Starting phenix.real_space_refine on Mon Sep 14 13:56:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mki_23895/09_2026/7mki_23895.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mki_23895/09_2026/7mki_23895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mki_23895/09_2026/7mki_23895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mki_23895/09_2026/7mki_23895.map" model { file = "/net/cci-nas-00/data/ceres_data/7mki_23895/09_2026/7mki_23895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mki_23895/09_2026/7mki_23895.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7mki_23895/09_2026/7mki_23895.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mki_23895/09_2026/7mki_23895.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 95 5.49 5 Mg 1 5.21 5 S 128 5.16 5 C 19111 2.51 5 N 5460 2.21 5 O 6122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30919 Number of models: 1 Model: "" Number of chains: 10 Chain: "P" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 998 Classifications: {'DNA': 49} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 48} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DT:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1808 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain: "H" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1714 Classifications: {'peptide': 223} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain breaks: 1 Chain: "I" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1280} Chain: "J" Number of atoms: 10377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10377 Classifications: {'peptide': 1335} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 54, 'TRANS': 1278} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "L" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3787 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 450} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "Q" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 957 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain breaks: 1 Chain: "I" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'1N7': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 2} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15536 SG CYS J 70 100.607 129.805 113.399 1.00 58.80 S ATOM 15550 SG CYS J 72 98.437 132.572 114.843 1.00 60.73 S ATOM 15658 SG CYS J 85 101.740 131.565 116.494 1.00 77.39 S ATOM 15682 SG CYS J 88 98.685 129.106 116.392 1.00 70.87 S ATOM 21365 SG CYS J 814 125.243 72.789 87.626 1.00 53.88 S ATOM 21930 SG CYS J 888 121.798 74.142 88.527 1.00 45.02 S ATOM 21981 SG CYS J 895 123.405 75.043 85.177 1.00 34.28 S ATOM 22002 SG CYS J 898 122.218 71.628 85.656 1.00 39.66 S Time building chain proxies: 5.82, per 1000 atoms: 0.19 Number of scatterers: 30919 At special positions: 0 Unit cell: (151.41, 182.31, 186.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 128 16.00 P 95 15.00 Mg 1 11.99 O 6122 8.00 N 5460 7.00 C 19111 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: 2.43 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " Number of angles added : 12 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6820 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 52 sheets defined 41.0% alpha, 12.5% beta 39 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 3.46 Creating SS restraints... Processing helix chain 'G' and resid 35 through 50 removed outlier: 3.700A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 4.017A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 212 through 228 Processing helix chain 'G' and resid 229 through 231 No H-bonds generated for 'chain 'G' and resid 229 through 231' Processing helix chain 'H' and resid 34 through 50 removed outlier: 4.089A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.523A pdb=" N ILE H 81 " --> pdb=" O ASP H 77 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 227 Processing helix chain 'I' and resid 28 through 39 Processing helix chain 'I' and resid 49 through 57 removed outlier: 3.660A pdb=" N SER I 55 " --> pdb=" O ALA I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.985A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 270 through 280 Processing helix chain 'I' and resid 288 through 293 removed outlier: 3.625A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 327 removed outlier: 3.845A pdb=" N GLN I 327 " --> pdb=" O ALA I 323 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 354 Processing helix chain 'I' and resid 358 through 371 removed outlier: 3.983A pdb=" N MET I 369 " --> pdb=" O GLU I 365 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 389 removed outlier: 3.787A pdb=" N GLU I 382 " --> pdb=" O ARG I 378 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 480 Processing helix chain 'I' and resid 495 through 508 removed outlier: 3.701A pdb=" N ALA I 501 " --> pdb=" O PRO I 497 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 527 Processing helix chain 'I' and resid 551 through 555 removed outlier: 4.067A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 removed outlier: 3.648A pdb=" N HIS I 673 " --> pdb=" O PHE I 670 " (cutoff:3.500A) Processing helix chain 'I' and resid 675 through 686 Processing helix chain 'I' and resid 687 through 689 No H-bonds generated for 'chain 'I' and resid 687 through 689' Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 738 through 741 removed outlier: 3.585A pdb=" N MET I 741 " --> pdb=" O GLU I 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 738 through 741' Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 898 through 907 Processing helix chain 'I' and resid 942 through 979 Processing helix chain 'I' and resid 995 through 1000 removed outlier: 4.266A pdb=" N LEU I 998 " --> pdb=" O ASP I 995 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU I 999 " --> pdb=" O ARG I 996 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU I1000 " --> pdb=" O TRP I 997 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 995 through 1000' Processing helix chain 'I' and resid 1007 through 1038 removed outlier: 4.613A pdb=" N GLU I1012 " --> pdb=" O GLN I1008 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLN I1013 " --> pdb=" O ASN I1009 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU I1026 " --> pdb=" O LYS I1022 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.671A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1138 through 1149 Processing helix chain 'I' and resid 1167 through 1176 removed outlier: 3.569A pdb=" N LEU I1172 " --> pdb=" O GLU I1168 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1243 Processing helix chain 'I' and resid 1271 through 1281 removed outlier: 3.909A pdb=" N TYR I1281 " --> pdb=" O ALA I1277 " (cutoff:3.500A) Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 4.333A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1321 through 1332 Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 96 through 100 Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'J' and resid 124 through 129 removed outlier: 3.632A pdb=" N LEU J 128 " --> pdb=" O ILE J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 140 removed outlier: 4.068A pdb=" N ARG J 137 " --> pdb=" O ARG J 133 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL J 138 " --> pdb=" O ASP J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 172 removed outlier: 3.551A pdb=" N GLU J 170 " --> pdb=" O LEU J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 192 Processing helix chain 'J' and resid 193 through 208 removed outlier: 3.560A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 264 through 286 Processing helix chain 'J' and resid 288 through 301 Processing helix chain 'J' and resid 303 through 306 Processing helix chain 'J' and resid 327 through 332 Processing helix chain 'J' and resid 336 through 341 removed outlier: 3.633A pdb=" N ASN J 341 " --> pdb=" O ARG J 337 " (cutoff:3.500A) Processing helix chain 'J' and resid 370 through 377 removed outlier: 3.542A pdb=" N PHE J 377 " --> pdb=" O ALA J 373 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 403 Processing helix chain 'J' and resid 407 through 417 removed outlier: 3.600A pdb=" N ILE J 411 " --> pdb=" O VAL J 407 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG J 417 " --> pdb=" O ASP J 413 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 removed outlier: 3.636A pdb=" N ASN J 489 " --> pdb=" O SER J 486 " (cutoff:3.500A) Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 573 through 580 removed outlier: 3.508A pdb=" N ALA J 577 " --> pdb=" O THR J 573 " (cutoff:3.500A) Processing helix chain 'J' and resid 598 through 612 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.755A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 removed outlier: 3.910A pdb=" N MET J 