Starting phenix.real_space_refine on Sun Jul 5 18:01:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fog_50622/07_2026/9fog_50622.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fog_50622/07_2026/9fog_50622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fog_50622/07_2026/9fog_50622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fog_50622/07_2026/9fog_50622.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fog_50622/07_2026/9fog_50622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fog_50622/07_2026/9fog_50622.map" } resolution = 2.51 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= 0.001 sd= 0.015 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 105 5.49 5 Mg 4 5.21 5 S 71 5.16 5 C 17829 2.51 5 N 5126 2.21 5 O 5579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28716 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1797 Classifications: {'peptide': 229} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 214} Chain: "B" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1797 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 214} Chain: "C" Number of atoms: 8675 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1096, 8642 Classifications: {'peptide': 1096} Link IDs: {'PCIS': 1, 'PTRANS': 69, 'TRANS': 1025} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1096, 8642 Classifications: {'peptide': 1096} Link IDs: {'PCIS': 1, 'PTRANS': 69, 'TRANS': 1025} Chain breaks: 2 bond proxies already assigned to first conformer: 8769 Chain: "D" Number of atoms: 10904 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1365, 10774 Classifications: {'peptide': 1365} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1296} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1371, 10817 Classifications: {'peptide': 1371} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1302} Chain breaks: 2 bond proxies already assigned to first conformer: 10866 Chain: "E" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 761 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 6, 'TRANS': 87} Chain: "F" Number of atoms: 2671 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 329, 2660 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 13, 'TRANS': 315} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 329, 2660 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 13, 'TRANS': 315} Chain breaks: 1 bond proxies already assigned to first conformer: 2689 Chain: "G" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 944 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain breaks: 1 Chain: "H" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1053 Classifications: {'DNA': 51} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 50} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 6, 34 Unusual residues: {' MG': 3, ' ZN': 2, '2TM': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 79 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 2, 79 Unusual residues: {'2TM': 1, 'G3A': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20145 SG CYS D1112 99.990 85.753 94.450 1.00 34.94 S ATOM 20789 SG CYS D1194 96.771 85.558 92.489 1.00 31.63 S ATOM 20845 SG CYS D1201 99.920 83.840 91.159 1.00 27.45 S ATOM 20869 SG CYS D1204 98.175 82.375 94.098 1.00 33.25 S ATOM 12758 SG CYS D 58 75.819 127.277 48.354 1.00 76.77 S ATOM 12769 SG CYS D 60 73.134 129.873 47.689 1.00 82.99 S ATOM 12880 SG CYS D 73 76.179 130.960 49.474 1.00 78.14 S ATOM 12906 SG CYS D 76 73.790 128.647 51.273 1.00 70.34 S Residues with excluded nonbonded symmetry interactions: 22 residue: pdb=" N AARG C 493 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 493 " occ=0.50 residue: pdb=" N AARG C 744 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 744 " occ=0.50 residue: pdb=" N AARG C 945 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 945 " occ=0.50 residue: pdb=" N AARG D 35 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 35 " occ=0.50 residue: pdb=" N AARG D 647 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 647 " occ=0.50 residue: pdb=" N AARG D 674 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 674 " occ=0.50 residue: pdb=" N AARG D1087 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D1087 " occ=0.50 residue: pdb=" N AGLN D1235 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN D1235 " occ=0.50 residue: pdb=" N ALEU D1236 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU D1236 " occ=0.50 residue: pdb=" N ATHR D1237 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR D1237 " occ=0.50 residue: pdb=" N AMET D1238 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET D1238 " occ=0.50 residue: pdb=" N AARG D1239 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D1239 " occ=0.50 ... (remaining 10 not shown) Time building chain proxies: 8.80, per 1000 atoms: 0.31 Number of scatterers: 28716 At special positions: 0 Unit cell: (140.878, 177.557, 137.544, 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 71 16.00 P 105 15.00 Mg 4 11.99 O 5579 8.00 N 5126 7.00 C 17829 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: 2.40 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1201 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1204 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1112 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1194 " pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 73 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 76 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 58 " Number of angles added : 12 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6222 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 50 sheets defined 44.0% alpha, 18.5% beta 31 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 3.15 Creating SS restraints... Processing helix chain 'A' and resid 31 through 47 Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 206 through 224 removed outlier: 3.716A pdb=" N TYR A 224 " --> pdb=" O GLU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'B' and resid 31 through 47 Proline residue: B 39 - end of helix Processing helix chain 'B' and resid 74 through 84 removed outlier: 3.738A pdb=" N GLU B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 152 through 157 removed outlier: 3.585A pdb=" N HIS B 156 " --> pdb=" O PRO B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 223 Processing helix chain 'B' and resid 224 through 226 No H-bonds generated for 'chain 'B' and resid 224 through 226' Processing helix chain 'C' and resid 19 through 31 removed outlier: 4.091A pdb=" N SER C 25 " --> pdb=" O ILE C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 39 removed outlier: 3.557A pdb=" N ARG C 39 " --> pdb=" O PRO C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 52 removed outlier: 3.557A pdb=" N ALA C 46 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 87 Processing helix chain 'C' and resid 193 through 201 Processing helix chain 'C' and resid 203 through 212 Processing helix chain 'C' and resid 216 through 222 Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 230 through 243 Processing helix chain 'C' and resid 249 through 262 Processing helix chain 'C' and resid 270 through 282 Processing helix chain 'C' and resid 302 through 315 Processing helix chain 'C' and resid 335 through 362 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 375 through 389 removed outlier: 3.569A pdb=" N SER C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 408 Processing helix chain 'C' and resid 431 through 435 Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 525 through 529 