Starting phenix.real_space_refine on Sun Jun 22 08:22:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hkc_34849/06_2025/8hkc_34849.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hkc_34849/06_2025/8hkc_34849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hkc_34849/06_2025/8hkc_34849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hkc_34849/06_2025/8hkc_34849.map" model { file = "/net/cci-nas-00/data/ceres_data/8hkc_34849/06_2025/8hkc_34849.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hkc_34849/06_2025/8hkc_34849.cif" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 83 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 15906 2.51 5 N 4583 2.21 5 O 5098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25779 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1756 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 9, 'TRANS': 220} Chain: "C" Number of atoms: 9345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1188, 9345 Classifications: {'peptide': 1188} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1134} Chain breaks: 2 Chain: "F" Number of atoms: 9068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1160, 9068 Classifications: {'peptide': 1160} Link IDs: {'PCIS': 2, 'PTRANS': 45, 'TRANS': 1112} Chain breaks: 2 Chain: "G" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 858 Classifications: {'DNA': 42} Link IDs: {'rna3p': 41} Chain breaks: 1 Chain: "H" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 844 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain breaks: 1 Chain: "E" Number of atoms: 2119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2119 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 257} Chain breaks: 1 Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13345 SG CYS F 70 44.600 87.044 60.144 1.00 61.00 S ATOM 13359 SG CYS F 72 44.396 90.091 58.044 1.00 68.30 S ATOM 13467 SG CYS F 85 42.520 87.023 56.878 1.00 68.63 S ATOM 13491 SG CYS F 88 46.243 87.082 56.597 1.00 63.21 S ATOM 19179 SG CYS F 814 83.109 29.764 66.322 1.00 54.46 S ATOM 19744 SG CYS F 888 83.604 33.534 66.239 1.00 46.75 S ATOM 19795 SG CYS F 895 82.554 31.746 69.513 1.00 39.20 S ATOM 19816 SG CYS F 898 85.997 31.387 68.282 1.00 38.51 S Time building chain proxies: 14.93, per 1000 atoms: 0.58 Number of scatterers: 25779 At special positions: 0 Unit cell: (157.435, 147.223, 162.541, 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 106 16.00 P 83 15.00 Mg 1 11.99 O 5098 8.00 N 4583 7.00 C 15906 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: 6.51 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F1501 " pdb="ZN ZN F1501 " - pdb=" SG CYS F 72 " pdb="ZN ZN F1501 " - pdb=" SG CYS F 85 " pdb="ZN ZN F1501 " - pdb=" SG CYS F 88 " pdb="ZN ZN F1501 " - pdb=" SG CYS F 70 " pdb=" ZN F1502 " pdb="ZN ZN F1502 " - pdb=" SG CYS F 898 " pdb="ZN ZN F1502 " - pdb=" SG CYS F 895 " pdb="ZN ZN F1502 " - pdb=" SG CYS F 814 " pdb="ZN ZN F1502 " - pdb=" SG CYS F 888 " Number of angles added : 12 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5676 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 41 sheets defined 45.0% alpha, 16.7% beta 24 base pairs and 61 stacking pairs defined. Time for finding SS restraints: 9.46 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.697A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 161 removed outlier: 3.650A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 228 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.854A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.682A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 212 through 233 removed outlier: 4.415A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N PHE B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 9 removed outlier: 3.829A pdb=" N LYS C 9 " --> pdb=" O TYR C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.726A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.588A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 4.060A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 378 through 390 removed outlier: 3.994A pdb=" N GLU C 382 " --> pdb=" O ARG C 378 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 437 Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.761A pdb=" N ARG C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 495 through 509 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.951A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 Processing helix chain 'C' and resid 608 through 612 removed outlier: 3.814A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 608 through 612' Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 664 through 668 removed outlier: 3.723A pdb=" N ILE C 668 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 713 removed outlier: 4.051A pdb=" N GLY C 713 " --> pdb=" O ALA C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 741 Processing helix chain 'C' and resid 811 through 815 removed outlier: 3.749A pdb=" N ASP C 814 " --> pdb=" O ASN C 811 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 860 through 864 removed outlier: 3.994A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 942 through 973 removed outlier: 4.007A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 1027 through 1038 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.609A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.602A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.632A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 3.722A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.787A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 34 Processing helix chain 'F' and resid 58 through 63 Processing helix chain 'F' and resid 94 through 100 removed outlier: 3.544A pdb=" N VAL F 97 " --> pdb=" O GLN F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 119 removed outlier: 3.597A pdb=" N SER F 119 " --> pdb=" O TRP F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 129 Processing helix chain 'F' and resid 131 through 140 Processing helix chain 'F' and resid 161 through 173 removed outlier: 3.538A pdb=" N GLU F 170 " --> pdb=" O LEU F 166 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU F 171 " --> pdb=" O ASP F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 192 removed outlier: 3.809A pdb=" N ILE F 185 " --> pdb=" O GLY F 181 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET F 192 " --> pdb=" O LEU F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 208 removed outlier: 3.685A pdb=" N GLU F 197 " --> pdb=" O ASP F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 231 Processing helix chain 'F' and resid 233 through 236 Processing helix chain 'F' and resid 246 through 250 Processing helix chain 'F' and resid 263 through 285 removed outlier: 4.066A pdb=" N ASP F 267 " --> pdb=" O SER F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 308 removed outlier: 3.541A pdb=" N VAL F 292 " --> pdb=" O PRO F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.625A pdb=" N MET F 330 " --> pdb=" O SER F 326 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE F 331 " --> pdb=" O LEU F 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 326 through 331' Processing helix chain 'F' and resid 336 through 342 Processing helix chain 'F' and resid 370 through 377 Processing