644 " --> pdb=" O ILE J 641 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 669 removed outlier: 3.746A pdb=" N ILE J 653 " --> pdb=" O LYS J 649 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 702 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 768 through 775 Processing helix chain 'J' and resid 776 through 804 removed outlier: 3.943A pdb=" N LEU J 788 " --> pdb=" O ALA J 784 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG J 798 " --> pdb=" O GLY J 794 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.559A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 876 removed outlier: 3.720A pdb=" N ASN J 875 " --> pdb=" O LEU J 871 " (cutoff:3.500A) Processing helix chain 'J' and resid 895 through 900 Processing helix chain 'J' and resid 915 through 925 Processing helix chain 'J' and resid 926 through 929 Processing helix chain 'J' and resid 1068 through 1072 removed outlier: 3.752A pdb=" N LYS J1072 " --> pdb=" O ALA J1069 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1146 removed outlier: 3.778A pdb=" N VAL J1141 " --> pdb=" O GLY J1137 " (cutoff:3.500A) Processing helix chain 'J' and resid 1216 through 1225 removed outlier: 3.510A pdb=" N ILE J1220 " --> pdb=" O ALA J1216 " (cutoff:3.500A) Processing helix chain 'J' and resid 1225 through 1245 removed outlier: 3.997A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1261 Processing helix chain 'J' and resid 1282 through 1294 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1319 through 1324 Processing helix chain 'J' and resid 1327 through 1338 removed outlier: 3.837A pdb=" N VAL J1331 " --> pdb=" O GLU J1327 " (cutoff:3.500A) Processing helix chain 'J' and resid 1347 through 1354 Processing helix chain 'J' and resid 1362 through 1373 Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 32 Processing helix chain 'K' and resid 45 through 57 Processing helix chain 'K' and resid 60 through 77 Processing helix chain 'K' and resid 78 through 80 No H-bonds generated for 'chain 'K' and resid 78 through 80' Processing helix chain 'L' and resid 98 through 108 removed outlier: 4.363A pdb=" N VAL L 108 " --> pdb=" O GLU L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 136 removed outlier: 3.777A pdb=" N ILE L 117 " --> pdb=" O ARG L 113 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU L 136 " --> pdb=" O CYS L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 153 removed outlier: 3.616A pdb=" N ALA L 153 " --> pdb=" O ASP L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 162 Processing helix chain 'L' and resid 215 through 235 Processing helix chain 'L' and resid 246 through 259 removed outlier: 3.635A pdb=" N PHE L 259 " --> pdb=" O VAL L 255 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 290 Processing helix chain 'L' and resid 298 through 307 removed outlier: 3.682A pdb=" N LEU L 305 " --> pdb=" O ASN L 301 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR L 307 " --> pdb=" O ILE L 303 " (cutoff:3.500A) Processing helix chain 'L' and resid 313 through 318 Processing helix chain 'L' and resid 319 through 323 removed outlier: 3.757A pdb=" N MET L 322 " --> pdb=" O ALA L 319 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASN L 323 " --> pdb=" O ILE L 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 319 through 323' Processing helix chain 'L' and resid 329 through 332 removed outlier: 3.685A pdb=" N ASP L 332 " --> pdb=" O LYS L 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 329 through 332' Processing helix chain 'L' and resid 333 through 352 removed outlier: 3.845A pdb=" N GLN L 342 " --> pdb=" O HIS L 338 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS L 343 " --> pdb=" O ARG L 339 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU L 348 " --> pdb=" O LEU L 344 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR L 351 " --> pdb=" O ILE L 347 " (cutoff:3.500A) Processing helix chain 'L' and resid 354 through 392 removed outlier: 5.383A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL L 387 " --> pdb=" O ASN L 383 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 418 Processing helix chain 'L' and resid 420 through 424 removed outlier: 4.106A pdb=" N ARG L 423 " --> pdb=" O GLU L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 426 through 447 removed outlier: 4.209A pdb=" N TYR L 430 " --> pdb=" O LYS L 426 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA L 447 " --> pdb=" O ILE L 443 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 475 removed outlier: 3.607A pdb=" N GLU L 473 " --> pdb=" O GLN L 469 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET L 474 " --> pdb=" O MET L 470 " (cutoff:3.500A) Processing helix chain 'L' and resid 479 through 487 Processing helix chain 'L' and resid 492 through 501 removed outlier: 4.037A pdb=" N ALA L 501 " --> pdb=" O VAL L 497 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 522 Processing helix chain 'L' and resid 530 through 550 removed outlier: 3.519A pdb=" N GLY L 550 " --> pdb=" O ASP L 546 " (cutoff:3.500A) Processing helix chain 'L' and resid 552 through 563 removed outlier: 3.591A pdb=" N PHE L 563 " --> pdb=" O LEU L 559 " (cutoff:3.500A) Processing helix chain 'L' and resid 572 through 580 Processing helix chain 'L' and resid 583 through 599 Processing helix chain 'L' and resid 603 through 609 removed outlier: 4.057A pdb=" N LEU L 607 " --> pdb=" O ARG L 603 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 17 removed outlier: 8.500A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR G 27 " --> pdb=" O ASP G 15 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLU G 204 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ILE G 183 " --> pdb=" O GLU G 204 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLU G 206 " --> pdb=" O GLU G 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 13 through 17 removed outlier: 8.500A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR G 27 " --> pdb=" O ASP G 15 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AA4, first strand: chain 'G' and resid 97 through 99 removed outlier: 6.784A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AA6, first strand: chain 'G' and resid 102 through 105 Processing sheet with id=AA7, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.702A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 13 through 17 removed outlier: 3.518A pdb=" N GLU H 29 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 98 through 99 removed outlier: 3.585A pdb=" N VAL H 98 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AB2, first strand: chain 'H' and resid 104 through 105 removed outlier: 3.700A pdb=" N LYS H 104 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE H 140 " --> pdb=" O LYS H 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'H' and resid 110 through 111 removed outlier: 3.724A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB5, first strand: chain 'H' and resid 180 through 182 removed outlier: 6.551A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.336A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 59 through 60 removed outlier: 7.043A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB9, first strand: chain 'I' and resid 147 through 148 removed outlier: 6.380A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'I' and resid 154 through 159 Processing sheet with id=AC2, first strand: chain 'I' and resid 284 through 286 removed outlier: 5.133A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 256 through 257 Processing sheet with id=AC4, first strand: chain 'I' and resid 301 through 302 removed outlier: 4.156A pdb=" N CYS I 311 " --> pdb=" O TYR I 301 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.595A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC7, first strand: chain 'I' and resid 633 through 635 Processing sheet with id=AC8, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.627A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 750 through 752 removed outlier: 6.774A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AD2, first strand: chain 'I' and resid 798 through 800 Processing sheet with id=AD3, first strand: chain 'I' and resid 1076 through 1080 removed outlier: 7.483A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 830 through 833 Processing sheet with id=AD5, first strand: chain 'I' and resid 830 through 833 removed outlier: 3.713A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.849A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 887 through 889 Processing sheet with id=AD8, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 7.599A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.648A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 1335 through 1340 Processing sheet with