Processing helix chain 'C' and resid 535 through 540 Processing helix chain 'C' and resid 543 through 547 Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 554 through 565 Processing helix chain 'C' and resid 566 through 568 No H-bonds generated for 'chain 'C' and resid 566 through 568' Processing helix chain 'C' and resid 583 through 591 Processing helix chain 'C' and resid 683 through 687 removed outlier: 4.080A pdb=" N ASP C 686 " --> pdb=" O ASN C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 697 Processing helix chain 'C' and resid 854 through 858 Processing helix chain 'C' and resid 874 through 880 removed outlier: 4.845A pdb=" N SER C 878 " --> pdb=" O LEU C 874 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG C 879 " --> pdb=" O GLY C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 898 Processing helix chain 'C' and resid 910 through 933 removed outlier: 4.211A pdb=" N ARG C 929 " --> pdb=" O TYR C 925 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU C 932 " --> pdb=" O LYS C 928 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY C 933 " --> pdb=" O ARG C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 951 Processing helix chain 'C' and resid 958 through 969 removed outlier: 3.560A pdb=" N GLN C 969 " --> pdb=" O GLU C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1004 Processing helix chain 'C' and resid 1033 through 1044 Processing helix chain 'C' and resid 1045 through 1054 Processing helix chain 'C' and resid 1059 through 1073 Processing helix chain 'C' and resid 1082 through 1095 removed outlier: 3.643A pdb=" N ARG C1086 " --> pdb=" O PRO C1082 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C1095 " --> pdb=" O GLU C1091 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 22 Processing helix chain 'D' and resid 46 through 51 Processing helix chain 'D' and resid 82 through 88 removed outlier: 3.529A pdb=" N VAL D 85 " --> pdb=" O LYS D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 107 Processing helix chain 'D' and resid 110 through 117 Processing helix chain 'D' and resid 119 through 128 Processing helix chain 'D' and resid 154 through 164 Processing helix chain 'D' and resid 372 through 376 Processing helix chain 'D' and resid 423 through 426 Processing helix chain 'D' and resid 456 through 468 removed outlier: 3.946A pdb=" N ALA D 460 " --> pdb=" O MET D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 481 Processing helix chain 'D' and resid 485 through 506 removed outlier: 3.717A pdb=" N VAL D 498 " --> pdb=" O LYS D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 511 Processing helix chain 'D' and resid 521 through 525 Processing helix chain 'D' and resid 538 through 560 removed outlier: 3.971A pdb=" N ASP D 542 " --> pdb=" O SER D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 583 Processing helix chain 'D' and resid 602 through 608 Processing helix chain 'D' and resid 612 through 618 Processing helix chain 'D' and resid 646 through 653 Processing helix chain 'D' and resid 653 through 664 Processing helix chain 'D' and resid 669 through 679 removed outlier: 3.865A pdb=" N ARG D 679 " --> pdb=" O ARG D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 683 Processing helix chain 'D' and resid 685 through 695 removed outlier: 3.780A pdb=" N ASP D 689 " --> pdb=" O ASP D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 711 No H-bonds generated for 'chain 'D' and resid 709 through 711' Processing helix chain 'D' and resid 729 through 731 No H-bonds generated for 'chain 'D' and resid 729 through 731' Processing helix chain 'D' and resid 732 through 737 Processing helix chain 'D' and resid 752 through 762 Processing helix chain 'D' and resid 764 through 768 Processing helix chain 'D' and resid 783 through 794 Processing helix chain 'D' and resid 808 through 819 Processing helix chain 'D' and resid 835 through 841 Processing helix chain 'D' and resid 845 through 855 Processing helix chain 'D' and resid 876 through 891 Processing helix chain 'D' and resid 892 through 900 Processing helix chain 'D' and resid 907 through 923 Processing helix chain 'D' and resid 923 through 945 removed outlier: 3.577A pdb=" N THR D 944 " --> pdb=" O THR D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 950 through 954 Processing helix chain 'D' and resid 958 through 980 removed outlier: 3.829A pdb=" N GLN D 962 " --> pdb=" O GLU D 958 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU D 972 " --> pdb=" O ASP D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 984 through 1015 Processing helix chain 'D' and resid 1018 through 1026 Processing helix chain 'D' and resid 1031 through 1040 Processing helix chain 'D' and resid 1066 through 1103 removed outlier: 3.859A pdb=" N HIS D1075 " --> pdb=" O PHE D1071 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY D1076 " --> pdb=" O ILE D1072 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA D1089 " --> pdb=" O ALA D1085 " (cutoff:3.500A) Processing helix chain 'D' and resid 1136 through 1145 Processing helix chain 'D' and resid 1167 through 1180 Processing helix chain 'D' and resid 1190 through 1194 Processing helix chain 'D' and resid 1202 through 1206 Processing helix chain 'D' and resid 1220 through 1236 Proline residue: D1232 - end of helix removed outlier: 3.597A pdb=" N AGLN D1235 " --> pdb=" O GLU D1231 " (cutoff:3.500A) Processing helix chain 'D' and resid 1255 through 1264 Processing helix chain 'D' and resid 1331 through 1339 Processing helix chain 'D' and resid 1340 through 1360 removed outlier: 3.501A pdb=" N VAL D1344 " --> pdb=" O GLY D1340 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL D1355 " --> pdb=" O GLU D1351 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR D1356 " --> pdb=" O ILE D1352 " (cutoff:3.500A) Processing helix chain 'D' and resid 1364 through 1376 removed outlier: 4.363A pdb=" N ILE D1368 " --> pdb=" O HIS D1364 " (cutoff:3.500A) Processing helix chain 'D' and resid 1397 through 1411 Processing helix chain 'D' and resid 1423 through 1430 Processing helix chain 'D' and resid 1433 through 1441 Processing helix chain 'D' and resid 1442 through 1454 Processing helix chain 'D' and resid 1461 through 1468 removed outlier: 4.050A pdb=" N ASN D1465 " --> pdb=" O GLY D1461 " (cutoff:3.500A) Processing helix chain 'D' and resid 1474 through 1478 Processing helix chain 'D' and resid 1489 through 1502 Processing helix chain 'E' and resid 5 through 12 Processing helix chain 'E' and resid 15 through 33 Processing helix chain 'E' and resid 59 through 71 removed outlier: 3.527A pdb=" N TRP E 63 " --> pdb=" O ASN E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 93 Processing helix chain 'F' and resid 79 through 90 removed outlier: 3.563A pdb=" N GLN F 83 " --> pdb=" O ASP F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 121 Processing helix chain 'F' and resid 123 through 137 Processing helix chain 'F' and resid 152 through 163 Processing helix chain 'F' and resid 170 through 200 removed outlier: 3.802A pdb=" N LEU F 174 " --> pdb=" O HIS F 170 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ARG F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL F 195 " --> pdb=" O ASN F 191 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL F 196 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 227 Processing helix chain 'F' and resid 228 through 232 removed outlier: 3.528A pdb=" N ARG F 231 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 255 removed outlier: 3.776A pdb=" N TYR F 238 " --> pdb=" O LYS F 234 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TRP