Starting phenix.real_space_refine on Sun May 3 05:53:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lhz_63108/05_2026/9lhz_63108.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lhz_63108/05_2026/9lhz_63108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lhz_63108/05_2026/9lhz_63108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lhz_63108/05_2026/9lhz_63108.map" model { file = "/net/cci-nas-00/data/ceres_data/9lhz_63108/05_2026/9lhz_63108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lhz_63108/05_2026/9lhz_63108.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.061 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 71 5.16 5 C 7106 2.51 5 N 1710 2.21 5 O 1865 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10753 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1322, 10395 Classifications: {'peptide': 1322} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 45, 'TRANS': 1273} Chain breaks: 2 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 439 Unresolved non-hydrogen angles: 559 Unresolved non-hydrogen dihedrals: 371 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'ASP:plan': 11, 'ARG:plan': 12, 'ASN:plan1': 4, 'HIS:plan': 2, 'GLN:plan1': 7, 'GLU:plan': 9, 'PHE:plan': 7, 'TYR:plan': 1, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 255 Chain: "H" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 202 Classifications: {'peptide': 27} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 22} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'LPE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Time building chain proxies: 2.84, per 1000 atoms: 0.26 Number of scatterers: 10753 At special positions: 0 Unit cell: (122.265, 115.425, 115.425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 71 16.00 P 1 15.00 O 1865 8.00 N 1710 7.00 C 7106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 343 " distance=2.04 Simple disulfide: pdb=" SG CYS A 709 " - pdb=" SG CYS A 717 " distance=2.04 Simple disulfide: pdb=" SG CYS A1011 " - pdb=" SG CYS A1030 " distance=2.03 Simple disulfide: pdb=" SG CYS A1368 " - pdb=" SG CYS A1381 " distance=2.03 Simple disulfide: pdb=" SG CYS H 3 " - pdb=" SG CYS H 17 " distance=2.04 Simple disulfide: pdb=" SG CYS H 4 " - pdb=" SG CYS H 11 " distance=2.02 Simple disulfide: pdb=" SG CYS H 6 " - pdb=" SG CYS H 22 " distance=2.03 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 Links applied BETA1-3 " BMA B 3 " - " BMA B 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG F 1 " - " NAG F 2 " BETA1-6 " BMA B 3 " - " BMA B 5 " NAG-ASN " NAG A1602 " - " ASN A 312 " " NAG A1603 " - " ASN A 300 " " NAG B 1 " - " ASN A 330 " " NAG F 1 " - " ASN A 308 " Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 564.6 milliseconds 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2556 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 3 sheets defined 71.8% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 50 through 57 Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.905A pdb=" N LYS A 99 " --> pdb=" O TYR A 96 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS A 100 " --> pdb=" O LYS A 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 96 through 100' Processing helix chain 'A' and resid 102 through 108 removed outlier: 3.751A pdb=" N THR A 106 " --> pdb=" O PHE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.965A pdb=" N SER A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 159 removed outlier: 3.572A pdb=" N SER A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 158 " --> pdb=" O CYS A 154 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET A 159 " --> pdb=" O ILE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 188 removed outlier: 3.823A pdb=" N ARG A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 216 removed outlier: 3.674A pdb=" N LEU A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP A 205 " --> pdb=" O TRP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 239 removed outlier: 4.114A pdb=" N ARG A 230 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL A 231 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 232 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG A 233 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 236 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 258 removed outlier: 4.215A pdb=" N ILE A 247 " --> pdb=" O GLY A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 280 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.729A pdb=" N THR A 285 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN A 286 " --> pdb=" O VAL A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 304 through 311 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.558A pdb=" N TRP A 316 " --> pdb=" O SER A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 374 Processing helix chain 'A' and resid 376 through 388 removed outlier: 4.150A pdb=" N LEU A 380 " --> pdb=" O TYR A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 392 through 404 removed outlier: 4.111A pdb=" N PHE A 396 " --> pdb=" O HIS A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 426 Processing helix chain 'A' and resid 428 through 435 removed outlier: 3.690A pdb=" N ALA A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 507 Processing helix chain 'A' and resid 507 through 517 removed outlier: 4.075A pdb=" N ALA A 511 " --> pdb=" O LYS A 507 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 537 removed outlier: 4.909A pdb=" N ALA A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 572 removed outlier: 3.656A pdb=" N ILE A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA A 566 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU A 568 " --> pdb=" O VAL A 564 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 