Starting phenix.real_space_refine on Wed Mar 4 05:02:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lkz_63189/03_2026/9lkz_63189.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lkz_63189/03_2026/9lkz_63189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lkz_63189/03_2026/9lkz_63189.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lkz_63189/03_2026/9lkz_63189.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lkz_63189/03_2026/9lkz_63189.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lkz_63189/03_2026/9lkz_63189.map" } resolution = 2.87 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= 0.009 sd= 0.113 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 7025 2.51 5 N 1679 2.21 5 O 1807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10583 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1246, 9969 Classifications: {'peptide': 1246} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 39, 'TRANS': 1204} Chain breaks: 2 Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 4, 'ARG:plan': 4, 'TRP:plan': 2, 'ASP:plan': 7, 'GLN:plan1': 5, 'HIS:plan': 2, 'GLU:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 162 Chain: "C" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 497 Classifications: {'peptide': 63} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 58} 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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.61, per 1000 atoms: 0.25 Number of scatterers: 10583 At special positions: 0 Unit cell: (121.136, 113.632, 117.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 1807 8.00 N 1679 7.00 C 7025 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, 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=2.03 Simple disulfide: pdb=" SG CYS A 709 " - pdb=" SG CYS A 717 " distance=2.03 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 C 12 " - pdb=" SG CYS C 63 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 36 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 46 " distance=2.03 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 48 " 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 " BETA1-6 " BMA B 3 " - " BMA B 5 " NAG-ASN " NAG A1601 " - " ASN A1034 " " NAG A1602 " - " ASN A 312 " " NAG A1603 " - " ASN A 308 " " NAG A1604 " - " ASN A 300 " " NAG B 1 " - " ASN A 330 " Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 548.9 milliseconds 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2486 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 6 sheets defined 70.6% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 130 through 139 Processing helix chain 'A' and resid 139 through 159 removed outlier: 3.854A pdb=" N SER A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 186 Processing helix chain 'A' and resid 199 through 218 removed outlier: 3.624A pdb=" N LEU A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP A 205 " --> pdb=" O TRP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 240 removed outlier: 3.502A pdb=" N ARG A 230 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 231 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 232 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG A 233 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 258 removed outlier: 4.052A 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 Processing helix chain 'A' and resid 295 through 299 removed outlier: 4.442A pdb=" N TRP A 298 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY A 299 " --> pdb=" O GLY A 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 295 through 299' Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.569A pdb=" N TRP A 316 " --> pdb=" O SER A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 360 through 374 Processing helix chain 'A' and resid 376 through 388 removed outlier: 4.227A 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: 3.850A pdb=" N PHE A 396 " --> pdb=" O HIS A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 427 Processing helix chain 'A' and resid 503 through 517 removed outlier: 3.720A pdb=" N VAL A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 538 removed outlier: 3.848A pdb=" N GLU A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 523 " --> pdb=" O PRO A 519 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 524 " --> pdb=" O PHE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 568 Processing helix chain 'A' and resid 574 through 579 removed outlier: 3.657A pdb=" N PHE A 579 " --> pdb=" O PRO A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 601 Processing helix chain 'A' and resid 607 through 622 removed outlier: 4.265A pdb=" N ARG A 610 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 614 " --> pdb=" O SER A 611 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS A 622 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 removed outlier: 3.508A pdb=" N MET A 634 " --> pdb=" O PHE A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 663 removed outlier: 3.866A pdb=" N ASN A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 670 removed outlier: 3.582A 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 Processing helix chain 'A' and resid 686 through 700 Processing helix chain 'A' and resid 702 