F 241 " --> pdb=" O THR F 237 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TRP F 242 " --> pdb=" O TYR F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 283 Processing helix chain 'F' and resid 287 through 296 removed outlier: 3.788A pdb=" N GLY F 296 " --> pdb=" O ALA F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 311 Processing helix chain 'F' and resid 328 through 333 Processing helix chain 'F' and resid 340 through 361 Processing helix chain 'F' and resid 362 through 373 Processing helix chain 'F' and resid 382 through 391 Processing helix chain 'F' and resid 393 through 414 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 16 removed outlier: 5.662A pdb=" N TYR A 20 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N THR A 201 " --> pdb=" O TYR A 20 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N GLU A 22 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE A 199 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N VAL A 24 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU A 197 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N GLU A 26 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU A 195 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N THR A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU A 186 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 104 removed outlier: 7.320A pdb=" N ASN A 139 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE A 58 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLU A 141 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL A 56 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ARG A 143 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 107 through 110 removed outlier: 6.640A pdb=" N LYS A 107 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N THR A 131 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL A 109 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 150 through 151 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 16 removed outlier: 6.163A pdb=" N ASP B 193 " --> pdb=" O PRO B 27 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N THR B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 186 " --> pdb=" O THR B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 104 removed outlier: 7.885A pdb=" N ASN B 139 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ILE B 58 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU B 141 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL B 56 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG B 143 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 89 Processing sheet with id=AA9, first strand: chain 'B' and resid 107 through 110 removed outlier: 6.311A pdb=" N LYS B 107 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR B 131 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 109 " --> pdb=" O ILE B 129 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 150 through 151 Processing sheet with id=AB2, first strand: chain 'C' and resid 2 through 5 Processing sheet with id=AB3, first strand: chain 'C' and resid 54 through 55 removed outlier: 5.475A pdb=" N LEU C 66 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE C 101 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N PHE C 68 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLN C 99 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU C 70 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ALA C 92 " --> pdb=" O HIS C 117 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N HIS C 117 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU C 94 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AB5, first strand: chain 'C' and resid 331 through 334 removed outlier: 6.484A pdb=" N SER C 138 " --> pdb=" O SER C 411 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 145 through 150 removed outlier: 6.660A pdb=" N TYR C 158 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL C 176 " --> pdb=" O TYR C 158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 291 through 294 Processing sheet with id=AB8, first strand: chain 'C' and resid 460 through 461 removed outlier: 5.470A pdb=" N GLU C 482 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL C 475 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C 480 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 460 through 461 Processing sheet with id=AC1, first strand: chain 'C' and resid 503 through 504 Processing sheet with id=AC2, first strand: chain 'C' and resid 595 through 596 removed outlier: 6.561A pdb=" N LEU C 595 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 620 through 624 removed outlier: 6.606A pdb=" N ARG C 610 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL C 606 " --> pdb=" O ARG C 610 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL C 612 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 629 through 630 Processing sheet with id=AC5, first strand: chain 'C' and resid 661 through 662 Processing sheet with id=AC6, first strand: chain 'C' and resid 971 through 972 removed outlier: 7.160A pdb=" N ILE C 688 " --> pdb=" O ALA C 850 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE C 852 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE C 690 " --> pdb=" O ILE C 852 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL C 689 " --> pdb=" O ILE C 870 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N VAL C 869 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU C 673 " --> pdb=" O VAL C 869 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU C 871 " --> pdb=" O LEU C 673 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA C 675 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL C 988 " --> pdb=" O ILE C 676 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 702 through 713 removed outlier: 8.163A pdb=" N ARG C 820 " --> pdb=" O ARG C 807 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ARG C 807 " --> pdb=" O ARG C 820 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL C 822 " --> pdb=" O ARG C 805 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ARG C 805 " --> pdb=" O VAL C 822 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ARG C 824 " --> pdb=" O THR C 803 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N THR C 803 " --> pdb=" O ARG C 824 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TYR C 826 " --> pdb=" O VAL C 801 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 721 through 722 removed outlier: 3.776A pdb=" N ARG C 721 " --> pdb=" O THR C 759 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 754 through 756 removed outlier: 6.724A pdb=" N LEU C 790 " --> pdb=" O LEU C 755 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1006 through 1008 removed outlier: 6.287A pdb=" N CYS D 642 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL D 721 " --> pdb=" O CYS D 642 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU D 644 " --> pdb=" O VAL D 721 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1031 through 1032 Processing sheet with id=AD3, first strand: chain 'C' and resid 1097 through 1102 Processing sheet with id=AD4, first strand: chain 'D' and resid 91 through 100 removed outlier: 10.204A pdb=" N LEU D 95 " --> pdb=" O PRO D 518 " (cutoff:3.500A) removed outlier: 10.768A pdb=" N THR D 97 " --> pdb=" O ALA D 516 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ALA D 516 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 152 through 153 removed outlier: 3.933A pdb=" N ASP D 453 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AD7, first strand: chain 