helix chain 'F' and resid 377 through 388 Processing helix chain 'F' and resid 393 through 404 Processing helix chain 'F' and resid 405 through 416 removed outlier: 3.794A pdb=" N TRP F 409 " --> pdb=" O GLU F 405 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP F 410 " --> pdb=" O ALA F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 432 No H-bonds generated for 'chain 'F' and resid 430 through 432' Processing helix chain 'F' and resid 450 through 452 No H-bonds generated for 'chain 'F' and resid 450 through 452' Processing helix chain 'F' and resid 453 through 458 Processing helix chain 'F' and resid 473 through 484 Processing helix chain 'F' and resid 485 through 489 Processing helix chain 'F' and resid 504 through 514 Processing helix chain 'F' and resid 529 through 539 Processing helix chain 'F' and resid 574 through 580 Processing helix chain 'F' and resid 581 through 583 No H-bonds generated for 'chain 'F' and resid 581 through 583' Processing helix chain 'F' and resid 588 through 592 Processing helix chain 'F' and resid 597 through 612 Processing helix chain 'F' and resid 614 through 636 removed outlier: 3.613A pdb=" N GLY F 636 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 644 removed outlier: 3.766A pdb=" N MET F 644 " --> pdb=" O ILE F 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 670 removed outlier: 3.557A pdb=" N SER F 670 " --> pdb=" O GLU F 666 " (cutoff:3.500A) Processing helix chain 'F' and resid 674 through 702 Processing helix chain 'F' and resid 720 through 729 Processing helix chain 'F' and resid 733 through 742 removed outlier: 3.668A pdb=" N GLN F 739 " --> pdb=" O ALA F 735 " (cutoff:3.500A) Processing helix chain 'F' and resid 768 through 805 removed outlier: 4.178A pdb=" N HIS F 777 " --> pdb=" O PHE F 773 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY F 778 " --> pdb=" O ILE F 774 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA F 779 " --> pdb=" O SER F 775 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR F 790 " --> pdb=" O THR F 786 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ALA F 791 " --> pdb=" O ALA F 787 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASN F 792 " --> pdb=" O LEU F 788 " (cutoff:3.500A) Processing helix chain 'F' and resid 835 through 840 Processing helix chain 'F' and resid 865 through 875 removed outlier: 3.576A pdb=" N ASN F 875 " --> pdb=" O LEU F 871 " (cutoff:3.500A) Processing helix chain 'F' and resid 896 through 900 Processing helix chain 'F' and resid 914 through 925 removed outlier: 3.665A pdb=" N ILE F 918 " --> pdb=" O ALA F 914 " (cutoff:3.500A) Processing helix chain 'F' and resid 926 through 930 removed outlier: 3.763A pdb=" N LEU F 930 " --> pdb=" O GLY F 927 " (cutoff:3.500A) Processing helix chain 'F' and resid 1137 through 1146 Processing helix chain 'F' and resid 1216 through 1225 removed outlier: 3.560A pdb=" N ILE F1220 " --> pdb=" O ALA F1216 " (cutoff:3.500A) Processing helix chain 'F' and resid 1225 through 1244 removed outlier: 3.895A pdb=" N VAL F1229 " --> pdb=" O GLY F1225 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL F1240 " --> pdb=" O GLU F1236 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN F1244 " --> pdb=" O VAL F1240 " (cutoff:3.500A) Processing helix chain 'F' and resid 1249 through 1261 removed outlier: 4.406A pdb=" N ILE F1253 " --> pdb=" O ASN F1249 " (cutoff:3.500A) Processing helix chain 'F' and resid 1282 through 1293 Processing helix chain 'F' and resid 1294 through 1297 removed outlier: 4.111A pdb=" N LYS F1297 " --> pdb=" O ALA F1294 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1294 through 1297' Processing helix chain 'F' and resid 1308 through 1315 Processing helix chain 'F' and resid 1318 through 1326 removed outlier: 3.523A pdb=" N ALA F1322 " --> pdb=" O SER F1318 " (cutoff:3.500A) Processing helix chain 'F' and resid 1327 through 1339 Processing helix chain 'F' and resid 1346 through 1354 removed outlier: 3.584A pdb=" N ASN F1350 " --> pdb=" O GLY F1346 " (cutoff:3.500A) Processing helix chain 'F' and resid 1359 through 1361 No H-bonds generated for 'chain 'F' and resid 1359 through 1361' Processing helix chain 'F' and resid 1362 through 1376 Processing helix chain 'E' and resid 15 through 26 removed outlier: 3.503A pdb=" N ARG E 21 " --> pdb=" O ASP E 17 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA E 22 " --> pdb=" O SER E 18 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP E 26 " --> pdb=" O ALA E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 45 removed outlier: 3.937A pdb=" N ALA E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU E 37 " --> pdb=" O GLU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 Processing helix chain 'E' and resid 57 through 66 removed outlier: 3.719A pdb=" N VAL E 61 " --> pdb=" O HIS E 57 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL E 62 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS E 63 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE E 64 " --> pdb=" O PHE E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 72 removed outlier: 5.061A pdb=" N GLY E 70 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR E 71 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY E 72 " --> pdb=" O ALA E 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 67 through 72' Processing helix chain 'E' and resid 74 through 92 Processing helix chain 'E' and resid 94 through 98 removed outlier: 3.501A pdb=" N VAL E 97 " --> pdb=" O ASN E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 121 removed outlier: 4.804A pdb=" N HIS E 107 " --> pdb=" O SER E 103 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TRP E 108 " --> pdb=" O PHE E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 143 removed outlier: 3.504A pdb=" N LYS E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE E 137 " --> pdb=" O ARG E 133 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN E 138 " --> pdb=" O LYS E 134 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG E 140 " --> pdb=" O PHE E 136 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LYS E 141 " --> pdb=" O PHE E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 162 removed outlier: 3.620A pdb=" N VAL E 154 " --> pdb=" O ASN E 150 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU E 155 " --> pdb=" O GLN E 151 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET E 156 " --> pdb=" O ASP E 152 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU E 160 " --> pdb=" O MET E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 177 removed outlier: 3.698A pdb=" N ALA E 176 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 232 removed outlier: 3.697A pdb=" N GLY E 211 " --> pdb=" O ASN E 207 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY E 231 " --> pdb=" O ASP E 227 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 245 Processing helix chain 'E' and resid 252 through 261 removed outlier: 3.625A pdb=" N LEU E 256 " --> pdb=" O THR E 252 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG E 259 " --> pdb=" O GLU E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 284 removed outlier: 3.941A pdb=" N LYS E 272 " --> pdb=" O ARG E 268 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN E 273 " --> pdb=" O GLN E 269 