through 713 removed outlier: 3.604A pdb=" N VAL A 712 " --> pdb=" O ASP A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 730 removed outlier: 3.561A pdb=" N PHE A 720 " --> pdb=" O SER A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 744 Processing helix chain 'A' and resid 839 through 854 removed outlier: 3.871A pdb=" N ILE A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 872 Processing helix chain 'A' and resid 873 through 876 removed outlier: 3.879A pdb=" N GLU A 876 " --> pdb=" O LEU A 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 873 through 876' Processing helix chain 'A' and resid 879 through 882 Processing helix chain 'A' and resid 883 through 919 removed outlier: 3.523A pdb=" N ALA A 899 " --> pdb=" O TYR A 895 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET A 905 " --> pdb=" O PHE A 901 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N PHE A 914 " --> pdb=" O PHE A 910 " (cutoff:3.500A) removed outlier: 9.344A pdb=" N LYS A 915 " --> pdb=" O ALA A 911 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS A 916 " --> pdb=" O VAL A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 942 removed outlier: 3.687A pdb=" N LEU A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP A 926 " --> pdb=" O TRP A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 952 removed outlier: 3.575A pdb=" N LEU A 952 " --> pdb=" O GLN A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 957 Processing helix chain 'A' and resid 958 through 964 removed outlier: 3.628A pdb=" N LYS A 964 " --> pdb=" O ARG A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 1005 removed outlier: 3.532A pdb=" N THR A 974 " --> pdb=" O VAL A 970 " (cutoff:3.500A) Proline residue: A 980 - end of helix removed outlier: 3.773A pdb=" N VAL A 995 " --> pdb=" O PHE A 991 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE A 996 " --> pdb=" O PHE A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1033 removed outlier: 3.589A pdb=" N GLU A1033 " --> pdb=" O ASP A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1059 removed outlier: 3.520A pdb=" N LEU A1052 " --> pdb=" O GLY A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1071 removed outlier: 3.893A 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: 3.553A pdb=" N PHE A1092 " --> pdb=" O MET A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1123 removed outlier: 3.730A pdb=" N CYS A1109 " --> pdb=" O LYS A1105 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN A1117 " --> pdb=" O ASP A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1144 removed outlier: 3.765A pdb=" N ILE A1135 " --> pdb=" O ARG A1131 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR A1136 " --> pdb=" O THR A1132 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG A1137 " --> pdb=" O GLN A1133 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A1144 " --> pdb=" O VAL A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1168 removed outlier: 3.632A pdb=" N LEU A1162 " --> pdb=" O HIS A1158 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A1166 " --> pdb=" O LEU A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1188 removed outlier: 3.527A pdb=" N GLU A1173 " --> pdb=" O ASN A1169 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR A1174 " --> pdb=" O ARG A1170 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A1179 " --> pdb=" O THR A1175 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE A1180 " --> pdb=" O MET A1176 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET A1187 " --> pdb=" O ASN A1183 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A1188 " --> pdb=" O VAL A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1205 Processing helix chain 'A' and resid 1205 through 1224 removed outlier: 3.726A pdb=" N PHE A1209 " --> pdb=" O LEU A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1250 removed outlier: 3.609A pdb=" N ILE A1235 " --> pdb=" O ASP A1231 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A1236 " --> pdb=" O PRO A1232 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A1242 " --> pdb=" O PHE A1238 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A1248 " --> pdb=" O ALA A1244 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET A1249 " --> pdb=" O ILE A1245 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A1250 " --> pdb=" O ALA A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1268 removed outlier: 3.832A pdb=" N ARG A1268 " --> pdb=" O LEU A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1276 removed outlier: 3.738A pdb=" N LEU A1275 " --> pdb=" O ARG A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1295 removed outlier: 3.757A pdb=" N LEU A1288 " --> pdb=" O GLY A1284 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1322 removed outlier: 3.522A pdb=" N MET A1322 " --> pdb=" O MET A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1350 Processing helix chain 'A' and resid 1354 through 1363 removed outlier: 3.580A pdb=" N VAL A1358 " --> pdb=" O GLY A1354 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA A1361 " --> pdb=" O GLY A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1398 Processing helix chain 'A' and resid 1403 through 1424 removed outlier: 4.321A pdb=" N ALA A1407 " --> pdb=" O ILE A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1427 through 1441 removed outlier: 3.518A pdb=" N ASP A1431 " --> pdb=" O ASP A1427 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE A1433 " --> pdb=" O ASP A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1452 through 1457 removed outlier: 3.518A pdb=" N LEU A1457 " --> pdb=" O LEU A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1458 through 1460 No H-bonds generated for 'chain 'A' and resid 1458 through 1460' Processing helix chain 'A' and resid 1470 through 1478 removed outlier: 3.660A pdb=" N LEU A1475 " --> pdb=" O LYS A1471 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN A1478 " --> pdb=" O ILE A1474 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1503 Processing helix chain 'C' and resid 24 through 30 Processing sheet with id=AA1, first strand: chain 'A' and resid 110 through 112 Processing sheet with id=AA2, first strand: chain 'A' and resid 287 through 290 Processing sheet with id=AA3, first strand: chain 'A' and resid 1010 through 1012 Processing sheet with id=AA4, first strand: chain 'A' and resid 1447 through 1449 Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.706A pdb=" N ALA C 4 " --> pdb=" O CYS C 48 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N CYS C 48 " --> pdb=" O ALA C 4 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 7 through 8 605 hydrogen bonds defined for protein. 1725 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: 1.64 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: 1.11 - 1.25: 1585 1.25 - 1.39: 2931 1.39 - 1.53: 5792 1.53 - 1.67: 449 1.67 - 1.81: 116 Bond restraints: 10873 Sorted by residual: bond pdb=" C HIS C 64 " pdb=" O HIS C 64 " ideal model delta sigma weight residual 1.235 1.113 0.122 1.26e-02 6.30e+03 9.38e+01 bond pdb=" CA CYS C 63 " pdb=" CB CYS C 63 " ideal model delta sigma weight residual 1.527 1.423 0.104 1.38e-02 5.25e+03 5.67e+01 bond pdb=" C CYS C 63 " pdb=" O CYS C 63 " ideal model delta sigma weight residual 1.236 1.147 0.088 1.21e-02 6.83e+03 5.35e+01 bond pdb=" N CYS C 63 " pdb=" CA CYS C 63 " ideal model delta sigma weight residual 1.458 1.380 0.077 1.24e-02 6.50e+03 3.89e+01 bond pdb=" CA HIS C 64 " pdb=" C HIS C 64 " ideal model delta sigma weight residual 1.523 1.445 0.079 1.34e-02 5.57e+03 3.44e+01 ... (remaining 10868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 14568 2.14 - 4.28: 180 4.28 - 6.42: 46 6.42 - 8.56: 7 8.56 - 10.70: 1 Bond angle restraints: 14802 Sorted by residual: angle pdb=" N ASP A1332 " pdb=" CA ASP A1332 " pdb=" C ASP A1332 " ideal model delta sigma weight residual 110.80 121.50 -10.70 2.13e+00 2.20e-01 2.52e+01 angle pdb=" C GLY A1379 " pdb=" N ASN A1380 " pdb=" CA ASN A1380 " ideal model delta sigma weight residual 124.82 132.15 -7.33 1.78e+00 3.16e-01 1.69e+01 angle pdb=" N SER A 331 " pdb=" CA SER A 331 " pdb=" C SER A 331 " ideal model delta sigma weight residual 110.55 105.05 5.50 1.35e+00 5.49e-01 1.66e+01 angle pdb=" N LYS C 41 " pdb=" CA LYS C 41 " pdb=" C LYS C 41 " ideal model delta sigma weight residual 114.04 109.43 4.61 1.24e+00 6.50e-01 1.38e+01 angle pdb=" O LYS C 62 " pdb=" C LYS C 62 " pdb=" N CYS C 63 " ideal model delta sigma weight residual 123.28 118.65 4.63 1.28e+00 6.10e-01 1.31e+01 ... (remaining 14797 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.82: 6061 24.82 - 49.64: 282 49.64 - 74.46: 43 74.46 - 99.29: 13 99.29 - 124.11: 16 Dihedral angle restraints: 6415 sinusoidal: 2558 harmonic: 3857 Sorted by residual: dihedral pdb=" N ASN A 330 " pdb=" C ASN A 330 " pdb=" CA ASN A 330 " pdb=" CB ASN A 330 " ideal model delta harmonic sigma weight residual 122.80 135.63 -12.83 0 2.50e+00 1.60e-01 2.63e+01 dihedral pdb=" C ASN A 330 " pdb=" N ASN A 330 " pdb=" CA ASN A 330 " pdb=" CB ASN A 330 " ideal model delta harmonic sigma weight residual -122.60 -134.33 11.73 0 2.50e+00 1.60e-01 2.20e+01 dihedral pdb=" CA THR A 127 " pdb=" C THR A 127 " pdb=" N PRO A 128 " pdb=" CA PRO A 128 " ideal model delta harmonic sigma weight residual -180.00 -158.97 -21.03 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 6412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.204: 1706 0.204 - 0.408: 6 0.408 - 0.612: 1 0.612 - 0.816: 0 0.816 - 1.020: 1 Chirality restraints: 1714 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 -1.38 -1.02 2.00e-01 2.50e+01 2.60e+01 chirality pdb=" CA ASN A 330 " pdb=" N ASN A 330 " pdb=" C ASN A 330 " pdb=" CB ASN A 330 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.28e+00 chirality pdb=" CA ASP A1332 " pdb=" N ASP A1332 " pdb=" C ASP A1332 " pdb=" CB ASP A1332 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 1711 not shown) Planarity restraints: 1817 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A1468 " 0.060 5.00e-02 4.00e+02 9.20e-02 1.35e+01 pdb=" N PRO A1469 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO A1469 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A1469 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 62 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.24e+01 pdb=" C LYS C 62 " -0.061 2.00e-02 2.50e+03 pdb=" O LYS C 62 " 0.022 2.00e-02 2.50e+03 pdb=" N CYS C 63 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 329 