'D' and resid 166 through 170 removed outlier: 7.028A pdb=" N VAL D 385 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL D 213 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU D 387 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL D 211 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU D 389 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N PHE D 207 " --> pdb=" O ALA D 391 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE D 393 " --> pdb=" O TYR D 205 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TYR D 205 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL D 395 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA D 203 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 166 through 170 removed outlier: 7.028A pdb=" N VAL D 385 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL D 213 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU D 387 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL D 211 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU D 389 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N PHE D 207 " --> pdb=" O ALA D 391 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE D 393 " --> pdb=" O TYR D 205 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TYR D 205 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL D 395 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA D 203 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 190 through 192 Processing sheet with id=AE1, first strand: chain 'D' and resid 352 through 353 removed outlier: 6.859A pdb=" N VAL D 377 " --> pdb=" O ILE D 367 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 398 through 402 removed outlier: 4.204A pdb=" N ASP D 413 " --> pdb=" O VAL D 435 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 420 through 422 removed outlier: 7.247A pdb=" N VAL D 427 " --> pdb=" O LEU D 421 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 527 through 529 Processing sheet with id=AE5, first strand: chain 'D' and resid 805 through 806 Processing sheet with id=AE6, first strand: chain 'D' and resid 842 through 843 Processing sheet with id=AE7, first strand: chain 'D' and resid 1106 through 1109 Processing sheet with id=AE8, first strand: chain 'D' and resid 1118 through 1121 Processing sheet with id=AE9, first strand: chain 'D' and resid 1123 through 1125 Processing sheet with id=AF1, first strand: chain 'D' and resid 1153 through 1155 Processing sheet with id=AF2, first strand: chain 'D' and resid 1300 through 1305 removed outlier: 3.667A pdb=" N LEU D1305 " --> pdb=" O LEU D1290 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU D1290 " --> pdb=" O LEU D1305 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY D1279 " --> pdb=" O VAL D1319 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 1394 through 1396 removed outlier: 5.511A pdb=" N VAL D1381 " --> pdb=" O LYS D1418 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS D1418 " --> pdb=" O VAL D1381 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 1484 through 1488 Processing sheet with id=AF5, first strand: chain 'E' and resid 47 through 49 1275 hydrogen bonds defined for protein. 3556 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 7.30 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7826 1.33 - 1.45: 5031 1.45 - 1.57: 16244 1.57 - 1.69: 202 1.69 - 1.81: 133 Bond restraints: 29436 Sorted by residual: bond pdb=" C3' DT H 19 " pdb=" C2' DT H 19 " ideal model delta sigma weight residual 1.516 1.551 -0.035 8.00e-03 1.56e+04 1.91e+01 bond pdb=" C3' DA G 18 " pdb=" C2' DA G 18 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.46e+01 bond pdb=" C3' DT H 27 " pdb=" C2' DT H 27 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.42e+01 bond pdb=" O3BA2TM G2102 " pdb=" PG A2TM G2102 " ideal model delta sigma weight residual 1.700 1.628 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C3' DC G 9 " pdb=" O3' DC G 9 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.15e+01 ... (remaining 29431 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 40005 2.88 - 5.75: 233 5.75 - 8.63: 13 8.63 - 11.51: 0 11.51 - 14.38: 4 Bond angle restraints: 40255 Sorted by residual: angle pdb=" N3 DT H 27 " pdb=" C4 DT H 27 " pdb=" O4 DT H 27 " ideal model delta sigma weight residual 119.90 122.79 -2.89 6.00e-01 2.78e+00 2.31e+01 angle pdb=" PA A2TM G2102 " pdb=" C1 A2TM G2102 " pdb=" PB A2TM G2102 " ideal model delta sigma weight residual 120.85 135.23 -14.38 3.00e+00 1.11e-01 2.30e+01 angle pdb=" PB A2TM G2102 " pdb=" O3BA2TM G2102 " pdb=" PG A2TM G2102 " ideal model delta sigma weight residual 132.18 146.39 -14.21 3.00e+00 1.11e-01 2.24e+01 angle pdb=" N3 DT H 5 " pdb=" C4 DT H 5 " pdb=" O4 DT H 5 " ideal model delta sigma weight residual 119.90 122.66 -2.76 6.00e-01 2.78e+00 2.12e+01 angle pdb=" O4 DT H 27 " pdb=" C4 DT H 27 " pdb=" C5 DT H 27 " ideal model delta sigma weight residual 124.90 121.70 3.20 7.00e-01 2.04e+00 2.08e+01 ... (remaining 40250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.74: 15997 25.74 - 51.49: 1566 51.49 - 77.23: 300 77.23 - 102.97: 43 102.97 - 128.71: 1 Dihedral angle restraints: 17907 sinusoidal: 8232 harmonic: 9675 Sorted by residual: dihedral pdb=" CA ASP C 268 " pdb=" C ASP C 268 " pdb=" N LEU C 269 " pdb=" CA LEU C 269 " ideal model delta harmonic sigma weight residual 180.00 155.79 24.21 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA SER A 46 " pdb=" C SER A 46 " pdb=" N SER A 47 " pdb=" CA SER A 47 " ideal model delta harmonic sigma weight residual -180.00 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA TYR D1207 " pdb=" C TYR D1207 " pdb=" N ASP D1208 " pdb=" CA ASP D1208 " ideal model delta harmonic sigma weight residual 180.00 157.04 22.96 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 17904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3667 0.059 - 0.117: 788 0.117 - 0.176: 68 0.176 - 0.234: 2 0.234 - 0.293: 1 Chirality restraints: 4526 Sorted by residual: chirality pdb=" P DA G 18 " pdb=" OP1 DA G 18 " pdb=" OP2 DA G 18 " pdb=" O5' DA G 18 " both_signs ideal model delta sigma weight residual True 2.34 -2.63 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" C1' DG G 17 " pdb=" O4' DG G 17 " pdb=" C2' DG G 17 " pdb=" N9 DG G 17 " both_signs ideal model delta sigma weight residual False 2.43 2.23 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C23 G3A G2101 " pdb=" C22 G3A G2101 " pdb=" C24 G3A G2101 " pdb=" O23 G3A G2101 " both_signs ideal model delta sigma weight residual False -2.44 -2.63 0.19 2.00e-01 2.50e+01 9.03e-01 ... (remaining 4523 not shown) Planarity restraints: 4914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 G3A G2101 " -0.021 2.00e-02 2.50e+03 6.86e-02 1.29e+02 pdb=" C14 G3A G2101 " -0.042 2.00e-02 2.50e+03 pdb=" C15 G3A G2101 " -0.020 2.00e-02 2.50e+03 pdb=" C16 G3A G2101 " 0.009 2.00e-02 2.50e+03 pdb=" C18 G3A G2101 " -0.058 2.00e-02 2.50e+03 pdb=" C21 G3A G2101 " 0.169 2.00e-02 2.50e+03 pdb=" N11 G3A G2101 " 0.006 2.00e-02 2.50e+03 pdb=" N13 G3A G2101 " -0.047 2.00e-02 2.50e+03 pdb=" N16 G3A G2101 " 0.100 2.00e-02 2.50e+03 pdb=" N17 G3A G2101 " -0.032 2.00e-02 2.50e+03 pdb=" N19 G3A G2101 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C32 G3A G2101 " -0.003 2.00e-02 2.50e+03 1.98e-02 1.18e+01 pdb=" C34 G3A G2101 " -0.025 2.00e-02 2.50e+03 pdb=" C35 G3A G2101 " -0.017 2.00e-02 2.50e+03 pdb=" C36 G3A G2101 " -0.006 2.00e-02 2.50e+03 pdb=" C38 G3A G2101 " -0.004 2.00e-02 2.50e+03 pdb=" C41 G3A G2101 " 0.046 2.00e-02 2.50e+03 pdb=" N31 G3A G2101 " 0.005 2.00e-02 2.50e+03 pdb=" N32 G3A