id=AE2, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.673A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 9.944A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 9.824A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AE4, first strand: chain 'J' and resid 252 through 254 removed outlier: 3.697A pdb=" N VAL J 253 " --> pdb=" O ALA J 261 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE J 260 " --> pdb=" O ILE L 505 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AE6, first strand: chain 'J' and resid 553 through 556 Processing sheet with id=AE7, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE8, first strand: chain 'J' and resid 825 through 826 removed outlier: 7.064A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 949 through 951 removed outlier: 7.376A pdb=" N ILE J 950 " --> pdb=" O VAL J1017 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL J1017 " --> pdb=" O ILE J 950 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'J' and resid 991 through 996 removed outlier: 3.979A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU J 984 " --> pdb=" O GLU J 993 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU J 981 " --> pdb=" O SER J 961 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY J 956 " --> pdb=" O VAL J1011 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AF3, first strand: chain 'J' and resid 1034 through 1036 removed outlier: 3.860A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 1046 through 1048 removed outlier: 3.578A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL J1107 " --> pdb=" O LEU J1059 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 1162 through 1164 Processing sheet with id=AF6, first strand: chain 'J' and resid 1173 through 1174 Processing sheet with id=AF7, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.630A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1189 hydrogen bonds defined for protein. 3384 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 96 hydrogen bonds 192 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 7.75 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6918 1.33 - 1.45: 6697 1.45 - 1.58: 17533 1.58 - 1.70: 196 1.70 - 1.82: 234 Bond restraints: 31578 Sorted by residual: bond pdb=" C19 1N7 J1504 " pdb=" C3 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.824 -0.292 2.00e-02 2.50e+03 2.13e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.821 -0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C19 1N7 I1402 " pdb=" C3 1N7 I1402 " ideal model delta sigma weight residual 1.532 1.821 -0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C3 1N7 J1504 " pdb=" C4 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.736 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C3 1N7 I1402 " pdb=" C4 1N7 I1402 " ideal model delta sigma weight residual 1.532 1.725 -0.193 2.00e-02 2.50e+03 9.32e+01 ... (remaining 31573 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 42234 2.36 - 4.72: 728 4.72 - 7.08: 70 7.08 - 9.45: 18 9.45 - 11.81: 5 Bond angle restraints: 43055 Sorted by residual: angle pdb=" C LEU J 903 " pdb=" N ALA J 904 " pdb=" CA ALA J 904 " ideal model delta sigma weight residual 121.54 132.56 -11.02 1.91e+00 2.74e-01 3.33e+01 angle pdb=" C LEU I 484 " pdb=" N ASP I 485 " pdb=" CA ASP I 485 " ideal model delta sigma weight residual 121.70 130.63 -8.93 1.80e+00 3.09e-01 2.46e+01 angle pdb=" N ARG L 603 " pdb=" CA ARG L 603 " pdb=" C ARG L 603 " ideal model delta sigma weight residual 114.75 108.61 6.14 1.26e+00 6.30e-01 2.37e+01 angle pdb=" C GLN I 517 " pdb=" N ASN I 518 " pdb=" CA ASN I 518 " ideal model delta sigma weight residual 122.86 115.42 7.44 1.53e+00 4.27e-01 2.37e+01 angle pdb=" N3 DT Q 22 " pdb=" C4 DT Q 22 " pdb=" O4 DT Q 22 " ideal model delta sigma weight residual 119.90 122.71 -2.81 6.00e-01 2.78e+00 2.19e+01 ... (remaining 43050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 18385 35.83 - 71.65: 761 71.65 - 107.48: 30 107.48 - 143.30: 0 143.30 - 179.13: 1 Dihedral angle restraints: 19177 sinusoidal: 8597 harmonic: 10580 Sorted by residual: dihedral pdb=" CA ASP J1184 " pdb=" C ASP J1184 " pdb=" N PRO J1185 " pdb=" CA PRO J1185 " ideal model delta harmonic sigma weight residual 180.00 -141.46 -38.54 0 5.00e+00 4.00e-02 5.94e+01 dihedral pdb=" CA ILE L 500 " pdb=" C ILE L 500 " pdb=" N ALA L 501 " pdb=" CA ALA L 501 " ideal model delta harmonic sigma weight residual 180.00 -149.17 -30.83 0 5.00e+00 4.00e-02 3.80e+01 dihedral pdb=" CA VAL K 32 " pdb=" C VAL K 32 " pdb=" N GLY K 33 " pdb=" CA GLY K 33 " ideal model delta harmonic sigma weight residual 180.00 -149.92 -30.08 0 5.00e+00 4.00e-02 3.62e+01 ... (remaining 19174 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 4569 0.092 - 0.184: 348 0.184 - 0.276: 8 0.276 - 0.368: 1 0.368 - 0.460: 3 Chirality restraints: 4929 Sorted by residual: chirality pdb=" C19 1N7 J1504 " pdb=" C18 1N7 J1504 " pdb=" C2 1N7 J1504 " pdb=" C3 1N7 J1504 " both_signs ideal model delta sigma weight residual False -2.53 -2.99 0.46 2.00e-01 2.50e+01 5.29e+00 chirality pdb=" C19 1N7 I1402 " pdb=" C18 1N7 I1402 " pdb=" C2 1N7 I1402 " pdb=" C3 1N7 I1402 " both_signs ideal model delta sigma weight residual False -2.53 -2.96 0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" C19 1N7 I1401 " pdb=" C18 1N7 I1401 " pdb=" C2 1N7 I1401 " pdb=" C3 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.53 -2.91 0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 4926 not shown) Planarity restraints: 5275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU I 898 " 0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C GLU I 898 " -0.061 2.00e-02 2.50e+03 pdb=" O GLU I 898 " 0.023 2.00e-02 2.50e+03 pdb=" N GLU I 899 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP J1184 " -0.043 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO J1185 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO J1185 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO J1185 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP I 189 " -0.036 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO I 190 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO I 190 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO I 190 " -0.031 5.00e-02 4.00e+02 ... (remaining 5272 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1445 2.72 - 3.26: 29053 3.26 - 3.81: 47627 3.81 - 4.35: 59431 4.35 - 4.90: 102759 Nonbonded interactions: 240315 Sorted by model distance: nonbonded pdb=" OG1 THR I 131 " pdb=" O THR I 135 " model vdw 2.170 3.040 nonbonded pdb=" OH TYR I 367 " pdb=" OE2 GLU I 374 " model vdw 2.179 3.040 nonbonded pdb=" OE1 GLU I1222 " pdb=" OH TYR J 512 " model vdw 2.180 3.040 nonbonded pdb=" NH2 ARG I 528 " pdb=" O SER I 576 " model vdw 2.190 3.120 nonbonded pdb=" O SER J 775 " pdb=" OG SER J 775 " model vdw 2.195 3.040 ... (remaining 240310 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 5 through 158 or resid 167 through 233)) selection = (chain 'H' and resid 5 through 233) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.060 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: 0.540 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 32.480 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 : 0.008 0.292 31586 Z= 0.404 Angle : 0.785 11.808 43067 Z= 0.492 Chirality : 0.050 0.460 4929 Planarity : 0.005 0.066 5275 Dihedral : 17.019 179.128 12357 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.15 % Favored : 92.83 % Rotamer: Outliers : 5.35 % Allowed : 11.74 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.17 % Twisted Proline : 0.70 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.13), residues: 3652 helix: -0.15 (0.14), residues: 1401 sheet: -1.40 (0.24), residues: 446 loop : -2.07 (0.13), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I1246 TYR 0.022 0.002 TYR G 177 PHE 0.021 0.002 PHE J 437 TRP 0.007 0.001 TRP J 33 HIS 0.009 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00803 / 0.40 (31578) covalent geometry : angle 0.78355 / 0.49 (43055) hydrogen bonds : bond 0.17213 / 18.00 ( 1271) hydrogen bonds : angle 6.57259 / 6.36 ( 3576) metal coordination : bond 0.01095 / 1.07 ( 8) metal coordination : angle 3.21439 / 5.47 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 273 time to evaluate : 1.082 Fit side-chains revert: symmetry clash REVERT: G 70 THR cc_start: 0.9005 (OUTLIER) cc_final: 0.8693 (t) REVERT: G 107 ILE cc_start: 0.8959 (pt) cc_final: 0.8703 (mt) REVERT: H 127 GLN cc_start: 0.8448 (mp10) cc_final: 0.8098 (mp10) REVERT: H 191 ARG cc_start: 0.8160 (ptm160) cc_final: 0.7793 (ptt90) REVERT: I 160 ASP cc_start: 0.7504 (t70) cc_final: 0.6900 (t0) REVERT: I 387 ASN cc_start: 0.8543 (t0) cc_final: 0.8268 (t0) REVERT: I 514 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.7679 (m-80) REVERT: I 516 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8569 (m-30) REVERT: I 524 ILE cc_start: 0.8490 (tt) cc_final: 0.8276 (tt) REVERT: I 601 ASP cc_start: 0.8100 (m-30) cc_final: 0.7625 (t0) REVERT: I 609 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8562 (mt) REVERT: I 829 THR cc_start: 0.9411 (OUTLIER) cc_final: 0.9192 (p) REVERT: I 1203 ASP cc_start: 0.5692 (OUTLIER) cc_final: 0.5472 (t70) REVERT: I 1212 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8828 (mp) REVERT: J 129 ASP cc_start: 0.7497 (t70) cc_final: 0.7202 (t0) REVERT: J 431 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7350 (ttm170) REVERT: J 1227 HIS cc_start: 0.7983 (m-70) cc_final: 0.7759 (m-70) REVERT: L 137 TYR cc_start: 0.2005 (OUTLIER) cc_final: 0.1305 (t80) REVERT: L 139 GLU cc_start: 0.6216 (OUTLIER) cc_final: 0.5681 (tt0) REVERT: L 381 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6707 (mt-10) REVERT: L 573 LEU cc_start: 0.6454 (OUTLIER) cc_final: 0.6244 (pp) outliers start: 168 outliers final: 85 residues processed: 428 average time/residue: 0.1881 time to fit residues: 132.7999 Evaluate side-chains 336 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 240 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 662 SER Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1203 ASP Chi-restraints excluded: chain I residue 1212 LEU Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 431 ARG Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1037 PHE Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 573 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 0.0370 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 554 HIS ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 200 GLN J 294 ASN ** J1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 406 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.162534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.132951 restraints weight = 35335.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.132296 restraints weight = 105236.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.129734 restraints weight = 46248.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.128753 restraints weight = 50791.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.129086 restraints weight = 42636.530| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31586 Z= 0.124 Angle : 0.589 12.395 43067 Z= 0.316 Chirality : 0.043 0.233 4929 Planarity : 0.005 0.051 5275 Dihedral : 16.256 177.571 5241 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.85 % Allowed : 13.84 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.17 % Twisted Proline : 0.70 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.14), residues: 3652 helix: 0.54 (0.14), residues: 1433 sheet: -1.23 (0.24), residues: 440 loop : -1.87 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 91 TYR 0.015 0.001 TYR G 177 PHE 0.017 0.001 PHE I 337 TRP 0.006 0.001 TRP I1276 HIS 0.006 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (31578) covalent geometry : angle 0.58659 / 0.32 (43055) hydrogen bonds : bond 0.04582 / 4.74 ( 1271) hydrogen bonds : angle 4.81682 / 4.74 ( 3576) metal coordination : bond 0.00537 / 0.54 ( 8) metal coordination : angle 2.90523 / 4.58 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 272 time to evaluate : 1.196 Fit side-chains revert: symmetry clash REVERT: G 70 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8704 (t) REVERT: H 65 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.6899 (mt) REVERT: H 191 ARG cc_start: 0.8066 (ptm160) cc_final: 0.7683 (ptt90) REVERT: H 198 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8384 (mm) REVERT: I 160 ASP cc_start: 0.7361 (t70) cc_final: 0.6890 (t0) REVERT: I 516 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.8140 (m-30) REVERT: I 751 TYR cc_start: 0.9073 (m-80) cc_final: 0.8819 (m-80) REVERT: I 960 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7821 (mm) REVERT: J 738 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7599 (ptp-170) REVERT: J 925 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8152 (tm-30) REVERT: K 3 ARG cc_start: 0.7667 (tpt170) cc_final: 0.7426 (mmt180) REVERT: K 55 GLU cc_start: 0.6553 (tt0) cc_final: 0.6277 (tt0) REVERT: L 100 MET cc_start: 0.8165 (mtt) cc_final: 0.7710 (mtt) REVERT: L 137 TYR cc_start: 0.1981 (OUTLIER) cc_final: 0.1303 (t80) REVERT: L 139 GLU cc_start: 0.5727 (OUTLIER) cc_final: 0.5514 (tt0) REVERT: L 288 MET cc_start: 0.5316 (tpp) cc_final: 0.3963 (tpp) REVERT: L 381 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6859 (mt-10) outliers start: 121 outliers final: 75 residues processed: 381 average time/residue: 0.1877 time to fit residues: 117.8697 Evaluate side-chains 325 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 241 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 533 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1040 ASP Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 738 ARG Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 925 GLU Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1037 PHE Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 488 LEU Chi-restraints excluded: chain L residue 558 VAL Chi-restraints excluded: chain L residue 587 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 213 optimal weight: 10.0000 chunk 317 optimal weight: 7.9990 chunk 319 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 343 optimal weight: 30.0000 chunk 101 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 324 optimal weight: 0.8980 chunk 347 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 127 GLN I 69 GLN ** I 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 200 GLN ** J1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** 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 = 0.3761 r_free = 0.3761 target = 0.159181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.123796 restraints weight = 35856.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.124778 restraints weight = 104323.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.125203 restraints weight = 44626.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.125831 restraints weight = 28538.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.126009 restraints weight = 25348.042| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 31586 Z= 0.228 Angle : 0.643 11.511 43067 Z= 0.338 Chirality : 0.045 0.259 4929 Planarity : 0.005 0.054 5275 Dihedral : 16.232 178.885 5181 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.71 % Favored : 93.24 % Rotamer: Outliers : 4.55 % Allowed : 14.70 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.17 % Twisted Proline : 0.70 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.14), residues: 3652 helix: 0.62 (0.14), residues: 1427 sheet: -1.20 (0.24), residues: 446 loop : -1.89 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 403 TYR 0.019 0.002 TYR G 177 PHE 0.016 0.002 PHE J 437 TRP 0.007 0.001 TRP L 315 HIS 0.007 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.23 (31578) covalent geometry : angle 0.64069 / 0.34 (43055) hydrogen bonds : bond 0.05042 / 5.22 ( 1271) hydrogen bonds : angle 4.63742 / 4.62 ( 3576) metal coordination : bond 0.01364 / 1.18 ( 8) metal coordination : angle 3.60195 / 5.72 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 241 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 70 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8647 (t) REVERT: H 31 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8309 (mt) REVERT: H 65 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.6988 (mt) REVERT: H 191 ARG cc_start: 0.8051 (ptm160) cc_final: 0.7658 (ptt90) REVERT: H 198 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8490 (mm) REVERT: I 160 ASP cc_start: 0.7407 (t70) cc_final: 0.6988 (t0) REVERT: I 514 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7607 (m-80) REVERT: I 516 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8068 (m-30) REVERT: I 694 ARG cc_start: 0.7160 (mtm180) cc_final: 0.6938 (mtp-110) REVERT: I 790 ASP cc_start: 0.7147 (t0) cc_final: 0.6942 (t70) REVERT: I 800 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7907 (mtp) REVERT: I 960 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7900 (mm) REVERT: J 225 GLU cc_start: 0.7844 (tt0) cc_final: 0.7537 (tt0) REVERT: J 235 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8190 (pt0) REVERT: J 925 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8395 (tm-30) REVERT: L 100 MET cc_start: 0.8202 (mtt) cc_final: 0.7953 (mtt) REVERT: L 137 TYR cc_start: 0.2231 (OUTLIER) cc_final: 0.1590 (t80) REVERT: L 381 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6905 (mt-10) REVERT: L 573 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6476 (pp) outliers start: 143 outliers final: 95 residues processed: 367 average time/residue: 0.1855 time to fit residues: 112.4669 Evaluate side-chains 344 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 237 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 525 THR Chi-restraints excluded: chain I residue 533 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 687 ARG Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1203 ASP Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 581 MET Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 738 ARG Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 925 GLU Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1037 PHE Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1190 ILE Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 131 GLN Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 488 LEU Chi-restraints excluded: chain L residue 558 VAL Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 587 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 254 optimal weight: 7.9990 chunk 300 optimal weight: 7.9990 chunk 357 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 297 optimal weight: 5.9990 chunk 318 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 127 GLN ** I 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 200 GLN ** J1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.160817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.124861 restraints weight = 35450.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.125909 restraints weight = 100920.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.126723 restraints weight = 46523.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.125842 restraints weight = 40272.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.127714 restraints weight = 27553.219| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 31586 Z= 0.166 Angle : 0.582 10.919 43067 Z= 0.309 Chirality : 0.043 0.259 4929 Planarity : 0.004 0.052 5275 Dihedral : 16.109 179.283 5172 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.58 % Allowed : 15.60 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.17 % Twisted Proline : 0.70 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.14), residues: 3652 helix: 0.75 (0.14), residues: 1441 sheet: -1.13 (0.24), residues: 450 loop : -1.82 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 3 TYR 0.017 0.001 TYR G 177 PHE 0.013 0.001 PHE J 437 TRP 0.019 0.001 TRP J1193 HIS 0.006 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (31578) covalent geometry : angle 0.57991 / 0.31 (43055) hydrogen bonds : bond 0.04427 / 4.58 ( 1271) hydrogen bonds : angle 4.41883 / 4.41 ( 3576) metal coordination : bond 0.01066 / 0.99 ( 8) metal coordination : angle 3.30398 / 5.35 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 255 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: G 70 THR cc_start: 0.8948 (OUTLIER) cc_final: 0.8641 (t) REVERT: H 31 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8304 (mt) REVERT: H 65 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6815 (mt) REVERT: H 191 ARG cc_start: 0.8039 (ptm160) cc_final: 0.7652 (ptt90) REVERT: H 198 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8473 (mm) REVERT: I 160 ASP cc_start: 0.7377 (t70) cc_final: 0.6891 (t0) REVERT: I 465 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6745 (ttm110) REVERT: I 514 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7636 (m-80) REVERT: I 516 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8103 (m-30) REVERT: I 524 ILE cc_start: 0.8604 (tt) cc_final: 0.8325 (tt) REVERT: I 790 ASP cc_start: 0.7149 (t0) cc_final: 0.6890 (t70) REVERT: I 800 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7896 (mtp) REVERT: I 903 ARG cc_start: 0.8203 (ttm-80) cc_final: 0.6799 (mtm110) REVERT: I 960 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7883 (mm) REVERT: I 1142 ARG cc_start: 0.8441 (ttm110) cc_final: 0.8198 (ttm110) REVERT: J 235 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8161 (pt0) REVERT: J 731 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.6890 (ttm-80) REVERT: J 925 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8164 (tm-30) REVERT: J 1236 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7069 (mm-30) REVERT: K 3 ARG cc_start: 0.7609 (mmt180) cc_final: 0.7326 (mmt180) REVERT: L 100 MET cc_start: 0.8186 (mtt) cc_final: 0.7963 (mtt) REVERT: L 137 TYR cc_start: 0.2061 (OUTLIER) cc_final: 0.1155 (t80) REVERT: L 381 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6911 (mt-10) REVERT: L 573 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6446 (pp) outliers start: 144 outliers final: 96 residues processed: 384 average time/residue: 0.1744 time to fit residues: 110.7223 Evaluate side-chains 353 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 244 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 525 THR Chi-restraints excluded: chain I residue 533 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 581 MET Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 738 ARG Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 925 GLU Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1037 PHE Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1190 ILE Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain L residue 93 ARG Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 131 GLN Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 417 ASP Chi-restraints excluded: chain L residue 488 LEU Chi-restraints excluded: chain L residue 558 VAL Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 587 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 77 optimal weight: 0.2980 chunk 277 optimal weight: 30.0000 chunk 330 optimal weight: 20.0000 chunk 343 optimal weight: 30.0000 chunk 115 optimal weight: 0.0030 chunk 194 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 127 GLN J 200 GLN ** J1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.163123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.127894 restraints weight = 35534.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.129415 restraints weight = 97416.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.129385 restraints weight = 43339.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.129510 restraints weight = 29411.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.130179 restraints weight = 24172.218| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 31586 Z= 0.108 Angle : 0.537 10.330 43067 Z= 0.286 Chirality : 0.042 0.258 4929 Planarity : 0.004 0.058 5275 Dihedral : 15.946 179.057 5170 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.91 % Allowed : 16.45 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.17 % Twisted Proline : 0.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.14), residues: 3652 helix: 1.05 (0.14), residues: 1438 sheet: -1.02 (0.24), residues: 448 loop : -1.69 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 3 TYR 0.015 0.001 TYR G 177 PHE 0.034 0.001 PHE I 337 TRP 0.019 0.001 TRP J1193 HIS 0.005 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (31578) covalent geometry : angle 0.53509 / 0.29 (43055) hydrogen bonds : bond 0.03899 / 4.03 ( 1271) hydrogen bonds : angle 4.21271 / 4.20 ( 3576) metal coordination : bond 0.00563 / 0.56 ( 8) metal coordination : angle 2.79334 / 4.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 256 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: G 226 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7587 (tm-30) REVERT: H 65 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6749 (mt) REVERT: H 80 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6698 (mt-10) REVERT: H 191 ARG cc_start: 0.8011 (ptm160) cc_final: 0.7633 (ptt90) REVERT: H 198 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8441 (mm) REVERT: I 160 ASP cc_start: 0.7298 (t70) cc_final: 0.6786 (t0) REVERT: I 189 ASP cc_start: 0.7469 (OUTLIER) cc_final: 0.7116 (t0) REVERT: I 369 MET cc_start: 0.8042 (ptm) cc_final: 0.7718 (ptm) REVERT: I 465 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6712 (ttp-110) REVERT: I 514 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7552 (m-80) REVERT: I 516 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8138 (m-30) REVERT: I 524 ILE cc_start: 0.8511 (tt) cc_final: 0.8250 (tt) REVERT: I 637 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8287 (ptt90) REVERT: I 751 TYR cc_start: 0.9077 (m-80) cc_final: 0.8759 (m-80) REVERT: I 800 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7803 (mtp) REVERT: I 960 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7831 (mm) REVERT: I 1142 ARG cc_start: 0.8369 (ttm110) cc_final: 0.8119 (ttm110) REVERT: J 154 LEU cc_start: 0.6289 (OUTLIER) cc_final: 