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.97e+00 pdb=" C GLY A 329 " 0.042 2.00e-02 2.50e+03 pdb=" O GLY A 329 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN A 330 " -0.014 2.00e-02 2.50e+03 ... (remaining 1814 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2752 2.79 - 3.32: 10067 3.32 - 3.85: 17037 3.85 - 4.37: 20152 4.37 - 4.90: 34871 Nonbonded interactions: 84879 Sorted by model distance: nonbonded pdb=" OD1 ASP A 714 " pdb=" OG SER A 716 " model vdw 2.266 3.040 nonbonded pdb=" OD1 ASN A1335 " pdb=" NE2 GLN A1341 " model vdw 2.283 3.120 nonbonded pdb=" OG1 THR A 101 " pdb=" O PHE A 112 " model vdw 2.287 3.040 nonbonded pdb=" O LYS A 915 " pdb=" OG1 THR A 919 " model vdw 2.305 3.040 nonbonded pdb=" O SER A 574 " pdb=" N PHE A 577 " model vdw 2.306 3.120 ... (remaining 84874 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.300 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 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 0.122 10891 Z= 0.238 Angle : 0.693 32.816 14847 Z= 0.325 Chirality : 0.050 1.020 1714 Planarity : 0.004 0.092 1812 Dihedral : 16.419 124.107 3902 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.76 % Favored : 93.01 % Rotamer: Outliers : 0.36 % Allowed : 0.55 % Favored : 99.09 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.24), residues: 1301 helix: 0.41 (0.18), residues: 841 sheet: -2.13 (1.06), residues: 22 loop : -1.57 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1225 TYR 0.012 0.001 TYR A 381 PHE 0.015 0.001 PHE A 189 TRP 0.009 0.001 TRP A1063 HIS 0.014 0.001 HIS C 64 Details of bonding type rmsd covalent geometry : bond 0.00388 (10873) covalent geometry : angle 0.59846 (14802) SS BOND : bond 0.00137 ( 9) SS BOND : angle 1.45901 ( 18) hydrogen bonds : bond 0.22532 ( 605) hydrogen bonds : angle 6.14408 ( 1725) link_BETA1-3 : bond 0.00386 ( 1) link_BETA1-3 : angle 1.77945 ( 3) link_BETA1-4 : bond 0.01365 ( 2) link_BETA1-4 : angle 6.26209 ( 6) link_BETA1-6 : bond 0.00524 ( 1) link_BETA1-6 : angle 18.98042 ( 3) link_NAG-ASN : bond 0.01864 ( 5) link_NAG-ASN : angle 5.54286 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 184 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 577 PHE cc_start: 0.7897 (m-80) cc_final: 0.7586 (m-10) REVERT: A 1137 ARG cc_start: 0.7057 (ttt90) cc_final: 0.6690 (ttp-110) REVERT: A 1176 MET cc_start: 0.8421 (mmp) cc_final: 0.8013 (mmp) REVERT: A 1237 ASP cc_start: 0.7570 (m-30) cc_final: 0.7203 (m-30) REVERT: A 1332 ASP cc_start: 0.6592 (p0) cc_final: 0.5905 (t0) REVERT: A 1461 GLN cc_start: 0.7636 (mt0) cc_final: 0.7316 (tt0) REVERT: A 1499 ASP cc_start: 0.8496 (t70) cc_final: 0.8227 (t0) REVERT: A 1503 ARG cc_start: 0.7381 (ptt90) cc_final: 0.7011 (ppt170) outliers start: 4 outliers final: 1 residues processed: 187 average time/residue: 0.4909 time to fit residues: 99.8351 Evaluate side-chains 129 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 ASN A 948 GLN A1002 GLN A1028 ASN A1335 ASN A1341 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.152621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.116538 restraints weight = 12678.769| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.59 r_work: 0.3213 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 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 : 0.005 0.047 10891 Z= 0.227 Angle : 0.793 16.576 14847 Z= 0.378 Chirality : 0.049 0.489 1714 Planarity : 0.005 0.068 1812 Dihedral : 13.811 111.477 1613 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.69 % Favored : 93.01 % Rotamer: Outliers : 2.64 % Allowed : 10.18 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.24), residues: 1301 helix: 0.72 (0.18), residues: 861 sheet: -2.14 (1.04), residues: 22 loop : -1.74 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 681 TYR 0.024 0.002 TYR A 381 PHE 0.023 0.002 PHE A 301 TRP 0.017 0.002 TRP A1063 HIS 0.014 0.002 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00543 (10873) covalent geometry : angle 0.75925 (14802) SS BOND : bond 0.00320 ( 9) SS BOND : angle 1.20220 ( 18) hydrogen bonds : bond 0.06369 ( 605) hydrogen bonds : angle 4.30601 ( 1725) link_BETA1-3 : bond 0.01204 ( 1) link_BETA1-3 : angle 2.86095 ( 3) link_BETA1-4 : bond 0.00979 ( 2) link_BETA1-4 : angle 5.26498 ( 6) link_BETA1-6 : bond 0.00121 ( 1) link_BETA1-6 : angle 3.69178 ( 3) link_NAG-ASN : bond 0.01575 ( 5) link_NAG-ASN : angle 6.09635 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.403 Fit side-chains REVERT: A 210 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8140 (mp) REVERT: A 336 MET cc_start: 0.8733 (mmm) cc_final: 0.8381 (mmp) REVERT: A 424 LYS cc_start: 0.8348 (ttpt) cc_final: 0.8122 (pttt) REVERT: A 631 MET cc_start: 0.8695 (mtm) cc_final: 0.8428 (mtp) REVERT: A 1102 PHE cc_start: 0.8598 (t80) cc_final: 0.7313 (m-80) REVERT: A 1137 ARG cc_start: 0.8299 (ttt90) cc_final: 0.7720 (ttp-110) REVERT: A 1144 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7805 (ptm) REVERT: A 1221 VAL cc_start: 0.8074 (OUTLIER) cc_final: 0.7817 (p) REVERT: A 1237 ASP cc_start: 0.7812 (m-30) cc_final: 0.7478 (m-30) REVERT: A 1322 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8707 (mtm) REVERT: A 1332 ASP cc_start: 0.7255 (p0) cc_final: 0.6631 (t0) REVERT: A 