G2101 " 0.007 2.00e-02 2.50e+03 pdb=" N33 G3A G2101 " -0.017 2.00e-02 2.50e+03 pdb=" N37 G3A G2101 " -0.004 2.00e-02 2.50e+03 pdb=" N39 G3A G2101 " -0.014 2.00e-02 2.50e+03 pdb=" O36 G3A G2101 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG C 230 " -0.041 5.00e-02 4.00e+02 6.18e-02 6.11e+00 pdb=" N PRO C 231 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 231 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 231 " -0.034 5.00e-02 4.00e+02 ... (remaining 4911 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 115 2.53 - 3.12: 20086 3.12 - 3.71: 44961 3.71 - 4.31: 64576 4.31 - 4.90: 105469 Nonbonded interactions: 235207 Sorted by model distance: nonbonded pdb=" OD1 ASP D 743 " pdb="MG MG D2003 " model vdw 1.932 2.170 nonbonded pdb=" OD1 ASP D 739 " pdb="MG MG D2003 " model vdw 1.989 2.170 nonbonded pdb=" O LYS D 840 " pdb="MG MG D2005 " model vdw 2.010 2.170 nonbonded pdb="MG MG D2003 " pdb=" O43 G3A G2101 " model vdw 2.139 2.170 nonbonded pdb="MG MG C1201 " pdb=" O1G G3A G2101 " model vdw 2.187 2.170 ... (remaining 235202 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.820 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: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 36.380 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 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 : 0.005 0.072 29444 Z= 0.280 Angle : 0.649 14.384 40267 Z= 0.397 Chirality : 0.047 0.293 4526 Planarity : 0.006 0.089 4914 Dihedral : 19.492 128.713 11685 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.42 % Allowed : 20.50 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.14), residues: 3355 helix: 1.57 (0.14), residues: 1294 sheet: 0.14 (0.24), residues: 444 loop : 0.09 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 232 TYR 0.029 0.002 TYR D1198 PHE 0.020 0.002 PHE A 179 TRP 0.015 0.002 TRP B 200 HIS 0.006 0.001 BHIS D1242 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.28 (29436) covalent geometry : angle 0.64855 / 0.40 (40255) hydrogen bonds : bond 0.14115 / 9.46 ( 1345) hydrogen bonds : angle 5.75922 / 4.06 ( 3712) metal coordination : bond 0.00347 / 0.20 ( 8) metal coordination : angle 2.07139 / 1.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 237 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 TYR cc_start: 0.8818 (m-10) cc_final: 0.8386 (m-10) REVERT: D 1286 THR cc_start: 0.9165 (m) cc_final: 0.8788 (p) REVERT: F 170 HIS cc_start: 0.8364 (m-70) cc_final: 0.8063 (m-70) outliers start: 10 outliers final: 1 residues processed: 246 average time/residue: 0.7815 time to fit residues: 218.9011 Evaluate side-chains 142 residues out of total 2833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 240 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 GLN D 994 GLN D1235 GLN B E 28 GLN E 78 ASN F 381 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.068995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.044164 restraints weight = 226150.675| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 3.71 r_work: 0.2559 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (14 function evaluations) r_final: 0.2555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9274 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29444 Z= 0.162 Angle : 0.601 10.103 40267 Z= 0.324 Chirality : 0.044 0.177 4526 Planarity : 0.005 0.063 4914 Dihedral : 16.730 130.301 4937 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.82 % Allowed : 20.25 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.14), residues: 3355 helix: 1.73 (0.14), residues: 1309 sheet: 0.18 (0.24), residues: 472 loop : 0.13 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 721 TYR 0.024 0.001 TYR D1198 PHE 0.018 0.001 PHE C 684 TRP 0.012 0.001 TRP B 200 HIS 0.007 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (29436) covalent geometry : angle 0.59960 / 0.32 (40255) hydrogen bonds : bond 0.05529 / 3.65 ( 1345) hydrogen bonds : angle 4.90244 / 3.46 ( 3712) metal coordination : bond 0.00386 / 0.21 ( 8) metal coordination : angle 2.13913 / 1.09 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 153 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 GLN cc_start: 0.8790 (mm-40) cc_final: 0.8122 (mm110) REVERT: D 421 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8388 (mp) REVERT: D 1317 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8108 (m-30) REVERT: E 87 LYS cc_start: 0.9351 (tmmm) cc_final: 0.9081 (tmmt) REVERT: F 170 HIS cc_start: 0.8488 (m-70) cc_final: 0.8255 (m-70) REVERT: F 290 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8726 (mp0) outliers start: 50 outliers final: 7 residues processed: 191 average time/residue: 0.7157 time to fit residues: 158.3632 Evaluate side-chains 150 residues out of total 2833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain D residue 1299 PHE Chi-restraints excluded: chain D residue 1317 ASP Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 367 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 300 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 189 optimal weight: 6.9990 chunk 262 optimal weight: 0.9990 chunk 309 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 326 optimal weight: 0.7980 chunk 217 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 292 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 670 GLN C 999 HIS D 350 HIS E 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.068341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.043753 restraints weight = 193002.563| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 3.16 r_work: 0.2574 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2573 r_free = 0.2573 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9273 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29444 Z= 0.163 Angle : 0.578 8.272 40267 Z= 0.310 Chirality : 0.044 0.171 4526 Planarity : 0.005 0.065 4914 Dihedral : 16.534 131.408 4937 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.57 % Allowed : 20.39 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.14), residues: 3355 helix: 1.83 (0.14), residues: 1309 sheet: 0.15 (0.24), residues: 475 loop : 0.23 (0.16), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 65 TYR 0.022 0.001 TYR D1198 PHE 0.028 0.001 PHE F 389 TRP 0.014 0.001 TRP B 200 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (29436) covalent geometry : angle 0.57707 / 0.31 (40255) hydrogen bonds : bond 0.05015 / 3.29 ( 1345) hydrogen bonds : angle 4.67904 / 3.30 ( 3712) metal coordination : bond 0.00449 / 0.27 ( 8) metal coordination : angle 2.10078 / 1.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 155 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8574 (mt-10) REVERT: A 229 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8191 (mm110) REVERT: B 159 LYS cc_start: 0.9224 (mttm) cc_final: 0.8973 (mtpm) REVERT: C 1 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.7034 (ppp) REVERT: C 101 ILE cc_start: 0.9429 (pt) cc_final: 0.9224 (pp) REVERT: C 284 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8278 (tpp-160) REVERT: C 762 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8873 (pttt) REVERT: E 52 GLU cc_start: 0.9007 (mp0) cc_final: 0.8614 (mp0) REVERT: E 87 LYS cc_start: 0.9299 (tmmm) cc_final: 0.9093 (tmmt) outliers start: 43 outliers final: 13 residues processed: 187 average time/residue: 0.7043 time to fit residues: 151.7564 Evaluate side-chains 154 residues out of total 2833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain C residue 762 LYS Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain D residue 1299 PHE Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 358 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 192 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 339 optimal weight: 10.0000 chunk 44 optimal weight: 0.1980 chunk 311 optimal weight: 2.9990 chunk 229 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 68 optimal weight: 0.2980 chunk 176 optimal weight: 0.0770 chunk 53 optimal weight: 4.9990 chunk 305 optimal weight: 9.