0.6038 (mt) REVERT: J 235 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8160 (pt0) REVERT: J 731 ARG cc_start: 0.8156 (ttm-80) cc_final: 0.6698 (ttm-80) REVERT: J 925 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8322 (tm-30) REVERT: L 100 MET cc_start: 0.8155 (mtt) cc_final: 0.7938 (mtt) REVERT: L 137 TYR cc_start: 0.2152 (OUTLIER) cc_final: 0.1292 (t80) REVERT: L 381 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6847 (mt-10) REVERT: L 387 VAL cc_start: 0.8372 (t) cc_final: 0.8143 (p) REVERT: L 573 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6454 (pp) outliers start: 123 outliers final: 79 residues processed: 362 average time/residue: 0.1825 time to fit residues: 109.2430 Evaluate side-chains 340 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 245 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 525 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 925 GLU Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1037 PHE Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1190 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain L residue 93 ARG Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 488 LEU Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 587 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 253 optimal weight: 0.7980 chunk 174 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 5 optimal weight: 0.0980 chunk 207 optimal weight: 7.9990 chunk 176 optimal weight: 0.8980 chunk 254 optimal weight: 10.0000 chunk 140 optimal weight: 0.3980 chunk 244 optimal weight: 4.9990 chunk 310 optimal weight: 6.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 799 ASN I1237 HIS J 200 GLN J1108 GLN ** L 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.164889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.129402 restraints weight = 35471.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.130831 restraints weight = 98306.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.131347 restraints weight = 43994.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.130542 restraints weight = 39956.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.132318 restraints weight = 27460.332| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 31586 Z= 0.100 Angle : 0.517 9.208 43067 Z= 0.276 Chirality : 0.041 0.260 4929 Planarity : 0.004 0.050 5275 Dihedral : 15.788 178.553 5161 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.50 % Allowed : 17.03 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.17 % Twisted Proline : 0.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.14), residues: 3652 helix: 1.29 (0.14), residues: 1441 sheet: -0.91 (0.24), residues: 444 loop : -1.58 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 67 TYR 0.014 0.001 TYR G 177 PHE 0.015 0.001 PHE I 337 TRP 0.022 0.001 TRP J1193 HIS 0.003 0.000 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.10 (31578) covalent geometry : angle 0.51535 / 0.28 (43055) hydrogen bonds : bond 0.03550 / 3.65 ( 1271) hydrogen bonds : angle 4.02627 / 4.03 ( 3576) metal coordination : bond 0.00491 / 0.50 ( 8) metal coordination : angle 2.46159 / 3.97 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 280 time to evaluate : 1.359 Fit side-chains revert: symmetry clash REVERT: G 70 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8682 (t) REVERT: G 226 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7671 (tm-30) REVERT: H 31 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8362 (mt) REVERT: H 65 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6653 (mt) REVERT: H 191 ARG cc_start: 0.7967 (ptm160) cc_final: 0.7605 (ptt90) REVERT: H 198 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8384 (mm) REVERT: I 160 ASP cc_start: 0.7205 (t70) cc_final: 0.6712 (t0) REVERT: I 189 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.7079 (t0) REVERT: I 369 MET cc_start: 0.8071 (ptm) cc_final: 0.7687 (ptm) REVERT: I 465 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6624 (ttp-110) REVERT: I 516 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8143 (m-30) REVERT: I 524 ILE cc_start: 0.8507 (tt) cc_final: 0.8272 (tt) REVERT: I 637 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8359 (ptt90) REVERT: I 751 TYR cc_start: 0.9047 (m-80) cc_final: 0.8692 (m-80) REVERT: I 1108 ASN cc_start: 0.8627 (p0) cc_final: 0.8400 (p0) REVERT: I 1142 ARG cc_start: 0.8342 (ttm110) cc_final: 0.8098 (ttm110) REVERT: J 154 LEU cc_start: 0.6307 (OUTLIER) cc_final: 0.6006 (mt) REVERT: J 442 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8194 (pt) REVERT: J 925 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8006 (tm-30) REVERT: K 3 ARG cc_start: 0.7675 (mmp-170) cc_final: 0.7445 (mmt180) REVERT: K 80 LEU cc_start: 0.2845 (OUTLIER) cc_final: 0.1172 (tp) REVERT: L 100 MET cc_start: 0.8186 (mtt) cc_final: 0.7935 (mtt) REVERT: L 137 TYR cc_start: 0.1944 (OUTLIER) cc_final: 0.1179 (t80) REVERT: L 277 MET cc_start: 0.5500 (tpt) cc_final: 0.5286 (tpp) REVERT: L 379 MET cc_start: 0.8405 (ttp) cc_final: 0.8200 (ttm) REVERT: L 573 LEU cc_start: 0.6751 (OUTLIER) cc_final: 0.6494 (pp) outliers start: 110 outliers final: 67 residues processed: 377 average time/residue: 0.1967 time to fit residues: 121.5768 Evaluate side-chains 338 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 256 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 738 ARG Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 925 GLU Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1037 PHE Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1190 ILE Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 131 GLN Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 430 TYR Chi-restraints excluded: chain L residue 488 LEU Chi-restraints excluded: chain L residue 573 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 158 optimal weight: 0.2980 chunk 172 optimal weight: 1.9990 chunk 213 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 227 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 336 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 354 optimal weight: 6.9990 chunk 105 optimal weight: 0.4980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 127 GLN J 200 GLN ** L 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 362 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.164208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.129245 restraints weight = 35559.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.130121 restraints weight = 103413.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.130774 restraints weight = 47744.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.130033 restraints weight = 39947.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.131147 restraints weight = 27994.383| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 31586 Z= 0.113 Angle : 0.522 8.888 43067 Z= 0.278 Chirality : 0.041 0.262 4929 Planarity : 0.004 0.054 5275 Dihedral : 15.717 178.503 5141 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.85 % Allowed : 16.80 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.17 % Twisted Proline : 0.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.14), residues: 3652 helix: 1.33 (0.14), residues: 1447 sheet: -0.89 (0.24), residues: 442 loop : -1.54 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 764 TYR 0.022 0.001 TYR J 144 PHE 0.015 0.001 PHE I 337 TRP 0.020 0.001 TRP J1193 HIS 0.004 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (31578) covalent geometry : angle 0.52103 / 0.28 (43055) hydrogen bonds : bond 0.03616 / 3.71 ( 1271) hydrogen bonds : angle 3.96984 / 3.98 ( 3576) metal coordination : bond 0.00542 / 0.57 ( 8) metal coordination : angle 2.38406 / 3.