1461 GLN cc_start: 0.8031 (mt0) cc_final: 0.7700 (tt0) REVERT: C 65 ARG cc_start: 0.6167 (OUTLIER) cc_final: 0.5726 (ppt-90) outliers start: 29 outliers final: 10 residues processed: 150 average time/residue: 0.5384 time to fit residues: 87.8994 Evaluate side-chains 135 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 636 LYS Chi-restraints excluded: chain A residue 925 LEU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1144 MET Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1335 ASN Chi-restraints excluded: chain C residue 65 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 77 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 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 629 ASN A 948 GLN A1028 ASN A1335 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.154920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.119340 restraints weight = 12821.714| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.66 r_work: 0.3245 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10891 Z= 0.133 Angle : 0.677 16.444 14847 Z= 0.322 Chirality : 0.044 0.375 1714 Planarity : 0.004 0.052 1812 Dihedral : 12.688 113.495 1612 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.38 % Favored : 93.47 % Rotamer: Outliers : 2.64 % Allowed : 12.82 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.24), residues: 1301 helix: 1.11 (0.18), residues: 854 sheet: -2.17 (1.00), residues: 22 loop : -1.59 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1225 TYR 0.018 0.001 TYR A 381 PHE 0.021 0.001 PHE A 301 TRP 0.009 0.001 TRP A1355 HIS 0.005 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00295 (10873) covalent geometry : angle 0.63917 (14802) SS BOND : bond 0.00186 ( 9) SS BOND : angle 0.84054 ( 18) hydrogen bonds : bond 0.04889 ( 605) hydrogen bonds : angle 4.01543 ( 1725) link_BETA1-3 : bond 0.00981 ( 1) link_BETA1-3 : angle 2.86709 ( 3) link_BETA1-4 : bond 0.00494 ( 2) link_BETA1-4 : angle 5.21862 ( 6) link_BETA1-6 : bond 0.00975 ( 1) link_BETA1-6 : angle 2.16007 ( 3) link_NAG-ASN : bond 0.00582 ( 5) link_NAG-ASN : angle 6.01413 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6762 (tt0) REVERT: A 210 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8077 (mp) REVERT: A 324 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6646 (mt-10) REVERT: A 336 MET cc_start: 0.8610 (mmm) cc_final: 0.8246 (mmp) REVERT: A 543 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7626 (ttm) REVERT: A 631 MET cc_start: 0.8683 (mtm) cc_final: 0.8410 (mtp) REVERT: A 1137 ARG cc_start: 0.8250 (ttt90) cc_final: 0.7660 (ttp-110) REVERT: A 1144 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7703 (ptm) REVERT: A 1237 ASP cc_start: 0.7772 (m-30) cc_final: 0.7472 (m-30) REVERT: A 1263 LEU cc_start: 0.8358 (tt) cc_final: 0.8096 (mp) REVERT: A 1283 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7708 (ttt180) REVERT: A 1322 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8671 (mtm) REVERT: A 1332 ASP cc_start: 0.7078 (p0) cc_final: 0.6495 (t0) REVERT: A 1335 ASN cc_start: 0.9182 (OUTLIER) cc_final: 0.8930 (p0) REVERT: A 1384 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7494 (ttp-110) REVERT: A 1423 GLU cc_start: 0.8254 (pm20) cc_final: 0.8001 (pt0) REVERT: A 1461 GLN cc_start: 0.8007 (mt0) cc_final: 0.7602 (tt0) REVERT: C 65 ARG cc_start: 0.6213 (OUTLIER) cc_final: 0.5648 (ppt-90) outliers start: 29 outliers final: 10 residues processed: 140 average time/residue: 0.5153 time to fit residues: 78.3218 Evaluate side-chains 142 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 636 LYS Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain A residue 925 LEU Chi-restraints excluded: chain A residue 1144 MET Chi-restraints excluded: chain A residue 1204 TYR Chi-restraints excluded: chain A residue 1283 ARG Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1335 ASN Chi-restraints excluded: chain A residue 1384 ARG Chi-restraints excluded: chain C residue 65 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 ASN A 643 ASN A 948 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.153401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.118015 restraints weight = 12744.526| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.52 r_work: 0.3228 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10891 Z= 0.169 Angle : 0.697 17.121 14847 Z= 0.331 Chirality : 0.046 0.388 1714 Planarity : 0.004 0.054 1812 Dihedral : 12.335 117.049 1612 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.69 % Favored : 93.08 % Rotamer: Outliers : 3.00 % Allowed : 13.45 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.24), residues: 1301 helix: 1.11 (0.18), residues: 860 sheet: -2.12 (1.01), residues: 22 loop : -1.64 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1142 TYR 0.020 0.001 TYR A 381 PHE 0.020 0.002 PHE A 301 TRP 0.008 0.001 TRP A1355 HIS 0.006 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00403 (10873) covalent geometry : angle 0.65994 (14802) SS BOND : bond 0.00294 ( 9) SS BOND : angle 0.98757 ( 18) hydrogen bonds : bond 0.05077 ( 605) hydrogen bonds : angle 3.97305 ( 1725) link_BETA1-3 : bond 0.00866 ( 1) link_BETA1-3 : angle 2.73912 ( 3) link_BETA1-4 : bond 0.00517 ( 2) link_BETA1-4 : angle 