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 670 GLN D 350 HIS E 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.069044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.044130 restraints weight = 249226.481| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 3.60 r_work: 0.2585 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2585 r_free = 0.2585 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2585 r_free = 0.2585 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9264 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29444 Z= 0.115 Angle : 0.543 9.280 40267 Z= 0.291 Chirality : 0.042 0.146 4526 Planarity : 0.004 0.072 4914 Dihedral : 16.376 131.332 4937 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.54 % Allowed : 20.36 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.15), residues: 3355 helix: 1.96 (0.14), residues: 1311 sheet: 0.24 (0.24), residues: 460 loop : 0.33 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 65 TYR 0.018 0.001 TYR D1198 PHE 0.027 0.001 PHE F 389 TRP 0.011 0.001 TRP B 200 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (29436) covalent geometry : angle 0.54243 / 0.29 (40255) hydrogen bonds : bond 0.04273 / 2.79 ( 1345) hydrogen bonds : angle 4.51867 / 3.19 ( 3712) metal coordination : bond 0.00249 / 0.16 ( 8) metal coordination : angle 1.87820 / 0.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8624 (mt-10) REVERT: A 229 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8193 (mm110) REVERT: D 351 MET cc_start: 0.8446 (ptp) cc_final: 0.8051 (ptp) outliers start: 42 outliers final: 10 residues processed: 187 average time/residue: 0.6930 time to fit residues: 149.5363 Evaluate side-chains 148 residues out of total 2833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain D residue 1299 PHE Chi-restraints excluded: chain E residue 89 MET Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 367 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 168 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 178 optimal weight: 10.0000 chunk 47 optimal weight: 0.0670 chunk 148 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 273 optimal weight: 1.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN C 390 GLN C 670 GLN D 143 ASN D 350 HIS E 78 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.068392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.043500 restraints weight = 247630.315| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 3.58 r_work: 0.2567 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2568 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2568 r_free = 0.2568 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2568 r_free = 0.2568 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2568 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9278 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29444 Z= 0.142 Angle : 0.554 12.276 40267 Z= 0.295 Chirality : 0.043 0.159 4526 Planarity : 0.004 0.066 4914 Dihedral : 16.309 131.976 4937 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.54 % Allowed : 20.15 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.15), residues: 3355 helix: 1.98 (0.14), residues: 1320 sheet: 0.30 (0.24), residues: 467 loop : 0.39 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 65 TYR 0.019 0.001 TYR D1198 PHE 0.017 0.001 PHE C 684 TRP 0.012 0.001 TRP B 200 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (29436) covalent geometry : angle 0.55326 / 0.30 (40255) hydrogen bonds : bond 0.04498 / 2.94 ( 1345) hydrogen bonds : angle 4.48803 / 3.18 ( 3712) metal coordination : bond 0.00400 / 0.24 ( 8) metal coordination : angle 1.94235 / 0.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 144 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8628 (mt-10) REVERT: A 186 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8994 (tp) REVERT: A 229 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8330 (mm-40) REVERT: D 973 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.7787 (mp10) REVERT: D 1362 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8565 (mmtp) REVERT: E 87 LYS cc_start: 0.9085 (tmmt) cc_final: 0.8821 (tmmm) REVERT: F 358 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8064 (tt) outliers start: 42 outliers final: 15 residues processed: 177 average time/residue: 0.7023 time to fit residues: 144.2909 Evaluate side-chains 155 residues out of total 2833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 973 GLN Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain D residue 1299 PHE Chi-restraints excluded: chain D residue 1362 LYS Chi-restraints excluded: chain D residue 1495 ILE Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 358 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 211 optimal weight: 2.9990 chunk 289 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 302 optimal weight: 8.9990 chunk 114 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 307 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 670 GLN D 143 ASN D 350 HIS E 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.067728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.042859 restraints weight = 233917.260| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 3.48 r_work: 0.2549 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2550 r_free = 0.2550 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2550 r_free = 0.2550 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9294 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 29444 Z= 0.183 Angle : 0.567 9.189 40267 Z= 0.303 Chirality : 0.044 0.194 4526 Planarity : 0.005 0.072 4914 Dihedral : 16.292 132.248 4936 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.02 % Favored : 97.95 % Rotamer: Outliers : 1.36 % Allowed : 20.43 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.15), residues: 3355 helix: 1.96 (0.14), residues: 1321 sheet: 0.25 (0.24), residues: 477 loop : 0.38 (0.16), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 8 TYR 0.020 0.001 TYR D1198 PHE 0.016 0.001 PHE C 684 TRP 0.013 0.001 TRP B 200 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (29436) covalent geometry : angle 0.56577 / 0.30 (40255) hydrogen bonds : bond 0.04820 / 3.15 ( 1345) hydrogen bonds : angle 4.52089 / 3.19 ( 3712) metal coordination : bond 0.00576 / 0.33 ( 8) metal coordination : angle 2.09692 / 1.