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 263 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 70 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8686 (t) REVERT: G 226 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: H 31 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8370 (mt) REVERT: H 65 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6591 (mt) REVERT: H 80 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6431 (mt-10) REVERT: H 191 ARG cc_start: 0.7975 (ptm160) cc_final: 0.7619 (ptt90) REVERT: H 198 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8388 (mm) REVERT: I 160 ASP cc_start: 0.7191 (t70) cc_final: 0.6693 (t0) REVERT: I 189 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7077 (t0) REVERT: I 369 MET cc_start: 0.8068 (ptm) cc_final: 0.7653 (ptm) REVERT: I 465 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6668 (ttp-110) REVERT: I 516 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8216 (m-30) REVERT: I 524 ILE cc_start: 0.8541 (tt) cc_final: 0.8304 (tt) REVERT: I 637 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8358 (ptt90) REVERT: I 751 TYR cc_start: 0.9038 (m-80) cc_final: 0.8693 (m-80) REVERT: I 800 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7805 (mtp) REVERT: I 1142 ARG cc_start: 0.8371 (ttm110) cc_final: 0.8110 (ttm110) REVERT: J 154 LEU cc_start: 0.6385 (OUTLIER) cc_final: 0.6106 (mt) REVERT: J 235 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8160 (pt0) REVERT: J 442 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8213 (pt) REVERT: J 925 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8260 (tm-30) REVERT: J 1236 GLU cc_start: 0.7347 (mm-30) cc_final: 0.7114 (mm-30) REVERT: K 3 ARG cc_start: 0.7634 (mmp-170) cc_final: 0.7386 (mmt180) REVERT: K 80 LEU cc_start: 0.2710 (OUTLIER) cc_final: 0.1256 (tp) REVERT: L 100 MET cc_start: 0.8178 (mtt) cc_final: 0.7964 (mtt) REVERT: L 137 TYR cc_start: 0.1925 (OUTLIER) cc_final: 0.1165 (t80) REVERT: L 379 MET cc_start: 0.8416 (ttp) cc_final: 0.8203 (ttm) REVERT: L 573 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6584 (pp) outliers start: 121 outliers final: 85 residues processed: 374 average time/residue: 0.1960 time to fit residues: 120.9270 Evaluate side-chains 358 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 255 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 525 THR Chi-restraints excluded: chain I residue 533 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain J residue 53 ARG Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 738 ARG Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 925 GLU Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1037 PHE Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1190 ILE Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 131 GLN Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 430 TYR Chi-restraints excluded: chain L residue 488 LEU Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 587 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 243 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 187 optimal weight: 3.9990 chunk 233 optimal weight: 9.9990 chunk 30 optimal weight: 0.2980 chunk 103 optimal weight: 0.0270 chunk 135 optimal weight: 10.0000 chunk 371 optimal weight: 50.0000 chunk 219 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 197 optimal weight: 10.0000 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 127 GLN I 799 ASN J 200 GLN ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1227 HIS ** L 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 338 HIS L 362 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.166045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.129914 restraints weight = 35417.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.130499 restraints weight = 98728.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.131596 restraints weight = 52731.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.131349 restraints weight = 34987.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.132360 restraints weight = 27934.404| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 31586 Z= 0.097 Angle : 0.507 8.602 43067 Z= 0.271 Chirality : 0.041 0.262 4929 Planarity : 0.004 0.048 5275 Dihedral : 15.634 178.567 5141 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.41 % Allowed : 17.35 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.17 % Twisted Proline : 0.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.14), residues: 3652 helix: 1.51 (0.14), residues: 1443 sheet: -0.74 (0.24), residues: 443 loop : -1.46 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 67 TYR 0.014 0.001 TYR G 177 PHE 0.008 0.001 PHE I 505 TRP 0.025 0.001 TRP J1193 HIS 0.003 0.000 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.10 (31578) covalent geometry : angle 0.50568 / 0.27 (43055) hydrogen bonds : bond 0.03350 / 3.43 ( 1271) hydrogen bonds : angle 3.85427 / 3.88 ( 3576) metal coordination : bond 0.00392 / 0.42 ( 8) metal coordination : angle 2.22721 / 3.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 280 time to evaluate : 1.185 Fit side-chains revert: symmetry clash REVERT: G 70 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8721 (t) REVERT: G 226 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7732 (tm-30) REVERT: H 65 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6561 (mt) REVERT: H 191 ARG cc_start: 0.7977 (ptm160) cc_final: 0.7623 (ptt90) REVERT: I 160 ASP cc_start: 0.7116 (t70) cc_final: 0.6614 (t0) REVERT: I 189 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7067 (t0) REVERT: I 369 MET cc_start: 0.8076 (ptm) cc_final: 0.7619 (ptm) REVERT: I 465 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6610 (ttm110) REVERT: I 514 PHE cc_start: 0.8067 (OUTLIER) cc_final: 0.7518 (m-80) REVERT: I 516 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8179 (m-30) REVERT: I 524 ILE cc_start: 0.8467 (tt) cc_final: 0.8223 (tt) REVERT: I 618 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7226 (tt0) REVERT: I 751 TYR cc_start: 0.9030 (m-80) cc_final: 0.8692 (m-80) REVERT: I 800 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7875 (mtp) REVERT: I 1142 ARG cc_start: 0.8262 (ttm110) cc_final: 0.8001 (ttm110) REVERT: J 154 LEU cc_start: 0.6291 (OUTLIER) cc_final: 0.5978 (mt) REVERT: J 235 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8152 (pt0) REVERT: J 442 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8255 (pt) REVERT: J 698 MET cc_start: 0.8187 (tpt) cc_final: 0.7852 (tpp) REVERT: J 925 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8108 (tm-30) REVERT: J 1316 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8306 (p) REVERT: K 55 GLU cc_start: 0.6518 (tt0) cc_final: 0.6138 (tt0) REVERT: K 80 LEU cc_start: 0.2740 (OUTLIER) cc_final: 0.1338 (tp) REVERT: L 100 MET cc_start: 0.8089 (mtt) cc_final: 0.7836 (mtt) REVERT: L 137 TYR cc_start: 0.1669 (OUTLIER) cc_final: 0.0854 (t80) REVERT: L 573 LEU cc_start: 0.6819 (OUTLIER) cc_final: 0.6578 (pp) outliers start: 107 outliers final: 72 residues processed: 373 average time/residue: 0.1859 time to fit residues: 114.5441 Evaluate side-chains 348 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 259 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 618 GLN Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 738 ARG Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 925 GLU Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1190 ILE Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 131 GLN Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 430 TYR Chi-restraints excluded: chain L residue 488 LEU Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 587 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 166 optimal weight: 7.9990 chunk 2 optimal weight: 30.0000 chunk 344 optimal weight: 9.9990 chunk 262 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 190 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 317 optimal weight: 2.9990 chunk 228 optimal weight: 0.8980 chunk 260 optimal weight: 8.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 922 ASN J 200 GLN J1227 HIS ** L 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 362 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.164218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.129622 restraints weight = 35383.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.131034 restraints weight = 97335.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.130928 restraints weight = 43342.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.131081 restraints weight = 30075.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.131648 restraints weight = 24574.253| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31586 Z= 0.130 Angle : 0.533 9.737 43067 Z= 0.282 Chirality : 0.042 0.264 4929 Planarity : 0.004 0.055 5275 Dihedral : 15.658 178.615 5135 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.25 % Allowed : 17.54 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.17 % Twisted Proline : 0.