5.42134 ( 6) link_BETA1-6 : bond 0.00841 ( 1) link_BETA1-6 : angle 1.93367 ( 3) link_NAG-ASN : bond 0.00459 ( 5) link_NAG-ASN : angle 6.00793 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8082 (mp) REVERT: A 324 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6704 (mt-10) REVERT: A 336 MET cc_start: 0.8697 (mmm) cc_final: 0.8346 (mmp) REVERT: A 631 MET cc_start: 0.8689 (mtm) cc_final: 0.8417 (mtp) REVERT: A 1137 ARG cc_start: 0.8338 (ttt90) cc_final: 0.7724 (ttp-110) REVERT: A 1144 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7726 (ptm) REVERT: A 1237 ASP cc_start: 0.7772 (m-30) cc_final: 0.7478 (m-30) REVERT: A 1263 LEU cc_start: 0.8384 (tt) cc_final: 0.8148 (mp) REVERT: A 1283 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7708 (ttt180) REVERT: A 1322 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8694 (mtm) REVERT: A 1332 ASP cc_start: 0.6820 (p0) cc_final: 0.6425 (t0) REVERT: A 1384 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7509 (ttp-110) REVERT: A 1423 GLU cc_start: 0.8168 (pm20) cc_final: 0.7954 (pt0) REVERT: A 1461 GLN cc_start: 0.8068 (mt0) cc_final: 0.7597 (tt0) REVERT: C 65 ARG cc_start: 0.6288 (OUTLIER) cc_final: 0.5727 (ppt-90) outliers start: 33 outliers final: 12 residues processed: 143 average time/residue: 0.5332 time to fit residues: 82.5344 Evaluate side-chains 139 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 636 LYS Chi-restraints excluded: chain A residue 925 LEU Chi-restraints excluded: chain A residue 1144 MET Chi-restraints excluded: chain A residue 1204 TYR Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain A residue 1283 ARG Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1384 ARG Chi-restraints excluded: chain C residue 65 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 11 optimal weight: 0.6980 chunk 54 optimal weight: 0.2980 chunk 114 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 14 optimal weight: 0.0870 chunk 85 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.156497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.120819 restraints weight = 12659.662| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.53 r_work: 0.3284 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10891 Z= 0.112 Angle : 0.621 16.214 14847 Z= 0.294 Chirality : 0.043 0.344 1714 Planarity : 0.004 0.055 1812 Dihedral : 11.244 116.436 1612 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.53 % Favored : 93.31 % Rotamer: Outliers : 3.18 % Allowed : 14.09 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.24), residues: 1301 helix: 1.41 (0.18), residues: 850 sheet: -2.17 (1.02), residues: 22 loop : -1.56 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1286 TYR 0.015 0.001 TYR A 381 PHE 0.018 0.001 PHE A 301 TRP 0.009 0.001 TRP A1355 HIS 0.004 0.001 HIS A1191 Details of bonding type rmsd covalent geometry : bond 0.00241 (10873) covalent geometry : angle 0.58368 (14802) SS BOND : bond 0.00410 ( 9) SS BOND : angle 0.82157 ( 18) hydrogen bonds : bond 0.03968 ( 605) hydrogen bonds : angle 3.79102 ( 1725) link_BETA1-3 : bond 0.00967 ( 1) link_BETA1-3 : angle 2.33511 ( 3) link_BETA1-4 : bond 0.00512 ( 2) link_BETA1-4 : angle 5.36178 ( 6) link_BETA1-6 : bond 0.01112 ( 1) link_BETA1-6 : angle 1.50141 ( 3) link_NAG-ASN : bond 0.00556 ( 5) link_NAG-ASN : angle 5.59470 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.8016 (mp) REVERT: A 324 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6506 (mt-10) REVERT: A 336 MET cc_start: 0.8587 (mmm) cc_final: 0.8238 (mmp) REVERT: A 542 ASP cc_start: 0.7486 (m-30) cc_final: 0.7264 (m-30) REVERT: A 636 LYS cc_start: 0.7257 (OUTLIER) cc_final: 0.7008 (pttp) REVERT: A 1137 ARG cc_start: 0.8289 (ttt90) cc_final: 0.7655 (ttp-110) REVERT: A 1237 ASP cc_start: 0.7711 (m-30) cc_final: 0.7442 (m-30) REVERT: A 1263 LEU cc_start: 0.8359 (tt) cc_final: 0.8054 (mt) REVERT: A 1277 ARG cc_start: 0.8145 (mtp180) cc_final: 0.7913 (ptp-170) REVERT: A 1283 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7678 (ttt180) REVERT: A 1322 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8682 (ttm) REVERT: A 1332 ASP cc_start: 0.6859 (p0) cc_final: 0.6549 (t0) REVERT: A 1384 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7463 (ttp-110) REVERT: A 1418 TYR cc_start: 0.8487 (m-80) cc_final: 0.8132 (m-80) REVERT: A 1423 GLU cc_start: 0.8010 (pm20) cc_final: 0.7802 (pt0) REVERT: A 1461 GLN cc_start: 0.8047 (mt0) cc_final: 0.7668 (tt0) REVERT: C 65 ARG cc_start: 0.6323 (OUTLIER) cc_final: 0.5716 (ppt-90) outliers start: 35 outliers final: 14 residues processed: 155 average time/residue: 0.4974 time to fit residues: 84.1383 Evaluate side-chains 147 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 636 LYS Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain A residue 925 LEU Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1204 TYR Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1283 ARG Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1384 ARG Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 65 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 2 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 112 optimal weight: 0.0470 chunk 90 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 ASN A 643 