581 through 600 removed outlier: 3.533A pdb=" N VAL A 585 " --> pdb=" O ASP A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 623 removed outlier: 3.504A pdb=" N SER A 611 " --> pdb=" O VAL A 608 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 614 " --> pdb=" O SER A 611 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 622 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 removed outlier: 4.078A pdb=" N SER A 637 " --> pdb=" O VAL A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 670 removed outlier: 5.822A pdb=" N MET A 665 " --> pdb=" O GLN A 661 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ASN A 666 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR A 667 " --> pdb=" O PHE A 663 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A 668 " --> pdb=" O GLY A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 678 Proline residue: A 675 - end of helix removed outlier: 4.005A pdb=" N ASP A 678 " --> pdb=" O PRO A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 700 removed outlier: 3.528A pdb=" N ALA A 697 " --> pdb=" O ILE A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 713 removed outlier: 3.624A pdb=" N VAL A 712 " --> pdb=" O ASP A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 731 removed outlier: 3.819A pdb=" N PHE A 720 " --> pdb=" O SER A 716 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL A 731 " --> pdb=" O VAL A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 743 removed outlier: 3.976A pdb=" N ASN A 743 " --> pdb=" O LEU A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 839 Processing helix chain 'A' and resid 840 through 847 removed outlier: 4.039A pdb=" N ASN A 844 " --> pdb=" O ARG A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 854 removed outlier: 3.607A pdb=" N LYS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 873 removed outlier: 3.793A pdb=" N GLN A 859 " --> pdb=" O ASN A 855 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 860 " --> pdb=" O LYS A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 879 through 882 Processing helix chain 'A' and resid 883 through 913 removed outlier: 3.891A pdb=" N ALA A 899 " --> pdb=" O TYR A 895 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL A 902 " --> pdb=" O THR A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 942 removed outlier: 3.561A pdb=" N TRP A 924 " --> pdb=" O SER A 920 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP A 926 " --> pdb=" O TRP A 922 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA A 942 " --> pdb=" O VAL A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 952 removed outlier: 3.533A pdb=" N ARG A 951 " --> pdb=" O LEU A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 957 Processing helix chain 'A' and resid 958 through 964 removed outlier: 3.595A pdb=" N LYS A 964 " --> pdb=" O ARG A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 978 removed outlier: 4.508A pdb=" N VAL A 971 " --> pdb=" O GLY A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1005 removed outlier: 3.853A pdb=" N VAL A 995 " --> pdb=" O PHE A 991 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE A 996 " --> pdb=" O PHE A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1033 removed outlier: 3.564A pdb=" N CYS A1030 " --> pdb=" O ASP A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1059 Processing helix chain 'A' and resid 1062 through 1073 removed outlier: 4.132A pdb=" N ILE A1066 " --> pdb=" O GLY A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1087 No H-bonds generated for 'chain 'A' and resid 1085 through 1087' Processing helix chain 'A' and resid 1088 through 1100 removed outlier: 3.775A pdb=" N PHE A1092 " --> pdb=" O MET A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1123 removed outlier: 4.245A pdb=" N CYS A1109 " --> pdb=" O LYS A1105 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A1110 " --> pdb=" O LEU A1106 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG A1120 " --> pdb=" O ARG A1116 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A1121 " --> pdb=" O GLN A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1144 removed outlier: 4.115A pdb=" N ILE A1135 " --> pdb=" O ARG A1131 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR A1136 " --> pdb=" O THR A1132 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET A1144 " --> pdb=" O VAL A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1169 removed outlier: 3.552A pdb=" N LEU A1162 " --> pdb=" O HIS A1158 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N MET A1163 " --> pdb=" O PRO A1159 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR A1164 " --> pdb=" O GLN A1160 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP A1165 " --> pdb=" O SER A1161 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A1166 " --> pdb=" O LEU A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1186 removed outlier: 3.577A pdb=" N GLU A1173 " --> pdb=" O ASN A1169 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET A1177 " --> pdb=" O GLU A1173 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A1180 " --> pdb=" O MET A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1187 through 1190 removed outlier: 3.729A pdb=" N ASP A1190 " --> pdb=" O MET A1187 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1187 through 1190' Processing helix chain 'A' and resid 1197 through 1224 removed outlier: 3.842A pdb=" N LEU A1205 " --> pdb=" O VAL A1201 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN A1206 " --> pdb=" O LEU A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1225 through 1230 removed outlier: 3.589A pdb=" N TYR A1228 " --> pdb=" O ARG A1225 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A1229 " --> pdb=" O