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 20 removed outlier: 6.613A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N HIS A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N THR A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL A 192 " --> pdb=" O THR A 196 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 198 " --> pdb=" O ALA A 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.604A pdb=" N MET A 142 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE A 140 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN A 147 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A 55 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.629A pdb=" N ARG A 91 " --> pdb=" O GLU A 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.887A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 13 through 18 removed outlier: 6.800A pdb=" N THR B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE B 16 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LYS B 25 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLN B 18 " --> pdb=" O HIS B 23 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N HIS B 23 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 105 removed outlier: 3.660A pdb=" N GLU B 58 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.494A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.813A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU C 106 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL C 114 " --> pdb=" O GLU C 106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.636A pdb=" N SER C 147 " --> pdb=" O ARG C 529 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 160 removed outlier: 3.819A pdb=" N LEU C 171 " --> pdb=" O ASP C 160 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 227 through 229 Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 7.195A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC1, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.537A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.186A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC4, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC5, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.201A pdb=" N ILE C 816 " --> pdb=" O LYS C1078 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ASN C1080 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.809A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 849 through 850 removed outlier: 3.534A pdb=" N GLU C 849 " --> pdb=" O VAL C 887 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.814A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD1, first strand: chain 'C' and resid 1251 through 1252 removed outlier: 4.652A pdb=" N TYR C1251 " --> pdb=" O ASP E 203 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 3.788A pdb=" N GLN C1268 " --> pdb=" O VAL F 347 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1335 through 1340 removed outlier: 3.511A pdb=" N ALA F 19 " --> pdb=" O GLU C1340 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 103 through 112 removed outlier: 10.222A pdb=" N LEU F 107 " --> pdb=" O PRO F 243 " (cutoff:3.500A) removed outlier: 10.750A pdb=" N SER F 109 " --> pdb=" O VAL F 241 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL F 241 " --> pdb=" O SER F 109 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 159 through 160 removed outlier: 6.840A pdb=" N ASP F 177 " --> pdb=" O ILE F 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 252 through 254 Processing sheet with id=AD7, first strand: chain 'F' and resid 526 through 527 Processing sheet with id=AD8, first strand: chain 'F' and resid 703 through 707 Processing sheet with id=AD9, first strand: chain 'F' and resid 809 through 811 Processing sheet with id=AE1, first strand: chain 'F' and resid 820 through 822 Processing sheet with id=AE2, first strand: chain 'F' and resid 825 through 827 removed outlier: 6.962A pdb=" N VAL F 825 " --> pdb=" O LYS F 832 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 1155 through 1156 Processing sheet with id=AE4, first strand: chain 'F' and resid 1177 through 1178 Processing sheet with id=AE5, first strand: chain 'F' and resid 1279 through 1281 removed outlier: 6.693A pdb=" N THR F1301 " --> pdb=" O VAL F1267 " (cutoff:3.500A) 1088 hydrogen bonds defined for protein. 3075 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 58 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 61 stacking parallelities Total time for adding SS restraints: 12.03 Time building geometry restraints manager: 7.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8431 1.34 - 1.46: 3821 1.46 - 1.58: 13750 1.58 - 1.70: 162 1.70 - 1.82: 185 Bond restraints: 26349 Sorted by residual: bond pdb=" C CYS F 366 " pdb=" N GLY F 367 " ideal model delta sigma weight residual 1.332 1.339 -0.007 5.00e-03 4.00e+04 1.81e+00 bond pdb=" C3' DA H 36 " pdb=" O3' DA H 36 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.56e+00 bond pdb=" C3' DT G 7 " pdb=" O3' DT G 7 " ideal model delta sigma weight residual 1.422 1.453 -0.031 3.00e-02 1.11e+03 1.05e+00 bond pdb=" N ILE F1190 " pdb=" CA ILE F1190 " ideal model delta sigma weight residual 1.454 1.462 -0.008 7.70e-03 1.69e+04 1.00e+00 bond pdb=" C3' DG H 42 " pdb=" O3' DG H 42 " ideal model delta sigma weight residual 1.422 1.451 -0.029 3.00e-02 1.11e+03 9.34e-01 ... (remaining 26344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 35601 2.02 - 4.04: 306 4.04 - 6.06: 23 6.06 - 8.08: 1 8.08 - 10.10: 1 Bond angle restraints: 35932 Sorted by residual: angle pdb=" C GLN F 504 " pdb=" CA GLN F 504 " pdb=" CB GLN F 504 " ideal model delta sigma weight residual 110.42 115.82 -5.40 1.99e+00 2.53e-01 7.37e+00 angle pdb=" C VAL C1186 " pdb=" N PHE C1187 " pdb=" CA PHE C1187 " ideal model delta sigma weight residual 121.54 126.06 -4.52 1.91e+00 2.74e-01 5.61e+00 angle pdb=" CB MET F 698 " pdb=" CG MET F 698 " pdb=" SD MET F 698 " ideal model delta sigma weight residual 112.70 119.63 -6.93 3.00e+00 1.11e-01 5.34e+00 angle pdb=" CA ARG C1034 " pdb=" CB ARG C1034 " pdb=" CG ARG C1034 " ideal model delta sigma weight residual 114.10 118.66 -4.56 2.00e+00 2.50e-01 5.20e+00 angle pdb=" CA TYR F 679 " pdb=" CB TYR F 679 " pdb=" CG TYR F 679 " ideal model delta sigma weight residual 113.90 117.95 -4.05 1.80e+00 3.09e-01 5.07e+00 ... (remaining 35927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.20: 15316 35.20 - 70.40: 566 70.40 - 105.60: 37 105.60 - 140.80: 7 140.80 - 176.00: 2 Dihedral angle restraints: 15928 sinusoidal: 7111 harmonic: 8817 Sorted by residual: dihedral pdb=" C4' DA H 48 " pdb=" C3' DA H 48 " pdb=" O3' DA H 48 " pdb=" P DA H 49 " ideal model delta sinusoidal sigma weight residual -140.00 36.00 -176.00 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC G 28 " pdb=" C3' DC G 28 " pdb=" O3' DC G 28 " pdb=" P DA G 29 " ideal model delta sinusoidal sigma weight residual 220.00 76.31 143.69 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" C4' DA H 36 " pdb=" C3' DA H 36 " pdb=" O3' DA H 36 " pdb=" P DA H 37 " ideal model delta sinusoidal sigma weight residual 220.00 80.83 139.17 1 3.50e+01 8.16e-04 1.38e+01 ... (remaining 15925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 3129 0.041 - 0.082: 661 0.082 - 0.123: 271 0.123 - 0.163: 9 0.163 - 0.204: 