc_final: 0.3750 (ppp) REVERT: D 1186 TYR cc_start: 0.8436 (m-10) cc_final: 0.8165 (m-10) REVERT: D 1189 MET cc_start: 0.8684 (ppp) cc_final: 0.8399 (ppp) REVERT: D 1219 ASP cc_start: 0.9185 (p0) cc_final: 0.8936 (p0) REVERT: D 1236 GLU cc_start: 0.8788 (tp30) cc_final: 0.8340 (tp30) REVERT: D 1254 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8157 (mt-10) REVERT: D 1327 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6762 (tp30) REVERT: E 7 GLN cc_start: 0.9240 (mm110) cc_final: 0.8912 (mm110) REVERT: E 43 ASN cc_start: 0.9557 (t0) cc_final: 0.9226 (t0) REVERT: E 62 GLN cc_start: 0.9606 (mp10) cc_final: 0.9402 (mp10) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1822 time to fit residues: 61.7642 Evaluate side-chains 165 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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: 7.9990 chunk 83 optimal weight: 9.9990 chunk 264 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 237 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 263 optimal weight: 9.9990 chunk 321 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 HIS C 327 GLN C 725 GLN ** C 799 ASN ** 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** E 75 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.059438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.041982 restraints weight = 150259.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.043232 restraints weight = 84667.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.044094 restraints weight = 57669.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.044640 restraints weight = 44585.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.045037 restraints weight = 37681.427| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 27074 Z= 0.296 Angle : 0.749 10.478 36910 Z= 0.386 Chirality : 0.045 0.250 4224 Planarity : 0.005 0.074 4556 Dihedral : 16.873 164.292 4407 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.39 % Favored : 89.55 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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 aren not related in a simple way. whole: -1.41 (0.15), residues: 3166 helix: 0.70 (0.16), residues: 1129 sheet: -1.49 (0.27), residues: 359 loop : -2.04 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 67 TYR 0.025 0.002 TYR D1241 PHE 0.023 0.002 PHE A 35 TRP 0.018 0.002 TRP C1276 HIS 0.008 0.001 HIS D 450 Details of bonding type rmsd covalent geometry : bond 0.00631 (27070) covalent geometry : angle 0.74864 (36910) hydrogen bonds : bond 0.04975 ( 1025) hydrogen bonds : angle 4.77915 ( 2843) metal coordination : bond 0.00555 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4414.73 seconds wall clock time: 77 minutes 4.42 seconds (4624.42 seconds total)