HIS A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1250 removed outlier: 3.879A pdb=" N MET A1249 " --> pdb=" O ILE A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1268 removed outlier: 3.725A pdb=" N ARG A1268 " --> pdb=" O LEU A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1281 removed outlier: 3.623A pdb=" N ARG A1274 " --> pdb=" O ARG A1271 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A1276 " --> pdb=" O GLY A1273 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ARG A1277 " --> pdb=" O ARG A1274 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR A1278 " --> pdb=" O LEU A1275 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N GLN A1280 " --> pdb=" O ARG A1277 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N SER A1281 " --> pdb=" O TYR A1278 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1321 removed outlier: 3.683A pdb=" N LEU A1288 " --> pdb=" O GLY A1284 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ARG A1297 " --> pdb=" O ARG A1293 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N THR A1298 " --> pdb=" O LYS A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1350 Processing helix chain 'A' and resid 1354 through 1363 removed outlier: 3.725A pdb=" N VAL A1358 " --> pdb=" O GLY A1354 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A1361 " --> pdb=" O GLY A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1399 Processing helix chain 'A' and resid 1404 through 1423 removed outlier: 3.584A pdb=" N ALA A1408 " --> pdb=" O ASN A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1439 removed outlier: 3.966A pdb=" N TYR A1430 " --> pdb=" O THR A1426 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN A1439 " --> pdb=" O GLU A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1452 through 1460 Processing helix chain 'A' and resid 1470 through 1477 removed outlier: 3.812A pdb=" N LEU A1475 " --> pdb=" O LYS A1471 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1505 Processing helix chain 'A' and resid 1508 through 1521 Proline residue: A1516 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 287 through 290 Processing sheet with id=AA2, first strand: chain 'A' and resid 1010 through 1012 Processing sheet with id=AA3, first strand: chain 'A' and resid 1447 through 1449 600 hydrogen bonds defined for protein. 1713 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.82 Time building geometry restraints manager: 1.21 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: 3272 1.34 - 1.46: 2737 1.46 - 1.58: 4904 1.58 - 1.70: 5 1.70 - 1.82: 116 Bond restraints: 11034 Sorted by residual: bond pdb=" N LPE H 101 " pdb=" C2N LPE H 101 " ideal model delta sigma weight residual 1.515 1.434 0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" N LPE H 101 " pdb=" C3N LPE H 101 " ideal model delta sigma weight residual 1.520 1.442 0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" N LPE H 101 " pdb=" C1N LPE H 101 " ideal model delta sigma weight residual 1.513 1.443 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C1 BMA B 3 " pdb=" C2 BMA B 3 " ideal model delta sigma weight residual 1.519 1.581 -0.062 2.00e-02 2.50e+03 9.50e+00 bond pdb=" N LPE H 101 " pdb=" C32 LPE H 101 " ideal model delta sigma weight residual 1.524 1.471 0.053 2.00e-02 2.50e+03 7.00e+00 ... (remaining 11029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 14852 2.77 - 5.54: 134 5.54 - 8.30: 25 8.30 - 11.07: 3 11.07 - 13.84: 3 Bond angle restraints: 15017 Sorted by residual: angle pdb=" CA PRO A1155 " pdb=" N PRO A1155 " pdb=" CD PRO A1155 " ideal model delta sigma weight residual 112.00 100.52 11.48 1.40e+00 5.10e-01 6.73e+01 angle pdb=" C ASP A 320 " pdb=" CA ASP A 320 " pdb=" CB ASP A 320 " ideal model delta sigma weight residual 116.63 110.20 6.43 1.16e+00 7.43e-01 3.07e+01 angle pdb=" N PRO A1155 " pdb=" CD PRO A1155 " pdb=" CG PRO A1155 " ideal model delta sigma weight residual 103.20 96.21 6.99 1.50e+00 4.44e-01 2.17e+01 angle pdb=" O31 LPE H 101 " pdb=" P LPE H 101 " pdb=" O32 LPE H 101 " ideal model delta sigma weight residual 122.76 108.92 13.84 3.00e+00 1.11e-01 2.13e+01 angle pdb=" CA ASP A 320 " pdb=" C ASP A 320 " pdb=" N ASP A 321 " ideal model delta sigma weight residual 119.63 116.69 2.94 8.10e-01 1.52e+00 1.32e+01 ... (remaining 15012 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.84: 6124 23.84 - 47.68: 340 47.68 - 71.52: 40 71.52 - 95.36: 18 95.36 - 119.20: 16 Dihedral angle restraints: 6538 sinusoidal: 2574 harmonic: 3964 Sorted by residual: dihedral pdb=" CB CYS A1368 " pdb=" SG CYS A1368 " pdb=" SG CYS A1381 " pdb=" CB CYS A1381 " ideal model delta sinusoidal sigma weight residual 93.00 149.69 -56.69 1 1.00e+01 1.00e-02 4.33e+01 dihedral pdb=" CA VAL A 564 " pdb=" C VAL A 564 " pdb=" N GLU A 565 " pdb=" CA GLU A 565 " ideal model delta harmonic sigma weight residual 180.00 149.66 30.34 0 5.00e+00 4.00e-02 3.68e+01 dihedral pdb=" CA SER A1020 " pdb=" C SER A1020 " pdb=" N HIS A1021 " pdb=" CA HIS A1021 " ideal model delta harmonic sigma weight residual -180.00 -151.01 -28.99 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 6535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 1729 0.158 - 0.315: 10 0.315 - 0.473: 0 0.473 - 0.631: 0 0.631 - 0.788: 1 Chirality restraints: 1740 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 330 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-01 2.50e+01 1.55e+01 chirality pdb=" C4 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" C5 NAG B 2 " pdb=" O4 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.53 -2.24 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C5 BMA B 4 " pdb=" C4 BMA B 4 " pdb=" C6 BMA B 4 " pdb=" O5 BMA B 4 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 