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 104 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8616 (mt-10) REVERT: A 229 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8397 (mm-40) REVERT: B 159 LYS cc_start: 0.9242 (mttm) cc_final: 0.8971 (mtpm) REVERT: C 1 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7321 (ppp) REVERT: C 108 ILE cc_start: 0.9487 (mt) cc_final: 0.9271 (mm) REVERT: C 762 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8872 (pttt) REVERT: D 973 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.7790 (mp10) REVERT: D 1362 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8590 (mmtp) REVERT: D 1403 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9174 (tm) REVERT: E 87 LYS cc_start: 0.9088 (tmmt) cc_final: 0.8885 (tmmm) REVERT: F 290 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8782 (mp0) REVERT: F 358 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8052 (tt) REVERT: F 403 LYS cc_start: 0.8828 (mmmm) cc_final: 0.8572 (mmmt) outliers start: 37 outliers final: 13 residues processed: 168 average time/residue: 0.7388 time to fit residues: 143.8545 Evaluate side-chains 161 residues out of total 2833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 731 GLU Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain C residue 762 LYS Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 973 GLN Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain D residue 1299 PHE Chi-restraints excluded: chain D residue 1362 LYS Chi-restraints excluded: chain D residue 1403 LEU Chi-restraints excluded: chain D residue 1495 ILE Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 358 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 30 optimal weight: 0.3980 chunk 157 optimal weight: 3.9990 chunk 256 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 335 optimal weight: 30.0000 chunk 75 optimal weight: 0.5980 chunk 236 optimal weight: 0.6980 chunk 190 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 670 GLN D 350 HIS E 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.068432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.043623 restraints weight = 227110.462| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 3.45 r_work: 0.2576 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2578 r_free = 0.2578 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2578 r_free = 0.2578 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9275 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29444 Z= 0.122 Angle : 0.547 12.179 40267 Z= 0.290 Chirality : 0.042 0.191 4526 Planarity : 0.004 0.065 4914 Dihedral : 16.219 131.898 4936 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.98 % Allowed : 20.64 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.15), residues: 3355 helix: 2.03 (0.14), residues: 1322 sheet: 0.30 (0.24), residues: 465 loop : 0.45 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 8 TYR 0.017 0.001 TYR D1198 PHE 0.034 0.001 PHE F 389 TRP 0.012 0.001 TRP B 200 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (29436) covalent geometry : angle 0.54574 / 0.29 (40255) hydrogen bonds : bond 0.04242 / 2.76 ( 1345) hydrogen bonds : angle 4.40143 / 3.11 ( 3712) metal coordination : bond 0.00325 / 0.19 ( 8) metal coordination : angle 1.86384 / 0.93 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8387 (mm-40) REVERT: B 159 LYS cc_start: 0.9229 (mttm) cc_final: 0.8994 (mtpm) REVERT: C 222 MET cc_start: 0.7590 (mmm) cc_final: 0.7374 (mmm) REVERT: C 361 MET cc_start: 0.8294 (ttm) cc_final: 0.8029 (tmm) REVERT: D 386 HIS cc_start: 0.8694 (m-70) cc_final: 0.8489 (m-70) REVERT: D 973 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.7751 (mp10) REVERT: D 1403 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9128 (tm) REVERT: E 87 LYS cc_start: 0.9088 (tmmt) cc_final: 0.8811 (tmmm) REVERT: F 290 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8766 (mp0) REVERT: F 358 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8031 (tt) REVERT: F 403 LYS cc_start: 0.8844 (mmmm) cc_final: 0.8576 (mmmt) outliers start: 26 outliers final: 9 residues processed: 169 average time/residue: 0.6832 time to fit residues: 133.8544 Evaluate side-chains 151 residues out of total 2833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 973 GLN Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain D residue 1299 PHE Chi-restraints excluded: chain D residue 1403 LEU Chi-restraints excluded: chain D residue 1495 ILE Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 358 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 121 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 302 optimal weight: 8.9990 chunk 301 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 326 optimal weight: 0.9980 chunk 240 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 670 GLN D 350 HIS E 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.067221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.043011 restraints weight = 202216.615| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 3.36 r_work: 0.2536 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9306 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 29444 Z= 0.201 Angle : 0.591 12.093 40267 Z= 0.313 Chirality : 0.044 0.177 4526 Planarity : 0.005 0.077 4914 Dihedral : 16.225 132.542 4936 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.91 % Allowed : 20.81 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.15), residues: 3355 helix: 1.95 (0.14), residues: 1321 sheet: 0.33 (0.24), residues: 464 loop : 0.38 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 8 TYR 0.021 0.001 TYR D1198 PHE 0.038 0.002 PHE F 389 TRP 0.013 0.001 TRP B 200 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (29436) covalent geometry : angle 0.59010 / 0.31 (40255) hydrogen bonds : bond 0.04973 / 3.26 ( 1345) hydrogen bonds : angle 4.52530 / 3.19 ( 3712) metal coordination : bond 0.00675 / 0.39 ( 8) metal coordination : angle 2.14934 / 1.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8440 (mm-40) REVERT: B 159 LYS cc_start: 0.9252 (mttm) cc_final: 0.8959 (mtpm) REVERT: C 222 MET cc_start: 0.7722 (mmm) cc_final: 0.7466 (mmm) REVERT: C 361 MET cc_start: 0.8369 (ttm) cc_final: 0.8132 (tmm) REVERT: C 762 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8851 (pttt) REVERT: D 973 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.7796 (mp10) REVERT: D 1362 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8637 (mmtt) REVERT: D 1403 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9169 (tm) REVERT: D 1493 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8670 (mppt) REVERT: F 173 TYR cc_start: 0.8682 (m-10) cc_final: 0.8397 (m-10) REVERT: F 290 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8722 (mp0) REVERT: F 358 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8008 (tt) REVERT: F 403 LYS cc_start: 0.8836 (mmmm) cc_final: 0.8572 (mmmt) outliers start: 24 outliers final: 11 residues processed: 160 average time/residue: 0.7291 time to fit residues: 134.4343 Evaluate side-chains 156 residues out of total 2833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain C residue 762 LYS Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 973 GLN Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain D residue 1299 PHE Chi-restraints excluded: chain D residue 1362 LYS Chi-restraints excluded: chain D residue 1403 LEU Chi-restraints excluded: chain D residue 1493 LYS Chi-restraints excluded: chain D residue 1495 ILE Chi-restraints excluded: chain E residue 89 MET Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 358 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 321 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 286 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 176 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 236 optimal weight: 0.