1 Chirality restraints: 4071 Sorted by residual: chirality pdb=" CB THR C1184 " pdb=" CA THR C1184 " pdb=" OG1 THR C1184 " pdb=" CG2 THR C1184 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA VAL E 198 " pdb=" N VAL E 198 " pdb=" C VAL E 198 " pdb=" CB VAL E 198 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.89e-01 chirality pdb=" CA ILE A 16 " pdb=" N ILE A 16 " pdb=" C ILE A 16 " pdb=" CB ILE A 16 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 4068 not shown) Planarity restraints: 4413 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 742 " 0.031 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO C 743 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 743 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 743 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 488 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO C 489 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 489 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 489 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 551 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO C 552 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 552 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 552 " 0.021 5.00e-02 4.00e+02 ... (remaining 4410 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 390 2.68 - 3.23: 23180 3.23 - 3.79: 38682 3.79 - 4.34: 52938 4.34 - 4.90: 86709 Nonbonded interactions: 201899 Sorted by model distance: nonbonded pdb=" OD1 ASP F 460 " pdb="MG MG F1503 " model vdw 2.123 2.170 nonbonded pdb=" OD1 ASP F 462 " pdb="MG MG F1503 " model vdw 2.138 2.170 nonbonded pdb=" OE1 GLU C1222 " pdb=" OH TYR F 512 " model vdw 2.225 3.040 nonbonded pdb=" OG1 THR C 843 " pdb=" O GLY C 846 " model vdw 2.247 3.040 nonbonded pdb=" O GLY F 613 " pdb=" OG1 THR F 617 " model vdw 2.256 3.040 ... (remaining 201894 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' and (resid 6 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 233)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.090 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: 1.030 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 71.200 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 : 0.002 0.044 26357 Z= 0.097 Angle : 0.456 10.100 35944 Z= 0.245 Chirality : 0.039 0.204 4071 Planarity : 0.003 0.048 4413 Dihedral : 17.034 176.002 10252 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.15), residues: 3045 helix: 1.68 (0.16), residues: 1169 sheet: 0.60 (0.27), residues: 379 loop : -0.36 (0.16), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 33 HIS 0.003 0.000 HIS F 651 PHE 0.009 0.001 PHE F1319 TYR 0.016 0.001 TYR F 679 ARG 0.004 0.000 ARG F 133 Details of bonding type rmsd hydrogen bonds : bond 0.19765 ( 1144) hydrogen bonds : angle 6.54284 ( 3187) metal coordination : bond 0.00311 ( 8) metal coordination : angle 2.80130 ( 12) covalent geometry : bond 0.00199 (26349) covalent geometry : angle 0.45365 (35932) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 2.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLN cc_start: 0.7011 (tp-100) cc_final: 0.6717 (tp-100) REVERT: C 968 GLU cc_start: 0.5574 (pt0) cc_final: 0.5358 (pp20) REVERT: C 1140 LYS cc_start: 0.6940 (mtmt) cc_final: 0.6726 (mtmm) REVERT: F 466 MET cc_start: 0.8181 (mtp) cc_final: 0.7963 (ttm) REVERT: F 1373 ARG cc_start: 0.7122 (ttm170) cc_final: 0.6083 (ttp80) REVERT: E 68 TYR cc_start: 0.8114 (m-80) cc_final: 0.7831 (m-80) REVERT: E 238 ASP cc_start: 0.5990 (t0) cc_final: 0.5497 (t70) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 1.5623 time to fit residues: 500.6509 Evaluate side-chains 203 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 264 optimal weight: 3.9990 chunk 237 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 160 optimal weight: 0.8980 chunk 126 optimal weight: 10.0000 chunk 245 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 149 optimal weight: 7.9990 chunk 182 optimal weight: 5.9990 chunk 284 optimal weight: 10.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 186 ASN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS C1136 GLN F 229 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.142701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.093238 restraints weight = 36181.799| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.05 r_work: 0.3066 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 26357 Z= 0.204 Angle : 0.627 9.000 35944 Z= 0.341 Chirality : 0.046 0.181 4071 Planarity : 0.005 0.052 4413 Dihedral : 16.490 174.464 4248 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.38 % Allowed : 6.76 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.15), residues: 3045 helix: 1.56 (0.15), residues: 1197 sheet: 0.34 (0.26), residues: 387 loop : -0.54 (0.15), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 217 HIS 0.010 0.001 HIS F 430 PHE 0.019 0.002 PHE C 812 TYR 0.019 0.002 TYR F 631 ARG 0.007 0.001 ARG F 337 Details of bonding type rmsd hydrogen bonds : bond 0.07651 ( 1144) hydrogen bonds : angle 4.90243 ( 3187) metal coordination : bond 0.00482 ( 8) metal coordination : angle 3.26191 ( 12) covalent geometry : bond 0.00480 (26349) covalent geometry : angle 0.62404 (35932) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 216 time to evaluate : 3.008 Fit side-chains revert: symmetry clash REVERT: A 18 GLN cc_start: 0.7047 (tp-100) cc_final: 0.6672 (tp-100) REVERT: B 13 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8129 (tt) REVERT: B 93 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.6709 (pm20) REVERT: B 95 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7339 (ptmt) REVERT: C 496 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7135 (ttpt) REVERT: C 541 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7010 (mm-30) REVERT: C 968 GLU cc_start: 0.5656 (pt0) cc_final: 0.5317 (pp20) REVERT: C 1034 ARG cc_start: 0.7490 (tpp-160) cc_final: 0.7117 (mmm160) REVERT: C 1303 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8302 (mtmp) REVERT: F 204 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7182 (tp30) REVERT: F 1373 ARG cc_start: 0.6881 (ttm170) cc_final: 0.5668 (ttp80) REVERT: E 68 TYR cc_start: 0.8449 (m-80) cc_final: 0.8088 (m-80) REVERT: E 238 ASP cc_start: 0.5679 (t0) cc_final: 0.5318 (t70) outliers start: 36 outliers final: 11 residues processed: 233 average time/residue: 1.6390 time to fit residues: 434.8065 Evaluate side-chains 219 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1303 LYS Chi-restraints excluded: chain F residue 825 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 199 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 168 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 216 optimal weight: 9.9990 chunk 257 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 146 optimal weight: 0.2980 chunk 44 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 186 ASN B 137 ASN C 83 GLN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN C 628 HIS C1136 GLN F 229 GLN E 269 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.143791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.095474 restraints weight = 36057.355| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.14 r_work: 0.3081 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26357 