1737 not shown) Planarity restraints: 1852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A1154 " 0.102 5.00e-02 4.00e+02 1.46e-01 3.39e+01 pdb=" N PRO A1155 " -0.251 5.00e-02 4.00e+02 pdb=" CA PRO A1155 " 0.076 5.00e-02 4.00e+02 pdb=" CD PRO A1155 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1063 " -0.030 2.00e-02 2.50e+03 2.71e-02 1.84e+01 pdb=" CG TRP A1063 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP A1063 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP A1063 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A1063 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1063 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A1063 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1063 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1063 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A1063 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 880 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.87e+00 pdb=" N PRO A 881 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 881 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 881 " 0.024 5.00e-02 4.00e+02 ... (remaining 1849 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1152 2.75 - 3.29: 10592 3.29 - 3.82: 16891 3.82 - 4.36: 19544 4.36 - 4.90: 34457 Nonbonded interactions: 82636 Sorted by model distance: nonbonded pdb=" OG1 THR A 177 " pdb=" OH TYR A 213 " model vdw 2.210 3.040 nonbonded pdb=" OG SER A1130 " pdb=" OE1 GLN A1133 " model vdw 2.238 3.040 nonbonded pdb=" O3 NAG B 2 " pdb=" O2 BMA B 3 " model vdw 2.290 3.040 nonbonded pdb=" OD1 ASN A 683 " pdb=" OG1 THR A 685 " model vdw 2.309 3.040 nonbonded pdb=" OE2 GLU A 876 " pdb=" NH2 ARG A 951 " model vdw 2.312 3.120 ... (remaining 82631 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.530 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.740 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:7.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 11051 Z= 0.189 Angle : 0.756 19.339 15060 Z= 0.371 Chirality : 0.048 0.788 1740 Planarity : 0.005 0.146 1848 Dihedral : 16.276 119.200 3958 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.28 % Favored : 91.28 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.23), residues: 1341 helix: 1.18 (0.19), residues: 840 sheet: 0.52 (1.22), residues: 10 loop : -2.46 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 230 TYR 0.019 0.001 TYR A 381 PHE 0.020 0.001 PHE A1488 TRP 0.073 0.001 TRP A1063 HIS 0.017 0.001 HIS A1021 Details of bonding type rmsd covalent geometry : bond 0.00416 (11034) covalent geometry : angle 0.71043 (15017) SS BOND : bond 0.00424 ( 8) SS BOND : angle 1.41671 ( 16) hydrogen bonds : bond 0.15280 ( 600) hydrogen bonds : angle 5.06135 ( 1713) link_BETA1-3 : bond 0.01013 ( 1) link_BETA1-3 : angle 1.14172 ( 3) link_BETA1-4 : bond 0.01452 ( 3) link_BETA1-4 : angle 5.65207 ( 9) link_BETA1-6 : bond 0.00463 ( 1) link_BETA1-6 : angle 1.22335 ( 3) link_NAG-ASN : bond 0.00851 ( 4) link_NAG-ASN : angle 7.61737 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.389 Fit side-chains REVERT: A 424 LYS cc_start: 0.7620 (ttmt) cc_final: 0.7310 (tmmt) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.6009 time to fit residues: 107.5022 Evaluate side-chains 137 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN A 345 GLN A 844 ASN A1034 ASN A1160 GLN A1191 HIS A1194 GLN A1341 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.170533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.131915 restraints weight = 11976.661| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.80 r_work: 0.3169 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11051 Z= 0.208 Angle : 0.751 19.113 15060 Z= 0.368 Chirality : 0.047 0.502 1740 Planarity : 0.005 0.076 1848 Dihedral : 12.981 118.131 1693 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.20 % Favored : 91.28 % Rotamer: Outliers : 2.69 % Allowed : 8.80 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.23), residues: 1341 helix: 1.07 (0.18), residues: 858 sheet: 0.41 (1.27), residues: 10 loop : -2.47 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 552 TYR 0.024 0.002 TYR A 381 PHE 0.030 0.002 PHE A1488 TRP 0.041 0.002 TRP A1063 HIS 0.010 0.001 HIS A1021 Details of bonding type rmsd covalent geometry : bond 0.00498 (11034) covalent geometry : angle 0.70671 (15017) SS BOND : bond 0.00541 ( 8) SS BOND : angle 1.46052 ( 16) hydrogen bonds : bond 0.07119 ( 600) hydrogen bonds : angle 4.42043 ( 1713) link_BETA1-3 : bond 0.01175 ( 1) link_BETA1-3 : angle 3.61444 ( 3) link_BETA1-4 : bond 0.00555 ( 3) link_BETA1-4 : angle 5.18563 ( 9) link_BETA1-6 : bond 0.00692 ( 1) link_BETA1-6 : angle 2.25980 ( 3) link_NAG-ASN : bond 0.00892 ( 4) link_NAG-ASN : angle 7.42986 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.420 Fit side-chains REVERT: A 318 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8007 (tp) REVERT: A 336 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8641 (mtt) REVERT: A 424 LYS cc_start: 0.7571 (ttmt) cc_final: 0.6894 (tmmt) REVERT: A 549 ARG cc_start: 0.7226 (ttm-80) cc_final: 0.7014 (ttm-80) REVERT: A 641 PHE cc_start: 0.7758 (m-80) cc_final: 0.7456 (m-80) REVERT: A 1029 ASP cc_start: 0.7554 (m-30) cc_final: 0.7158 (m-30) outliers start: 29 outliers final: 11 residues processed: 155 average time/residue: 0.5228 time to fit residues: 88.1110 Evaluate side-chains 149 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1021 HIS Chi-restraints excluded: chain A residue 1160 GLN Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1421 SER Chi-restraints excluded: chain A residue 1502 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 11 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 4 optimal weight: 40.0000 