ASN A 948 GLN A1028 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.156028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.119633 restraints weight = 12755.691| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.51 r_work: 0.3272 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10891 Z= 0.120 Angle : 0.631 16.230 14847 Z= 0.297 Chirality : 0.043 0.364 1714 Planarity : 0.004 0.057 1812 Dihedral : 10.930 117.055 1612 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.69 % Favored : 93.16 % Rotamer: Outliers : 3.27 % Allowed : 14.00 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.24), residues: 1301 helix: 1.40 (0.18), residues: 861 sheet: -2.22 (1.01), residues: 22 loop : -1.71 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1131 TYR 0.020 0.001 TYR A 578 PHE 0.016 0.001 PHE A 301 TRP 0.007 0.001 TRP A1355 HIS 0.004 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00269 (10873) covalent geometry : angle 0.59434 (14802) SS BOND : bond 0.00177 ( 9) SS BOND : angle 0.83210 ( 18) hydrogen bonds : bond 0.04092 ( 605) hydrogen bonds : angle 3.77549 ( 1725) link_BETA1-3 : bond 0.00691 ( 1) link_BETA1-3 : angle 2.41955 ( 3) link_BETA1-4 : bond 0.00450 ( 2) link_BETA1-4 : angle 5.39022 ( 6) link_BETA1-6 : bond 0.00807 ( 1) link_BETA1-6 : angle 1.62885 ( 3) link_NAG-ASN : bond 0.00505 ( 5) link_NAG-ASN : angle 5.59368 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8025 (mp) REVERT: A 324 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6539 (mt-10) REVERT: A 336 MET cc_start: 0.8646 (mmm) cc_final: 0.8300 (mmp) REVERT: A 596 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7959 (mt) REVERT: A 1137 ARG cc_start: 0.8307 (ttt90) cc_final: 0.7663 (ttp-110) REVERT: A 1237 ASP cc_start: 0.7708 (m-30) cc_final: 0.7447 (m-30) REVERT: A 1263 LEU cc_start: 0.8322 (tt) cc_final: 0.8037 (mt) REVERT: A 1277 ARG cc_start: 0.8193 (mtp180) cc_final: 0.7945 (ptp-170) REVERT: A 1283 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7067 (mmt-90) REVERT: A 1322 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8691 (ttm) REVERT: A 1332 ASP cc_start: 0.6827 (p0) cc_final: 0.6597 (t0) REVERT: A 1384 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7459 (ttp-110) REVERT: A 1418 TYR cc_start: 0.8507 (m-80) cc_final: 0.8150 (m-80) REVERT: A 1423 GLU cc_start: 0.8058 (pm20) cc_final: 0.7858 (pt0) REVERT: A 1461 GLN cc_start: 0.7976 (mt0) cc_final: 0.7638 (tt0) REVERT: C 65 ARG cc_start: 0.6329 (OUTLIER) cc_final: 0.5710 (ppt-90) outliers start: 36 outliers final: 15 residues processed: 147 average time/residue: 0.5275 time to fit residues: 84.2958 Evaluate side-chains 148 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain A residue 925 LEU Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1204 TYR Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1283 ARG Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1384 ARG Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 65 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 117 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 ASN A 643 ASN A 948 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.155750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.119387 restraints weight = 12630.826| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.50 r_work: 0.3269 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10891 Z= 0.125 Angle : 0.639 16.379 14847 Z= 0.302 Chirality : 0.043 0.367 1714 Planarity : 0.004 0.059 1812 Dihedral : 10.726 117.566 1612 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.69 % Favored : 93.16 % Rotamer: Outliers : 2.73 % Allowed : 14.91 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.24), residues: 1301 helix: 1.39 (0.18), residues: 864 sheet: -2.20 (1.02), residues: 22 loop : -1.64 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1325 TYR 0.017 0.001 TYR A 578 PHE 0.015 0.001 PHE A 301 TRP 0.007 0.001 TRP A1355 HIS 0.005 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00284 (10873) covalent geometry : angle 0.60260 (14802) SS BOND : bond 0.00189 ( 9) SS BOND : angle 0.84658 ( 18) hydrogen bonds : bond 0.04149 ( 605) hydrogen bonds : angle 3.75748 ( 1725) link_BETA1-3 : bond 0.00727 ( 1) link_BETA1-3 : angle 2.38386 ( 3) link_BETA1-4 : bond 0.00365 ( 2) link_BETA1-4 : angle 5.47072 ( 6) link_BETA1-6 : bond 0.00731 ( 1) link_BETA1-6 : angle 1.73878 ( 3) link_NAG-ASN : bond 0.00506 ( 5) link_NAG-ASN : angle 5.61904 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.8022 (mp) REVERT: A 324 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6529 (mt-10) REVERT: A 336 MET cc_start: 0.8592 (mmm) cc_final: 0.8213 (mmp) REVERT: A 580 LYS cc_start: 0.7889 (mttt) cc_final: 0.7589 (mmtm) REVERT: A 1137 ARG cc_start: 0.8339 (ttt90) cc_final: 0.7668 (ttp-110) REVERT: A 1237 ASP cc_start: 0.7734 (m-30) cc_final: 0.7462 (m-30) REVERT: A 1263 LEU cc_start: 0.8333 (tt) cc_final: 0.8077 (mt) REVERT: A 1277 ARG cc_start: 0.8185 (mtp180) cc_final: 0.7944 (ptp-170) REVERT: A 1283 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7079 (mmt-90) REVERT: A 1332 ASP cc_start: 0.6790 (p0) cc_final: 0.6551 (t0) REVERT: A 1384 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7454 (ttp-110) REVERT: A 1418 TYR cc_start: 