Z= 0.147 Angle : 0.545 9.300 35944 Z= 0.297 Chirality : 0.043 0.167 4071 Planarity : 0.004 0.047 4413 Dihedral : 16.415 173.667 4248 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.38 % Allowed : 9.29 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.15), residues: 3045 helix: 1.69 (0.15), residues: 1207 sheet: 0.33 (0.27), residues: 364 loop : -0.50 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 409 HIS 0.008 0.001 HIS F 430 PHE 0.015 0.001 PHE C 812 TYR 0.015 0.001 TYR F 631 ARG 0.004 0.000 ARG F 337 Details of bonding type rmsd hydrogen bonds : bond 0.05878 ( 1144) hydrogen bonds : angle 4.59325 ( 3187) metal coordination : bond 0.00388 ( 8) metal coordination : angle 3.10128 ( 12) covalent geometry : bond 0.00336 (26349) covalent geometry : angle 0.54223 (35932) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 217 time to evaluate : 2.710 Fit side-chains revert: symmetry clash REVERT: A 18 GLN cc_start: 0.6791 (tp-100) cc_final: 0.6533 (tp-100) REVERT: B 10 LYS cc_start: 0.8193 (mttt) cc_final: 0.7987 (mttt) REVERT: B 13 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8157 (tt) REVERT: B 93 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7357 (pm20) REVERT: C 160 ASP cc_start: 0.8047 (t0) cc_final: 0.7700 (t0) REVERT: C 337 PHE cc_start: 0.7328 (t80) cc_final: 0.7126 (t80) REVERT: C 349 GLU cc_start: 0.7348 (tm-30) cc_final: 0.7140 (tm-30) REVERT: C 541 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6944 (mm-30) REVERT: C 955 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: C 968 GLU cc_start: 0.5568 (pt0) cc_final: 0.5265 (pp20) REVERT: C 1035 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7820 (mtmm) REVERT: F 151 MET cc_start: 0.5654 (OUTLIER) cc_final: 0.5236 (pp-130) REVERT: F 204 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7208 (tp30) REVERT: F 820 ILE cc_start: 0.8804 (pt) cc_final: 0.8568 (pp) REVERT: F 1373 ARG cc_start: 0.6890 (ttm170) cc_final: 0.5756 (ttp80) REVERT: E 68 TYR cc_start: 0.8400 (m-80) cc_final: 0.8073 (m-80) REVERT: E 238 ASP cc_start: 0.5651 (t0) cc_final: 0.5312 (t70) outliers start: 36 outliers final: 12 residues processed: 237 average time/residue: 1.6094 time to fit residues: 434.5879 Evaluate side-chains 228 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 893 THR Chi-restraints excluded: chain C residue 955 GLN Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1035 LYS Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain F residue 825 VAL Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 245 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 101 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 283 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 274 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN B 137 ASN B 147 GLN C 83 GLN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 387 ASN C 628 HIS F 229 GLN F 320 ASN E 269 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.141816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.091596 restraints weight = 36294.720| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.98 r_work: 0.3043 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 26357 Z= 0.237 Angle : 0.645 8.387 35944 Z= 0.349 Chirality : 0.047 0.180 4071 Planarity : 0.005 0.058 4413 Dihedral : 16.581 173.014 4248 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.84 % Allowed : 10.60 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.15), residues: 3045 helix: 1.48 (0.15), residues: 1198 sheet: 0.23 (0.27), residues: 372 loop : -0.64 (0.15), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 409 HIS 0.011 0.001 HIS F 430 PHE 0.016 0.002 PHE C 812 TYR 0.017 0.002 TYR F 631 ARG 0.008 0.001 ARG F 337 Details of bonding type rmsd hydrogen bonds : bond 0.07262 ( 1144) hydrogen bonds : angle 4.76424 ( 3187) metal coordination : bond 0.00546 ( 8) metal coordination : angle 3.68803 ( 12) covalent geometry : bond 0.00575 (26349) covalent geometry : angle 0.64113 (35932) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 213 time to evaluate : 3.009 Fit side-chains revert: symmetry clash REVERT: A 18 GLN cc_start: 0.6761 (tp-100) cc_final: 0.6498 (tp-100) REVERT: B 10 LYS cc_start: 0.8195 (mttt) cc_final: 0.7952 (mttt) REVERT: B 13 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8110 (tt) REVERT: B 93 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.6705 (pm20) REVERT: B 181 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7741 (mt-10) REVERT: C 160 ASP cc_start: 0.7967 (t0) cc_final: 0.7678 (t0) REVERT: C 349 GLU cc_start: 0.7306 (tm-30) cc_final: 0.7077 (tm-30) REVERT: C 491 ASP cc_start: 0.8281 (m-30) cc_final: 0.8072 (m-30) REVERT: C 541 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6992 (mm-30) REVERT: C 542 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.7012 (mtm-85) REVERT: C 955 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7885 (tt0) REVERT: C 968 GLU cc_start: 0.5734 (pt0) cc_final: 0.5385 (pp20) REVERT: C 1034 ARG cc_start: 0.7636 (tpp-160) cc_final: 0.7267 (mmm160) REVERT: F 151 MET cc_start: 0.5701 (OUTLIER) cc_final: 0.5385 (pp-130) REVERT: F 204 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7128 (tp30) REVERT: F 1284 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7564 (mmt180) REVERT: F 1373 ARG cc_start: 0.6875 (ttm170) cc_final: 0.5711 (ttp80) REVERT: E 68 TYR cc_start: 0.8445 (m-80) cc_final: 0.8069 (m-80) REVERT: E 144 GLN cc_start: 0.6919 (OUTLIER) cc_final: 0.6679 (tp-100) REVERT: E 238 ASP cc_start: 0.5554 (t0) cc_final: 0.5189 (t70) outliers start: 48 outliers final: 21 residues processed: 241 average time/residue: 1.6087 time to fit residues: 443.2077 Evaluate side-chains 235 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 893 THR Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 955 GLN Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain F residue 667 GLN Chi-restraints excluded: chain F residue 825 VAL Chi-restraints excluded: chain F residue 1155 ILE Chi-restraints excluded: chain F residue 1260 MET Chi-restraints excluded: chain F residue 1284 ARG Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 144 GLN Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 262 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 221 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 295 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 273 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 205 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 277 optimal weight: 0.4980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN C 628 HIS C1136 GLN F 229 GLN F 320 ASN F 430 HIS E 269 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.143826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.093467 restraints weight = 36321.811| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.99 r_work: 0.3089 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26357 Z= 0.126 Angle : 0.531 9.451 35944 Z= 0.288 Chirality : 0.042 0.171 4071 Planarity : 0.004 0.063 4413 Dihedral : 16.459 174.330 4248 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.46 % Allowed : 11.98 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.15), residues: 3045 helix: 1.76 (0.15), residues: 1208 sheet: 0.23 (0.27), residues: 367 loop : -0.52 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 409 HIS 0.004 0.001 HIS A 66 PHE 0.014 0.001 PHE C 812 TYR 0.015 0.001 TYR F 631 ARG 0.010 0.000 ARG C 478 Details of bonding type rmsd hydrogen bonds : bond 0.05284 ( 1144) hydrogen bonds : angle 4.48161 ( 3187) metal coordination : bond 0.00321 ( 8) metal coordination : angle 3.09079 ( 12) covalent geometry : bond 0.00279 (26349) covalent geometry : angle 0.52823 (35932) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 218 time to evaluate : 3.114 Fit side-chains revert: symmetry clash REVERT: B 10 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7927 (mttt) REVERT: B 13 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8142 (tt) REVERT: B 181 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: C 160 ASP cc_start: 0.7909 (t0) cc_final: 0.7577 (t0) REVERT: C 349 GLU cc_start: 0.7332 (tm-30) cc_final: 0.7099 (tm-30) REVERT: C 369 MET cc_start: 0.7202 (tmm) cc_final: 0.6894 (ppp) REVERT: C 541 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6968 (mm-30) REVERT: C 955 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7869 (tt0) REVERT: C 968 GLU cc_start: 0.5611 (pt0) cc_final: 0.5292 (pp20) REVERT: C 1034 ARG cc_start: 0.7702 (tpp-160) cc_final: 0.7289 (mmm160) REVERT: C 1035 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7867 (mtmm) REVERT: C 1140 LYS cc_start: 0.7434 (mtmt) cc_final: 0.7210 (mtmt) REVERT: F 151 MET cc_start: 0.5738 (OUTLIER) cc_final: 0.5400 (pp-130) REVERT: F 204 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7146 (tp30) REVERT: F 289 ASP cc_start: 0.7654 (p0) cc_final: 0.7304 (m-30) REVERT: F 820 ILE cc_start: 0.8783 (pt) cc_final: 0.8566 (pp) REVERT: F 1373 ARG cc_start: 0.6918 (ttm170) cc_final: 0.5768 (ttp80) REVERT: E 68 TYR cc_start: 0.8391 (m-80) cc_final: 0.7981 (m-80) REVERT: E 238 ASP cc_start: 0.5584 (t0) cc_final: 0.5229 (t70) outliers start: 38 outliers final: 15 residues processed: 242 average time/residue: 1.6477 time to fit residues: 454.5404 Evaluate side-chains 230 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 208 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 893 THR Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 955 GLN Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1035 LYS Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain F residue 825 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 245 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 213 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 109 optimal weight: 0.0870 chunk 105 optimal weight: 8.9990 chunk 300 optimal weight: 10.0000 chunk 138 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 overall best weight: 3.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN C 83 GLN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS C1136 GLN F 229 GLN F 320 ASN F 430 HIS E 269 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.142574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.092110 restraints weight = 36096.957| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.00 r_work: 0.3058 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 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 : 0.005 0.050 26357 Z= 0.188 Angle : 0.593 8.719 35944 Z= 0.320 Chirality : 0.045 0.159 4071 Planarity : 0.004 0.048 4413 Dihedral : 16.513 173.900 4248 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.73 % Allowed : 12.21 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.15), residues: 3045 helix: 1.65 (0.15), residues: 1206 sheet: 0.22 (0.26), residues: 376 loop : -0.58 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 409 HIS 0.013 0.001 HIS F 430 PHE 0.014 0.002 PHE C 812 TYR 0.017 0.002 TYR F 631 ARG 0.006 0.000 ARG F 431 Details of bonding type rmsd hydrogen bonds : bond 0.06275 ( 1144) hydrogen bonds : angle 4.57110 ( 3187) metal coordination : bond 0.00479 ( 8) metal coordination : angle 3.45773 ( 12) covalent geometry : bond 0.00451 (26349) covalent geometry : angle 0.58945 (35932) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 212 time to evaluate : 2.868 Fit side-chains revert: symmetry clash REVERT: B 10 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7921 (mttt) REVERT: B 13 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8134 (tt) REVERT: B 93 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.6542 (pm20) REVERT: B 181 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7751 (mt-10) REVERT: C 160 ASP cc_start: 0.7916 (t0) cc_final: 0.7613 (t0) REVERT: C 349 GLU cc_start: 0.7368 (tm-30) cc_final: 0.7135 (tm-30) REVERT: C 369 MET cc_start: 0.7220 (tmm) cc_final: 0.6902 (ppp) REVERT: C 541 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7110 (mm-30) REVERT: C 955 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: C 968 GLU cc_start: 0.5643 (pt0) cc_final: 0.5349 (pp20) REVERT: C 1034 ARG cc_start: 0.7685 (tpp-160) cc_final: 0.7264 (mmm160) REVERT: F 151 MET cc_start: 0.5762 (OUTLIER) cc_final: 0.5407 (pp-130) REVERT: F 204 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7206 (tp30) REVERT: F 289 ASP cc_start: 0.7671 (p0) cc_final: 0.7363 (m-30) REVERT: F 820 ILE cc_start: 0.8813 (pt) cc_final: 0.8581 (pp) REVERT: F 1373 ARG cc_start: 0.6889 (ttm170) cc_final: 0.5796 (ttp80) REVERT: E 68 TYR cc_start: 0.8411 (m-80) cc_final: 0.8001 (m-80) REVERT: E 144 GLN cc_start: 0.6939 (OUTLIER) cc_final: 0.6674 (tp40) REVERT: E 238 ASP cc_start: 0.5595 (t0) cc_final: 0.5237 (t70) outliers start: 45 outliers final: 22 residues processed: 241 average time/residue: 1.8628 time to fit residues: 515.6784 Evaluate side-chains 235 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 3.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 893 THR Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 955 GLN Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain F residue 667 GLN Chi-restraints excluded: chain F residue 825 VAL Chi-restraints excluded: chain F residue 1155 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 144 GLN Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 262 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 109 optimal weight: 0.0770 chunk 301 optimal weight: 3.9990 chunk 308 optimal weight: 0.8980 chunk 179 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 251 optimal weight: 0.8980 chunk 310 optimal weight: 30.0000 chunk 72 optimal weight: 20.0000 overall best weight: 2.