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 128 optimal weight: 0.0980 chunk 15 optimal weight: 0.9990 chunk 56 optimal weight: 0.3980 chunk 113 optimal weight: 0.0570 overall best weight: 0.4500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 ASN A1034 ASN A1191 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.174180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.136353 restraints weight = 12033.290| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.81 r_work: 0.3262 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 11051 Z= 0.123 Angle : 0.630 17.201 15060 Z= 0.308 Chirality : 0.042 0.412 1740 Planarity : 0.004 0.052 1848 Dihedral : 11.773 117.963 1693 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.53 % Favored : 92.10 % Rotamer: Outliers : 2.31 % Allowed : 12.41 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.24), residues: 1341 helix: 1.39 (0.18), residues: 858 sheet: 0.51 (1.35), residues: 10 loop : -2.35 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1137 TYR 0.016 0.001 TYR A1390 PHE 0.019 0.001 PHE A 900 TRP 0.015 0.001 TRP A1063 HIS 0.007 0.001 HIS A1021 Details of bonding type rmsd covalent geometry : bond 0.00248 (11034) covalent geometry : angle 0.58625 (15017) SS BOND : bond 0.00285 ( 8) SS BOND : angle 0.90183 ( 16) hydrogen bonds : bond 0.05049 ( 600) hydrogen bonds : angle 4.13467 ( 1713) link_BETA1-3 : bond 0.00900 ( 1) link_BETA1-3 : angle 2.77647 ( 3) link_BETA1-4 : bond 0.00593 ( 3) link_BETA1-4 : angle 4.87581 ( 9) link_BETA1-6 : bond 0.01189 ( 1) link_BETA1-6 : angle 1.94109 ( 3) link_NAG-ASN : bond 0.00681 ( 4) link_NAG-ASN : angle 6.81730 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.420 Fit side-chains REVERT: A 318 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8016 (tp) REVERT: A 424 LYS cc_start: 0.7471 (ttmt) cc_final: 0.6805 (tmmt) REVERT: A 841 MET cc_start: 0.5892 (OUTLIER) cc_final: 0.5626 (ttt) REVERT: A 915 LYS cc_start: 0.6217 (pmtt) cc_final: 0.5722 (pmmt) REVERT: A 992 PHE cc_start: 0.8658 (m-80) cc_final: 0.8425 (m-80) REVERT: A 1029 ASP cc_start: 0.7356 (m-30) cc_final: 0.6933 (m-30) outliers start: 25 outliers final: 6 residues processed: 156 average time/residue: 0.5137 time to fit residues: 87.5273 Evaluate side-chains 146 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1021 HIS Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1421 SER Chi-restraints excluded: chain A residue 1502 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 2 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 118 optimal weight: 0.0070 chunk 82 optimal weight: 0.0070 chunk 52 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 ASN A1034 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.175720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.137910 restraints weight = 12201.882| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.83 r_work: 0.3290 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 11051 Z= 0.112 Angle : 0.606 16.523 15060 Z= 0.296 Chirality : 0.042 0.383 1740 Planarity : 0.003 0.043 1848 Dihedral : 10.826 118.187 1693 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.61 % Favored : 92.10 % Rotamer: Outliers : 2.22 % Allowed : 13.89 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.24), residues: 1341 helix: 1.56 (0.18), residues: 859 sheet: 0.29 (1.40), residues: 10 loop : -2.32 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1137 TYR 0.019 0.001 TYR A1450 PHE 0.020 0.001 PHE A 900 TRP 0.011 0.001 TRP A1063 HIS 0.008 0.001 HIS A1021 Details of bonding type rmsd covalent geometry : bond 0.00227 (11034) covalent geometry : angle 0.56316 (15017) SS BOND : bond 0.00241 ( 8) SS BOND : angle 1.01648 ( 16) hydrogen bonds : bond 0.04490 ( 600) hydrogen bonds : angle 3.96579 ( 1713) link_BETA1-3 : bond 0.00466 ( 1) link_BETA1-3 : angle 2.47231 ( 3) link_BETA1-4 : bond 0.00570 ( 3) link_BETA1-4 : angle 4.88609 ( 9) link_BETA1-6 : bond 0.00972 ( 1) link_BETA1-6 : angle 1.83719 ( 3) link_NAG-ASN : bond 0.00668 ( 4) link_NAG-ASN : angle 6.47476 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.436 Fit side-chains REVERT: A 249 ASP cc_start: 0.8046 (m-30) cc_final: 0.7749 (m-30) REVERT: A 318 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.7994 (tp) REVERT: A 424 LYS cc_start: 0.7429 (ttmt) cc_final: 0.6764 (tmmt) REVERT: A 573 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6568 (tt) REVERT: A 915 LYS cc_start: 0.6139 (pmtt) cc_final: 0.5669 (pmmt) REVERT: A 1029 ASP cc_start: 0.7255 (m-30) cc_final: 0.6952 (m-30) REVERT: A 1160 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.6505 (tp40) outliers start: 24 outliers final: 6 residues processed: 158 average time/residue: 0.5088 time to fit residues: 87.7227 Evaluate side-chains 149 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1021 HIS Chi-restraints excluded: chain A residue 1160 GLN Chi-restraints excluded: chain A residue 1415 LEU Chi-restraints excluded: chain A residue 1421 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 ASN A1034 ASN A1191 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.168490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.120706 restraints weight = 12020.942| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.87 r_work: 0.3121 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 11051 Z= 0.271 Angle : 0.796 19.785 15060 Z= 0.392 Chirality : 0.050 0.471 1740 Planarity : 0.004 0.042 1848 Dihedral : 11.540 122.092 1693 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.10 % Favored : 90.53 % Rotamer: Outliers : 2.87 % Allowed : 15.46 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.23), residues: 1341 helix: 1.00 (0.18), residues: 863 sheet: 0.18 (1.30), residues: 10 loop : -2.45 