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN C 670 GLN D 350 HIS E 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.067577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.043490 restraints weight = 195552.266| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 3.24 r_work: 0.2560 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9291 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29444 Z= 0.154 Angle : 0.574 11.359 40267 Z= 0.303 Chirality : 0.043 0.198 4526 Planarity : 0.004 0.065 4914 Dihedral : 16.183 132.195 4936 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.91 % Allowed : 20.71 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.15), residues: 3355 helix: 1.99 (0.14), residues: 1321 sheet: 0.27 (0.24), residues: 467 loop : 0.41 (0.16), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 185 TYR 0.019 0.001 TYR D1198 PHE 0.041 0.001 PHE F 389 TRP 0.013 0.001 TRP B 200 HIS 0.007 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (29436) covalent geometry : angle 0.57266 / 0.30 (40255) hydrogen bonds : bond 0.04592 / 3.00 ( 1345) hydrogen bonds : angle 4.46185 / 3.15 ( 3712) metal coordination : bond 0.00474 / 0.28 ( 8) metal coordination : angle 2.04592 / 1.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 1.045 Fit side-chains REVERT: A 229 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8453 (mm-40) REVERT: B 159 LYS cc_start: 0.9236 (mttm) cc_final: 0.8990 (mtpm) REVERT: C 361 MET cc_start: 0.8325 (ttm) cc_final: 0.8123 (tmm) REVERT: D 973 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.7765 (mp10) REVERT: D 1362 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8600 (mmtt) REVERT: D 1403 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9146 (tm) REVERT: D 1493 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8483 (mmtm) REVERT: E 86 GLN cc_start: 0.9078 (tp40) cc_final: 0.8572 (tp-100) REVERT: F 173 TYR cc_start: 0.8680 (m-10) cc_final: 0.8344 (m-10) REVERT: F 290 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8721 (mp0) REVERT: F 358 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8002 (tt) REVERT: F 403 LYS cc_start: 0.8862 (mmmm) cc_final: 0.8576 (mmmt) REVERT: F 405 LEU cc_start: 0.9448 (pp) cc_final: 0.9245 (mm) outliers start: 24 outliers final: 12 residues processed: 162 average time/residue: 0.7156 time to fit residues: 133.5983 Evaluate side-chains 154 residues out of total 2833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 607 LEU Chi-restraints excluded: chain D residue 973 GLN Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain D residue 1362 LYS Chi-restraints excluded: chain D residue 1403 LEU Chi-restraints excluded: chain D residue 1493 LYS Chi-restraints excluded: chain D residue 1495 ILE Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 358 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 137 optimal weight: 1.9990 chunk 231 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 223 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 233 optimal weight: 2.9990 chunk 269 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 139 ASN ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 670 GLN D 350 HIS E 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.067454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.042519 restraints weight = 233914.059| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 3.49 r_work: 0.2543 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2545 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2545 r_free = 0.2545 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2545 r_free = 0.2545 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9301 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29444 Z= 0.168 Angle : 0.586 10.148 40267 Z= 0.309 Chirality : 0.043 0.200 4526 Planarity : 0.005 0.081 4914 Dihedral : 16.167 132.355 4936 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.80 % Allowed : 20.95 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.15), residues: 3355 helix: 2.00 (0.14), residues: 1315 sheet: 0.32 (0.24), residues: 462 loop : 0.39 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 84 TYR 0.019 0.001 TYR D1198 PHE 0.044 0.001 PHE F 389 TRP 0.013 0.001 TRP B 200 HIS 0.007 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (29436) covalent geometry : angle 0.58470 / 0.31 (40255) hydrogen bonds : bond 0.04690 / 3.07 ( 1345) hydrogen bonds : angle 4.47882 / 3.16 ( 3712) metal coordination : bond 0.00532 / 0.31 ( 8) metal coordination : angle 2.05694 / 1.02 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.966 Fit side-chains REVERT: A 229 GLN cc_start: 0.8915 (mm-40) cc_final: 0.8465 (mm-40) REVERT: B 5 LYS cc_start: 0.8691 (tppp) cc_final: 0.8203 (tmtt) REVERT: B 159 LYS cc_start: 0.9241 (mttm) cc_final: 0.8993 (mtpm) REVERT: C 361 MET cc_start: 0.8345 (ttm) cc_final: 0.8132 (tmm) REVERT: D 973 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7783 (mp10) REVERT: D 1362 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8605 (mmtt) REVERT: D 1403 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9180 (tm) REVERT: D 1493 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8635 (mmtm) REVERT: E 86 GLN cc_start: 0.9102 (tp40) cc_final: 0.8593 (tp-100) REVERT: F 173 TYR cc_start: 0.8708 (m-10) cc_final: 0.8424 (m-10) REVERT: F 290 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8729 (mp0) REVERT: F 358 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8004 (tt) REVERT: F 403 LYS cc_start: 0.8863 (mmmm) cc_final: 0.8576 (mmmt) REVERT: F 405 LEU cc_start: 0.9450 (pp) cc_final: 0.9244 (mm) outliers start: 21 outliers final: 13 residues processed: 156 average time/residue: 0.6982 time to fit residues: 126.5039 Evaluate side-chains 157 residues out of total 2833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 607 LEU Chi-restraints excluded: chain D residue 973 GLN Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain D residue 1362 LYS Chi-restraints excluded: chain D residue 1403 LEU Chi-restraints excluded: chain D residue 1424 VAL Chi-restraints excluded: chain D residue 1493 LYS Chi-restraints excluded: chain D residue 1495 ILE Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 358 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 148 optimal weight: 0.8980 chunk 224 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 159 optimal weight: 0.0570 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 272 optimal weight: 0.0970 chunk 218 optimal weight: 2.9990 chunk 254 optimal weight: 4.9990 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN C 670 GLN D 350 HIS E 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.067756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.042942 restraints weight = 223535.141| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 3.42 r_work: 0.2559 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2562 r_free = 0.2562 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2562 r_free = 0.2562 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9290 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29444 Z= 0.141 Angle : 0.569 12.507 40267 Z= 0.300 Chirality : 0.043 0.208 4526 Planarity : 0.004 0.065 4914 Dihedral : 16.116 132.281 4936 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.91 % Allowed : 20.81 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.15), residues: 3355 helix: 2.07 (0.14), residues: 1313 sheet: 0.29 (0.24), residues: 465 loop : 0.42 (0.16), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 185 TYR 0.018 0.001 TYR D1198 PHE 0.043 0.001 PHE F 389 TRP 0.013 0.001 TRP B 200 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (29436) covalent geometry : angle 0.56778 / 0.30 (40255) hydrogen bonds : bond 0.04408 / 2.88 ( 1345) hydrogen bonds : angle 4.39324 / 3.10 ( 3712) metal coordination : bond 0.00413 / 0.24 ( 8) metal coordination : angle 1.95007 / 0.97 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9948.29 seconds wall clock time: 169 minutes 33.22 seconds (10173.22 seconds total)