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN C 83 GLN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS F 229 GLN F 320 ASN E 269 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.143392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.093085 restraints weight = 36295.000| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.86 r_work: 0.3092 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26357 Z= 0.145 Angle : 0.554 10.581 35944 Z= 0.299 Chirality : 0.043 0.169 4071 Planarity : 0.004 0.086 4413 Dihedral : 16.469 174.262 4248 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.46 % Allowed : 12.98 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.15), residues: 3045 helix: 1.78 (0.15), residues: 1201 sheet: 0.28 (0.26), residues: 373 loop : -0.56 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 409 HIS 0.004 0.001 HIS A 66 PHE 0.013 0.001 PHE C 812 TYR 0.016 0.001 TYR F 631 ARG 0.013 0.000 ARG C 478 Details of bonding type rmsd hydrogen bonds : bond 0.05531 ( 1144) hydrogen bonds : angle 4.47194 ( 3187) metal coordination : bond 0.00381 ( 8) metal coordination : angle 3.26155 ( 12) covalent geometry : bond 0.00337 (26349) covalent geometry : angle 0.55094 (35932) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 206 time to evaluate : 2.967 Fit side-chains revert: symmetry clash REVERT: B 10 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7919 (mttt) REVERT: B 13 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8149 (tt) REVERT: B 181 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7689 (mt-10) REVERT: C 160 ASP cc_start: 0.7904 (t0) cc_final: 0.7595 (t0) REVERT: C 349 GLU cc_start: 0.7343 (tm-30) cc_final: 0.7096 (tm-30) REVERT: C 369 MET cc_start: 0.7195 (tmm) cc_final: 0.6884 (ppp) REVERT: C 541 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7079 (mm-30) REVERT: C 955 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7739 (tt0) REVERT: C 968 GLU cc_start: 0.5679 (pt0) cc_final: 0.5388 (pp20) REVERT: C 1034 ARG cc_start: 0.7694 (tpp-160) cc_final: 0.7292 (mmm160) REVERT: C 1035 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7862 (mtmm) REVERT: F 151 MET cc_start: 0.5791 (OUTLIER) cc_final: 0.5454 (pp-130) REVERT: F 204 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7170 (tp30) REVERT: F 289 ASP cc_start: 0.7612 (p0) cc_final: 0.7302 (m-30) REVERT: F 820 ILE cc_start: 0.8763 (pt) cc_final: 0.8554 (pp) REVERT: F 1373 ARG cc_start: 0.6964 (ttm170) cc_final: 0.5883 (ttp80) REVERT: E 68 TYR cc_start: 0.8388 (m-80) cc_final: 0.7975 (m-80) outliers start: 38 outliers final: 21 residues processed: 232 average time/residue: 1.8061 time to fit residues: 477.4919 Evaluate side-chains 229 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 893 THR Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 955 GLN Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1035 LYS Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain F residue 591 ILE Chi-restraints excluded: chain F residue 667 GLN Chi-restraints excluded: chain F residue 825 VAL Chi-restraints excluded: chain F residue 849 LEU Chi-restraints excluded: chain F residue 1155 ILE Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 262 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 98 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 297 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN C 83 GLN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS C1136 GLN F 229 GLN F 320 ASN F 430 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.143051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.092605 restraints weight = 36106.185| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.86 r_work: 0.3087 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26357 Z= 0.161 Angle : 0.570 11.837 35944 Z= 0.307 Chirality : 0.044 0.164 4071 Planarity : 0.004 0.070 4413 Dihedral : 16.480 173.999 4248 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.65 % Allowed : 13.28 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.15), residues: 3045 helix: 1.75 (0.15), residues: 1200 sheet: 0.23 (0.26), residues: 376 loop : -0.57 (0.16), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 409 HIS 0.004 0.001 HIS F1366 PHE 0.013 0.001 PHE C 812 TYR 0.017 0.001 TYR F 631 ARG 0.012 0.000 ARG C 478 Details of bonding type rmsd hydrogen bonds : bond 0.05779 ( 1144) hydrogen bonds : angle 4.48455 ( 3187) metal coordination : bond 0.00426 ( 8) metal coordination : angle 3.36043 ( 12) covalent geometry : bond 0.00378 (26349) covalent geometry : angle 0.56659 (35932) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 210 time to evaluate : 2.748 Fit side-chains revert: symmetry clash REVERT: B 10 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7928 (mttt) REVERT: B 13 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8153 (tt) REVERT: B 181 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7703 (mt-10) REVERT: C 160 ASP cc_start: 0.7883 (t0) cc_final: 0.7571 (t0) REVERT: C 349 GLU cc_start: 0.7344 (tm-30) cc_final: 0.7102 (tm-30) REVERT: C 369 MET cc_start: 0.7189 (tmm) cc_final: 0.6869 (ppp) REVERT: C 541 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7179 (mm-30) REVERT: C 955 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7748 (tt0) REVERT: C 968 GLU cc_start: 0.5664 (pt0) cc_final: 0.5367 (pp20) REVERT: C 1034 ARG cc_start: 0.7684 (tpp-160) cc_final: 0.7282 (mmm160) REVERT: F 151 MET cc_start: 0.5826 (OUTLIER) cc_final: 0.5531 (pp-130) REVERT: F 204 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7130 (tp30) REVERT: F 289 ASP cc_start: 0.7620 (p0) cc_final: 0.7313 (m-30) REVERT: F 820 ILE cc_start: 0.8751 (pt) cc_final: 0.8546 (pp) REVERT: F 1373 ARG cc_start: 0.6955 (ttm170) cc_final: 0.5878 (ttp80) REVERT: E 68 TYR cc_start: 0.8394 (m-80) cc_final: 0.7992 (m-80) REVERT: E 144 GLN cc_start: 0.6982 (OUTLIER) cc_final: 0.6715 (tp40) outliers start: 43 outliers final: 23 residues processed: 238 average time/residue: 1.5656 time to fit residues: 428.8636 Evaluate side-chains 235 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 3.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 893 THR Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 955 GLN Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain F residue 591 ILE Chi-restraints excluded: chain F residue 667 GLN Chi-restraints excluded: chain F residue 825 VAL Chi-restraints excluded: chain F residue 1155 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 144 GLN Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 262 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 288 optimal weight: 10.0000 chunk 273 optimal weight: 0.2980 chunk 55 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 248 optimal weight: 6.9990 chunk 296 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 281 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 chunk 229 optimal weight: 9.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN C 83 GLN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS F 229 GLN F 320 ASN F 430 HIS F 907 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.141745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.092362 restraints weight = 36070.885| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.11 r_work: 0.3040 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 26357 Z= 0.243 Angle : 0.657 12.612 35944 Z= 0.354 Chirality : 0.047 0.171 4071 Planarity : 0.005 0.072 4413 Dihedral : 16.605 172.983 4248 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.57 % Allowed : 13.59 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.15), residues: 3045 helix: 1.47 (0.15), residues: 1205 sheet: 0.04 (0.27), residues: 370 loop : -0.68 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 217 HIS 0.006 0.001 HIS C1313 PHE 0.014 0.002 PHE C 812 TYR 0.018 0.002 TYR F 631 ARG 0.009 0.001 ARG C 478 Details of bonding type rmsd hydrogen bonds : bond 0.07015 ( 1144) hydrogen bonds : angle 4.68446 ( 3187) metal coordination : bond 0.00541 ( 8) metal coordination : angle 3.82096 ( 12) covalent geometry : bond 0.00590 (26349) covalent geometry : angle 0.65378 (35932) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 204 time to evaluate : 3.194 Fit side-chains revert: symmetry clash REVERT: B 10 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7905 (mttt) REVERT: B 13 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8141 (tt) REVERT: B 93 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.6489 (pm20) REVERT: B 181 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7758 (mt-10) REVERT: C 160 ASP cc_start: 0.7979 (t0) cc_final: 0.7666 (t0) REVERT: C 349 GLU cc_start: 0.7401 (tm-30) cc_final: 0.7166 (tm-30) REVERT: C 369 MET cc_start: 0.7141 (tmm) cc_final: 0.6820 (ppp) REVERT: C 541 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7083 (mm-30) REVERT: C 955 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7883 (tt0) REVERT: C 968 GLU cc_start: 0.5842 (pt0) cc_final: 0.5494 (pp20) REVERT: F 151 MET cc_start: 0.6034 (OUTLIER) cc_final: 0.5745 (pp-130) REVERT: F 204 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7157 (tp30) REVERT: F 289 ASP cc_start: 0.7676 (p0) cc_final: 0.7430 (m-30) REVERT: F 1373 ARG cc_start: 0.6921 (ttm170) cc_final: 0.5810 (ttp80) REVERT: E 68 TYR cc_start: 0.8455 (m-80) cc_final: 0.8042 (m-80) REVERT: E 144 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6692 (tp40) outliers start: 41 outliers final: 26 residues processed: 233 average time/residue: 1.6150 time to fit residues: 431.3301 Evaluate side-chains 236 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 201 time to evaluate : 3.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 893 THR Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 955 GLN Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain F residue 667 GLN Chi-restraints excluded: chain F residue 825 VAL Chi-restraints excluded: chain F residue 1155 ILE Chi-restraints excluded: chain F residue 1260 MET Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 144 GLN Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 262 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 101 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 133 optimal weight: 10.0000 chunk 267 optimal weight: 5.9990 chunk 202 optimal weight: 8.9990 chunk 212 optimal weight: 1.9990 chunk 302 optimal weight: 10.0000 chunk 172 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 113 optimal weight: 0.7980 chunk 72 optimal weight: 20.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN B 137 ASN C 83 GLN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** C1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 229 GLN F 320 ASN F 430 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.143039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.092686 restraints weight = 35877.060| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.85 r_work: 0.3087 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26357 Z= 0.159 Angle : 0.586 12.459 35944 Z= 0.313 Chirality : 0.044 0.162 4071 Planarity : 0.004 0.088 4413 Dihedral : 16.518 173.507 4248 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.42 % Allowed : 14.13 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.15), residues: 3045 helix: 1.68 (0.15), residues: 1200 sheet: 0.08 (0.27), residues: 370 loop : -0.62 (0.15), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 409 HIS 0.005 0.001 HIS F1366 PHE 0.014 0.001 PHE C 812 TYR 0.016 0.001 TYR F 631 ARG 0.020 0.000 ARG C 478 Details of bonding type rmsd hydrogen bonds : bond 0.05724 ( 1144) hydrogen bonds : angle 4.52484 ( 3187) metal coordination : bond 0.00399 ( 8) metal coordination : angle 3.38980 ( 12) covalent geometry : bond 0.00373 (26349) covalent geometry : angle 0.58287 (35932) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 206 time to evaluate : 2.990 Fit side-chains revert: symmetry clash REVERT: B 10 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7920 (mttt) REVERT: B 13 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8128 (tt) REVERT: B 93 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.6468 (pm20) REVERT: B 181 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: C 160 ASP cc_start: 0.7869 (t0) cc_final: 0.7556 (t0) REVERT: C 349 GLU cc_start: 0.7357 (tm-30) cc_final: 0.7118 (tm-30) REVERT: C 369 MET cc_start: 0.7134 (tmm) cc_final: 0.6804 (ppp) REVERT: C 541 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7140 (mm-30) REVERT: C 951 MET cc_start: 0.7945 (mpp) cc_final: 0.7599 (mmm) REVERT: C 955 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7821 (tt0) REVERT: C 968 GLU cc_start: 0.5799 (pt0) cc_final: 0.5467 (pp20) REVERT: C 1034 ARG cc_start: 0.7657 (tpp-160) cc_final: 0.7276 (mmm160) REVERT: F 151 MET cc_start: 0.6046 (OUTLIER) cc_final: 0.5741 (pp-130) REVERT: F 204 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7139 (tp30) REVERT: F 289 ASP cc_start: 0.7571 (p0) cc_final: 0.7328 (m-30) REVERT: F 820 ILE cc_start: 0.8761 (pt) cc_final: 0.8551 (pp) REVERT: F 1373 ARG cc_start: 0.6975 (ttm170) cc_final: 0.5883 (ttp80) REVERT: E 68 TYR cc_start: 0.8418 (m-80) cc_final: 0.8019 (m-80) REVERT: E 144 GLN cc_start: 0.7000 (OUTLIER) cc_final: 0.6728 (tp40) outliers start: 37 outliers final: 23 residues processed: 229 average time/residue: 1.5192 time to fit residues: 397.9748 Evaluate side-chains 232 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 893 THR Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 955 GLN Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain F residue 667 GLN Chi-restraints excluded: chain F residue 825 VAL Chi-restraints excluded: chain F residue 1155 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 144 GLN Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 262 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 217 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 145 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 290 optimal weight: 20.0000 chunk 310 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN B 137 ASN C 83 GLN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** C1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 229 GLN F 320 ASN F 430 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.142436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.093118 restraints weight = 36039.022| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.10 r_work: 0.3052 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 26357 Z= 0.190 Angle : 0.616 10.638 35944 Z= 0.330 Chirality : 0.045 0.162 4071 Planarity : 0.005 0.071 4413 Dihedral : 16.542 172.662 4248 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.54 % Allowed : 14.01 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.15), residues: 3045 helix: 1.60 (0.15), residues: 1200 sheet: 0.12 (0.27), residues: 376 loop : -0.67 (0.15), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 409 HIS 0.005 0.001 HIS F 777 PHE 0.014 0.002 PHE C 812 TYR 0.017 0.002 TYR F 631 ARG 0.024 0.000 ARG C 478 Details of bonding type rmsd hydrogen bonds : bond 0.06270 ( 1144) hydrogen bonds : angle 4.58229 ( 3187) metal coordination : bond 0.00457 ( 8) metal coordination : angle 3.54305 ( 12) covalent geometry : bond 0.00454 (26349) covalent geometry : angle 0.61236 (35932) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26862.83 seconds wall clock time: 460 minutes 51.12 seconds (27651.12 seconds total)