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1137 TYR 0.026 0.002 TYR A 381 PHE 0.031 0.002 PHE A1488 TRP 0.010 0.002 TRP A 715 HIS 0.009 0.002 HIS A1021 Details of bonding type rmsd covalent geometry : bond 0.00675 (11034) covalent geometry : angle 0.74887 (15017) SS BOND : bond 0.00638 ( 8) SS BOND : angle 1.77587 ( 16) hydrogen bonds : bond 0.07820 ( 600) hydrogen bonds : angle 4.33885 ( 1713) link_BETA1-3 : bond 0.00782 ( 1) link_BETA1-3 : angle 2.73358 ( 3) link_BETA1-4 : bond 0.00526 ( 3) link_BETA1-4 : angle 5.80340 ( 9) link_BETA1-6 : bond 0.00425 ( 1) link_BETA1-6 : angle 2.28293 ( 3) link_NAG-ASN : bond 0.01032 ( 4) link_NAG-ASN : angle 7.85054 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.388 Fit side-chains REVERT: A 261 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8442 (mm) REVERT: A 318 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8072 (tp) REVERT: A 424 LYS cc_start: 0.7747 (ttmt) cc_final: 0.7006 (tmmt) REVERT: A 573 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6743 (tt) REVERT: A 915 LYS cc_start: 0.6120 (OUTLIER) cc_final: 0.5158 (pmtt) REVERT: A 1029 ASP cc_start: 0.7787 (m-30) cc_final: 0.7421 (m-30) REVERT: A 1202 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8326 (mp) outliers start: 31 outliers final: 14 residues processed: 151 average time/residue: 0.4978 time to fit residues: 82.0337 Evaluate side-chains 151 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 915 LYS Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1021 HIS Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1421 SER Chi-restraints excluded: chain A residue 1502 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 64 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 114 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 ASN ** A1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.172567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.134791 restraints weight = 12025.381| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.84 r_work: 0.3211 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11051 Z= 0.134 Angle : 0.652 18.037 15060 Z= 0.319 Chirality : 0.044 0.402 1740 Planarity : 0.004 0.043 1848 Dihedral : 10.994 118.264 1693 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.90 % Favored : 91.80 % Rotamer: Outliers : 2.59 % Allowed : 16.67 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.24), residues: 1341 helix: 1.31 (0.18), residues: 865 sheet: 0.19 (1.34), residues: 10 loop : -2.34 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1137 TYR 0.017 0.001 TYR A 381 PHE 0.022 0.001 PHE A 900 TRP 0.008 0.001 TRP A1063 HIS 0.007 0.001 HIS A1021 Details of bonding type rmsd covalent geometry : bond 0.00287 (11034) covalent geometry : angle 0.60577 (15017) SS BOND : bond 0.00330 ( 8) SS BOND : angle 1.05044 ( 16) hydrogen bonds : bond 0.05379 ( 600) hydrogen bonds : angle 4.08925 ( 1713) link_BETA1-3 : bond 0.00684 ( 1) link_BETA1-3 : angle 2.13014 ( 3) link_BETA1-4 : bond 0.00443 ( 3) link_BETA1-4 : angle 5.12249 ( 9) link_BETA1-6 : bond 0.00854 ( 1) link_BETA1-6 : angle 1.92805 ( 3) link_NAG-ASN : bond 0.00703 ( 4) link_NAG-ASN : angle 7.11139 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.418 Fit side-chains REVERT: A 261 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8391 (mm) REVERT: A 304 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6973 (tm-30) REVERT: A 318 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8016 (tp) REVERT: A 424 LYS cc_start: 0.7563 (ttmt) cc_final: 0.6796 (tmmt) REVERT: A 573 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6688 (tt) REVERT: A 641 PHE cc_start: 0.7647 (m-80) cc_final: 0.7318 (m-80) REVERT: A 841 MET cc_start: 0.5920 (OUTLIER) cc_final: 0.5645 (ttt) REVERT: A 915 LYS cc_start: 0.6114 (OUTLIER) cc_final: 0.5887 (pmtt) REVERT: A 992 PHE cc_start: 0.8677 (m-80) cc_final: 0.8416 (m-80) REVERT: A 1029 ASP cc_start: 0.7359 (m-30) cc_final: 0.7005 (m-30) REVERT: A 1423 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6871 (mp0) outliers start: 28 outliers final: 13 residues processed: 153 average time/residue: 0.4970 time to fit residues: 83.2869 Evaluate side-chains 150 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 915 LYS Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1021 HIS Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1147 LYS Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1421 SER Chi-restraints excluded: chain A residue 1423 GLU Chi-restraints excluded: chain A residue 1502 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 0 optimal weight: 40.0000 chunk 50 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 126 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 ASN A1034 ASN A1191 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.172502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.134229 restraints weight = 12021.858| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.82 r_work: 0.3204 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11051 Z= 0.136 Angle : 0.661 17.889 15060 Z= 0.320 Chirality : 0.044 0.394 1740 Planarity : 0.004 0.043 1848 Dihedral : 10.782 118.557 1693 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.50 % Favored : 91.20 % Rotamer: Outliers : 2.78 % Allowed : 16.85 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.24), residues: 1341 helix: 1.37 (0.18), residues: 865 sheet: 0.12 (1.33), residues: 10 loop : -2.32 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1137 TYR 0.018 0.001 TYR A1450 PHE 0.023 0.001 PHE A 900 TRP 0.007 0.001 TRP A1355 HIS 0.007 0.001 HIS A1021 Details of bonding type rmsd covalent geometry : bond 0.00301 (11034) covalent geometry : angle 0.61598 (15017) SS BOND : bond 0.00322 ( 8) SS BOND : angle 1.01097 ( 16) hydrogen bonds : bond 0.05378 ( 600) hydrogen bonds : angle 4.04632 ( 1713) link_BETA1-3 : bond 0.00660 ( 1) link_BETA1-3 : angle 2.13015 ( 3) link_BETA1-4 : bond 0.00439 ( 3) link_BETA1-4 : angle 5.19361 ( 9) link_BETA1-6 : bond 0.00790 ( 1) link_BETA1-6 : angle 1.90792 ( 3) link_NAG-ASN : bond 0.00743 ( 4) link_NAG-ASN : angle 7.02578 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.399 Fit side-chains REVERT: A 261 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8394 (mm) REVERT: A 318 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8011 (tp) REVERT: A 424 LYS cc_start: 0.7566 (ttmt) cc_final: 0.6790 (tmmt) REVERT: A 573 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6608 (tt) REVERT: A 641 PHE cc_start: 0.7666 (m-80) cc_final: 0.7322 (m-80) REVERT: A 841 MET cc_start: 0.5913 (OUTLIER) cc_final: 0.5643 (ttt) REVERT: A 915 LYS cc_start: 0.6089 (OUTLIER) cc_final: 0.5829 (pmtt) REVERT: A 992 PHE cc_start: 0.8683 (m-80) cc_final: 0.8412 (m-80) REVERT: A 1029 ASP cc_start: 0.7407 (m-30) cc_final: 0.7021 (m-30) REVERT: A 1423 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6830 (mp0) outliers start: 30 outliers final: 14 residues processed: 155 average time/residue: 0.5094 time to fit residues: 86.2493 Evaluate side-chains 154 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 915 LYS Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1021 HIS Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1147 LYS Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1421 SER Chi-restraints excluded: chain A residue 1423 GLU Chi-restraints excluded: chain A residue 1502 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 79 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 30.0000 chunk 9 optimal weight: 0.0770 chunk 77 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 ASN A 844 ASN A1034 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.173759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.135999 restraints weight = 11984.232| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.77 r_work: 0.3233 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11051 Z= 0.123 Angle : 0.636 17.325 15060 Z= 0.309 Chirality : 0.043 0.380 1740 Planarity : 0.003 0.043 1848 Dihedral : 10.329 117.183 1693 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.98 % Favored : 91.72 % Rotamer: Outliers : 2.22 % Allowed : 18.06 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.24), residues: 1341 helix: 1.49 (0.18), residues: 866 sheet: 0.11 (1.35), residues: 10 loop : -2.27 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1137 TYR 0.017 0.001 TYR A1390 PHE 0.023 0.001 PHE A 900 TRP 0.007 0.001 TRP A1355 HIS 0.008 0.001 HIS A1021 Details of bonding type rmsd covalent geometry : bond 0.00265 (11034) covalent geometry : angle 0.59266 (15017) SS BOND : bond 0.00280 ( 8) SS BOND : angle 0.92206 ( 16) hydrogen bonds : bond 0.04843 ( 600) hydrogen bonds : angle 3.95507 ( 1713) link_BETA1-3 : bond 0.00734 ( 1) link_BETA1-3 : angle 1.88455 ( 3) link_BETA1-4 : bond 0.00535 ( 3) link_BETA1-4 : angle 5.14136 ( 9) link_BETA1-6 : bond 0.00731 ( 1) link_BETA1-6 : angle 1.97472 ( 3) link_NAG-ASN : bond 0.00710 ( 4) link_NAG-ASN : angle 6.75335 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.418 Fit side-chains REVERT: A 261 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8406 (mm) REVERT: A 318 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.7998 (tp) REVERT: A 424 LYS cc_start: 0.7547 (ttmt) cc_final: 0.6808 (tmmt) REVERT: A 573 LEU cc_start: 0.6905 (OUTLIER) cc_final: 0.6660 (tt) REVERT: A 877 ASP cc_start: 0.8308 (p0) cc_final: 0.7610 (m-30) REVERT: A 915 LYS cc_start: 0.6037 (OUTLIER) cc_final: 0.5790 (pmtt) REVERT: A 1029 ASP cc_start: 0.7308 (m-30) cc_final: 0.6833 (m-30) REVERT: A 1423 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6924 (mp0) outliers start: 24 outliers final: 13 residues processed: 158 average time/residue: 0.4899 time to fit residues: 84.6248 Evaluate side-chains 157 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 915 LYS Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1021 HIS Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1421 SER Chi-restraints excluded: chain A residue 1423 GLU Chi-restraints excluded: chain A residue 1502 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 104 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 70 optimal weight: 0.0980 chunk 99 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 ASN A 844 ASN A1034 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.173572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.135653 restraints weight = 11932.231| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.76 r_work: 0.3227 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11051 Z= 0.126 Angle : 0.647 17.335 15060 Z= 0.312 Chirality : 0.043 0.381 1740 Planarity : 0.003 0.043 1848 Dihedral : 10.237 117.169 1693 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.13 % Favored : 91.57 % Rotamer: Outliers : 2.13 % Allowed : 18.43 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.24), residues: 1341 helix: 1.55 (0.18), residues: 860 sheet: 0.09 (1.33), residues: 10 loop : -2.28 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1137 TYR 0.018 0.001 TYR A1450 PHE 0.024 0.001 PHE A 900 TRP 0.007 0.001 TRP A1063 HIS 0.007 0.001 HIS A1021 Details of bonding type rmsd covalent geometry : bond 0.00275 (11034) covalent geometry : angle 0.60388 (15017) SS BOND : bond 0.00297 ( 8) SS BOND : angle 0.92899 ( 16) hydrogen bonds : bond 0.04957 ( 600) hydrogen bonds : angle 3.95714 ( 1713) link_BETA1-3 : bond 0.00696 ( 1) link_BETA1-3 : angle 1.92574 ( 3) link_BETA1-4 : bond 0.00429 ( 3) link_BETA1-4 : angle 5.17758 ( 9) link_BETA1-6 : bond 0.00724 ( 1) link_BETA1-6 : angle 2.00253 ( 3) link_NAG-ASN : bond 0.00733 ( 4) link_NAG-ASN : angle 6.75894 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 261 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8373 (mm) REVERT: A 318 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.7999 (tp) REVERT: A 424 LYS cc_start: 0.7572 (ttmt) cc_final: 0.6846 (tmmt) REVERT: A 573 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6665 (tt) REVERT: A 877 ASP cc_start: 0.8311 (p0) cc_final: 0.7623 (m-30) REVERT: A 915 LYS cc_start: 0.5987 (OUTLIER) cc_final: 0.4922 (pmtt) REVERT: A 1029 ASP cc_start: 0.7364 (m-30) cc_final: 0.6866 (m-30) REVERT: A 1423 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6990 (mp0) outliers start: 23 outliers final: 14 residues processed: 157 average time/residue: 0.5162 time to fit residues: 88.7136 Evaluate side-chains 156 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 915 LYS Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1021 HIS Chi-restraints excluded: chain A residue 1034 ASN Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1421 SER Chi-restraints excluded: chain A residue 1423 GLU Chi-restraints excluded: chain A residue 1502 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 49 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 chunk 122 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 ASN A1227 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.173470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.135657 restraints weight = 11920.182| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.76 r_work: 0.3228 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 11051 Z= 0.158 Angle : 0.889 59.199 15060 Z= 0.484 Chirality : 0.045 0.572 1740 Planarity : 0.004 0.043 1848 Dihedral : 10.237 117.192 1693 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.13 % Favored : 91.57 % Rotamer: Outliers : 2.04 % Allowed : 18.80 % Favored : 79.17 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.24), residues: 1341 helix: 1.54 (0.18), residues: 860 sheet: -2.28 (0.92), residues: 22 loop : -2.26 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1137 TYR 0.018 0.001 TYR A1390 PHE 0.023 0.001 PHE A 900 TRP 0.006 0.001 TRP A1355 HIS 0.007 0.001 HIS A1021 Details of bonding type rmsd covalent geometry : bond 0.00340 (11034) covalent geometry : angle 0.85818 (15017) SS BOND : bond 0.00334 ( 8) SS BOND : angle 0.94904 ( 16) hydrogen bonds : bond 0.05019 ( 600) hydrogen bonds : angle 3.95712 ( 1713) link_BETA1-3 : bond 0.00734 ( 1) link_BETA1-3 : angle 1.87207 ( 3) link_BETA1-4 : bond 0.00459 ( 3) link_BETA1-4 : angle 5.28085 ( 9) link_BETA1-6 : bond 0.00666 ( 1) link_BETA1-6 : angle 2.00016 ( 3) link_NAG-ASN : bond 0.00745 ( 4) link_NAG-ASN : angle 6.76757 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 261 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8369 (mm) REVERT: A 318 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.7997 (tp) REVERT: A 424 LYS cc_start: 0.7570 (ttmt) cc_final: 0.6845 (tmmt) REVERT: A 573 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6663 (tt) REVERT: A 877 ASP cc_start: 0.8301 (p0) cc_final: 0.7611 (m-30) REVERT: A 915 LYS cc_start: 0.5995 (OUTLIER) cc_final: 0.4919 (pmtt) REVERT: A 1029 ASP cc_start: 0.7335 (m-30) cc_final: 0.6842 (m-30) REVERT: A 1034 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7820 (m110) REVERT: A 1423 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6989 (mp0) outliers start: 22 outliers final: 14 residues processed: 150 average time/residue: 0.5439 time to fit residues: 88.8444 Evaluate side-chains 158 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 915 LYS Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1021 HIS Chi-restraints excluded: chain A residue 1034 ASN Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1198 PHE Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1421 SER Chi-restraints excluded: chain A residue 1423 GLU Chi-restraints excluded: chain A residue 1502 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 47 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 35 optimal weight: 0.0870 chunk 82 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 ASN A1227 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.173436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.135537 restraints weight = 11998.828| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.76 r_work: 0.3226 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 11051 Z= 0.158 Angle : 0.889 59.199 15060 Z= 0.484 Chirality : 0.045 0.572 1740 Planarity : 0.004 0.043 1848 Dihedral : 10.237 117.192 1693 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.13 % Favored : 91.57 % Rotamer: Outliers : 1.85 % Allowed : 19.07 % Favored : 79.07 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.24), residues: 1341 helix: 1.54 (0.18), residues: 860 sheet: -2.28 (0.92), residues: 22 loop : -2.26 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1137 TYR 0.018 0.001 TYR A1390 PHE 0.023 0.001 PHE A 900 TRP 0.006 0.001 TRP A1355 HIS 0.007 0.001 HIS A1021 Details of bonding type rmsd covalent geometry : bond 0.00340 (11034) covalent geometry : angle 0.85818 (15017) SS BOND : bond 0.00334 ( 8) SS BOND : angle 0.94904 ( 16) hydrogen bonds : bond 0.05019 ( 600) hydrogen bonds : angle 3.95712 ( 1713) link_BETA1-3 : bond 0.00734 ( 1) link_BETA1-3 : angle 1.87207 ( 3) link_BETA1-4 : bond 0.00459 ( 3) link_BETA1-4 : angle 5.28085 ( 9) link_BETA1-6 : bond 0.00666 ( 1) link_BETA1-6 : angle 2.00016 ( 3) link_NAG-ASN : bond 0.00745 ( 4) link_NAG-ASN : angle 6.76757 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4101.25 seconds wall clock time: 70 minutes 26.78 seconds (4226.78 seconds total)