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.14), residues: 3652 helix: 1.42 (0.14), residues: 1453 sheet: -0.75 (0.24), residues: 453 loop : -1.47 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J1371 TYR 0.020 0.001 TYR J 144 PHE 0.014 0.001 PHE I 337 TRP 0.022 0.001 TRP J1193 HIS 0.004 0.001 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (31578) covalent geometry : angle 0.53225 / 0.28 (43055) hydrogen bonds : bond 0.03604 / 3.70 ( 1271) hydrogen bonds : angle 3.87655 / 3.90 ( 3576) metal coordination : bond 0.00601 / 0.64 ( 8) metal coordination : angle 2.19650 / 3.65 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 257 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: G 70 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8733 (t) REVERT: G 226 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7761 (tm-30) REVERT: H 65 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6526 (mt) REVERT: H 191 ARG cc_start: 0.7926 (ptm160) cc_final: 0.7598 (ptt90) REVERT: I 160 ASP cc_start: 0.7164 (t70) cc_final: 0.6669 (t0) REVERT: I 189 ASP cc_start: 0.7426 (OUTLIER) cc_final: 0.7072 (t0) REVERT: I 369 MET cc_start: 0.8148 (ptm) cc_final: 0.7698 (ptm) REVERT: I 465 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.6706 (ttm110) REVERT: I 514 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7604 (m-80) REVERT: I 516 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8159 (m-30) REVERT: I 524 ILE cc_start: 0.8556 (tt) cc_final: 0.8259 (tt) REVERT: I 637 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8453 (ptt90) REVERT: I 800 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7709 (mtp) REVERT: I 1142 ARG cc_start: 0.8365 (ttm110) cc_final: 0.8097 (ttm110) REVERT: J 53 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7370 (ttm-80) REVERT: J 154 LEU cc_start: 0.6373 (OUTLIER) cc_final: 0.6092 (mt) REVERT: J 235 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8171 (pt0) REVERT: J 442 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8233 (pt) REVERT: J 698 MET cc_start: 0.8208 (tpt) cc_final: 0.7894 (tpp) REVERT: J 925 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8211 (tm-30) REVERT: J 1316 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8311 (p) REVERT: K 80 LEU cc_start: 0.2729 (OUTLIER) cc_final: 0.1329 (tp) REVERT: L 100 MET cc_start: 0.8120 (mtt) cc_final: 0.7826 (mtt) REVERT: L 137 TYR cc_start: 0.1684 (OUTLIER) cc_final: 0.0788 (t80) REVERT: L 573 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6605 (pp) outliers start: 102 outliers final: 77 residues processed: 345 average time/residue: 0.1932 time to fit residues: 109.5775 Evaluate side-chains 348 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 253 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain J residue 53 ARG Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 738 ARG Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 925 GLU Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1190 ILE Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 131 GLN Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 488 LEU Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 587 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 143 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 303 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 281 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 chunk 335 optimal weight: 20.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 65 ASN I 922 ASN J 200 GLN J1227 HIS ** L 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 362 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.162233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.127006 restraints weight = 35294.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.128231 restraints weight = 102410.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.128362 restraints weight = 45031.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.129153 restraints weight = 28381.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.129296 restraints weight = 25470.474| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31586 Z= 0.170 Angle : 0.576 10.370 43067 Z= 0.302 Chirality : 0.043 0.265 4929 Planarity : 0.004 0.047 5275 Dihedral : 15.780 179.251 5131 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.28 % Allowed : 17.66 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.17 % Twisted Proline : 0.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.14), residues: 3652 helix: 1.26 (0.14), residues: 1456 sheet: -0.74 (0.25), residues: 438 loop : -1.51 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 936 TYR 0.018 0.001 TYR G 177 PHE 0.011 0.001 PHE J 437 TRP 0.023 0.001 TRP J1193 HIS 0.005 0.001 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (31578) covalent geometry : angle 0.57440 / 0.30 (43055) hydrogen bonds : bond 0.04064 / 4.18 ( 1271) hydrogen bonds : angle 3.97048 / 4.01 ( 3576) metal coordination : bond 0.00844 / 0.85 ( 8) metal coordination : angle 2.47574 / 4.16 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 256 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: G 70 THR cc_start: 0.8950 (OUTLIER) cc_final: 0.8699 (t) REVERT: G 226 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7750 (tm-30) REVERT: H 65 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6536 (mt) REVERT: H 191 ARG cc_start: 0.7943 (ptm160) cc_final: 0.7573 (ptt90) REVERT: I 160 ASP cc_start: 0.7271 (t70) cc_final: 0.6757 (t0) REVERT: I 189 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7126 (t0) REVERT: I 369 MET cc_start: 0.8231 (ptm) cc_final: 0.7798 (ptm) REVERT: I 465 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.6732 (ttm110) REVERT: I 514 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7641 (m-80) REVERT: I 516 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8108 (m-30) REVERT: I 524 ILE cc_start: 0.8657 (tt) cc_final: 0.8372 (tt) REVERT: I 637 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8454 (ptt90) REVERT: I 800 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7900 (mtp) REVERT: I 903 ARG cc_start: 0.8175 (ttm-80) cc_final: 0.6728 (mtm110) REVERT: I 1142 ARG cc_start: 0.8451 (ttm110) cc_final: 0.8179 (ttm110) REVERT: J 53 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7371 (ttm-80) REVERT: J 154 LEU cc_start: 0.6322 (OUTLIER) cc_final: 0.5982 (mt) REVERT: J 235 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8218 (pt0) REVERT: J 442 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8205 (pt) REVERT: J 925 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8099 (tm-30) REVERT: J 1316 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8366 (p) REVERT: K 80 LEU cc_start: 0.2761 (OUTLIER) cc_final: 0.1310 (tp) REVERT: L 100 MET cc_start: 0.8167 (mtt) cc_final: 0.7965 (mtt) REVERT: L 137 TYR cc_start: 0.1577 (OUTLIER) cc_final: 0.0669 (t80) REVERT: L 573 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.6540 (pp) outliers start: 103 outliers final: 73 residues processed: 348 average time/residue: 0.1908 time to fit residues: 109.4245 Evaluate side-chains 341 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 250 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 525 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain J residue 53 ARG Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 738 ARG Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 925 GLU Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1037 PHE Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1190 ILE Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 488 LEU Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 587 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 8 optimal weight: 0.9980 chunk 363 optimal weight: 10.0000 chunk 235 optimal weight: 0.7980 chunk 287 optimal weight: 7.9990 chunk 305 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 200 GLN J1227 HIS ** L 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 362 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.163838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.128455 restraints weight = 35551.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.129995 restraints weight = 99432.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.130369 restraints weight = 44409.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.129610 restraints weight = 40528.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.130883 restraints weight = 27479.294| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31586 Z= 0.120 Angle : 0.534 10.639 43067 Z= 0.282 Chirality : 0.041 0.264 4929 Planarity : 0.004 0.049 5275 Dihedral : 15.678 179.566 5131 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.18 % Allowed : 17.76 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.17 % Twisted Proline : 0.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.14), residues: 3652 helix: 1.41 (0.14), residues: 1449 sheet: -0.70 (0.25), residues: 446 loop : -1.48 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J1371 TYR 0.019 0.001 TYR J 144 PHE 0.015 0.001 PHE I 337 TRP 0.022 0.001 TRP J1193 HIS 0.004 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (31578) covalent geometry : angle 0.53268 / 0.28 (43055) hydrogen bonds : bond 0.03687 / 3.78 ( 1271) hydrogen bonds : angle 3.90604 / 3.94 ( 3576) metal coordination : bond 0.00575 / 0.59 ( 8) metal coordination : angle 2.41024 / 4.00 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4945.39 seconds wall clock time: 86 minutes 26.87 seconds (5186.87 seconds total)