0.8517 (m-80) cc_final: 0.8149 (m-80) REVERT: A 1461 GLN cc_start: 0.7987 (mt0) cc_final: 0.7641 (tt0) REVERT: C 65 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.5674 (ppt-90) outliers start: 30 outliers final: 17 residues processed: 148 average time/residue: 0.5210 time to fit residues: 84.0997 Evaluate side-chains 152 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 925 LEU Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1204 TYR Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain A residue 1283 ARG Chi-restraints excluded: chain A residue 1384 ARG Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 65 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 33 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 chunk 91 optimal weight: 0.0870 chunk 51 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 110 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 120 optimal weight: 0.0870 chunk 26 optimal weight: 1.9990 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 ASN A 643 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.159019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.122986 restraints weight = 12699.035| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.52 r_work: 0.3327 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10891 Z= 0.099 Angle : 0.596 15.712 14847 Z= 0.281 Chirality : 0.042 0.341 1714 Planarity : 0.003 0.061 1812 Dihedral : 9.999 116.213 1612 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.61 % Favored : 93.24 % Rotamer: Outliers : 2.64 % Allowed : 15.27 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.25), residues: 1301 helix: 1.56 (0.18), residues: 857 sheet: -2.26 (1.04), residues: 22 loop : -1.55 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1131 TYR 0.017 0.001 TYR A 578 PHE 0.013 0.001 PHE A 301 TRP 0.008 0.001 TRP A1355 HIS 0.003 0.001 HIS A1191 Details of bonding type rmsd covalent geometry : bond 0.00204 (10873) covalent geometry : angle 0.56013 (14802) SS BOND : bond 0.00128 ( 9) SS BOND : angle 0.72820 ( 18) hydrogen bonds : bond 0.03420 ( 605) hydrogen bonds : angle 3.65859 ( 1725) link_BETA1-3 : bond 0.00979 ( 1) link_BETA1-3 : angle 2.20288 ( 3) link_BETA1-4 : bond 0.00463 ( 2) link_BETA1-4 : angle 5.23376 ( 6) link_BETA1-6 : bond 0.00871 ( 1) link_BETA1-6 : angle 2.23871 ( 3) link_NAG-ASN : bond 0.00620 ( 5) link_NAG-ASN : angle 5.31888 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7114 (tt0) REVERT: A 210 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7988 (mp) REVERT: A 336 MET cc_start: 0.8363 (mmm) cc_final: 0.8000 (mmp) REVERT: A 1137 ARG cc_start: 0.8364 (ttt90) cc_final: 0.7700 (ttp-110) REVERT: A 1237 ASP cc_start: 0.7642 (m-30) cc_final: 0.7361 (m-30) REVERT: A 1263 LEU cc_start: 0.8293 (tt) cc_final: 0.8024 (mt) REVERT: A 1277 ARG cc_start: 0.8039 (mtp180) cc_final: 0.7798 (ptp-170) REVERT: A 1283 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7002 (mmt-90) REVERT: A 1332 ASP cc_start: 0.6708 (p0) cc_final: 0.6505 (t0) REVERT: A 1384 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7370 (ttp-110) REVERT: A 1418 TYR cc_start: 0.8429 (m-80) cc_final: 0.8111 (m-80) REVERT: A 1432 MET cc_start: 0.7917 (tmm) cc_final: 0.6163 (mmm) REVERT: A 1461 GLN cc_start: 0.7932 (mt0) cc_final: 0.7639 (tt0) REVERT: C 65 ARG cc_start: 0.6297 (OUTLIER) cc_final: 0.5631 (ppt-90) outliers start: 29 outliers final: 14 residues processed: 151 average time/residue: 0.5097 time to fit residues: 83.7437 Evaluate side-chains 145 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 925 LEU Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1204 TYR Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain A residue 1283 ARG Chi-restraints excluded: chain A residue 1384 ARG Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 65 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 110 optimal weight: 4.9990 chunk 76 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 123 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 ASN A 643 ASN A1028 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.153922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.118203 restraints weight = 12774.875| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.54 r_work: 0.3214 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10891 Z= 0.166 Angle : 0.682 17.193 14847 Z= 0.322 Chirality : 0.045 0.389 1714 Planarity : 0.004 0.060 1812 Dihedral : 10.420 123.223 1612 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.76 % Favored : 93.01 % Rotamer: Outliers : 2.00 % Allowed : 16.45 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.24), residues: 1301 helix: 1.32 (0.18), residues: 865 sheet: -2.12 (1.02), residues: 22 loop : -1.68 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1265 TYR 0.019 0.001 TYR A 381 PHE 0.017 0.002 PHE A 687 TRP 0.007 0.001 TRP A 924 HIS 0.006 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00398 (10873) covalent geometry : angle 0.64433 (14802) SS BOND : bond 0.00273 ( 9) SS BOND : angle 0.97979 ( 18) hydrogen bonds : bond 0.04783 ( 605) hydrogen bonds : angle 3.82540 ( 1725) link_BETA1-3 : bond 0.00463 ( 1) link_BETA1-3 : angle 2.48584 ( 3) link_BETA1-4 : bond 0.00228 ( 2) link_BETA1-4 : angle 5.65154 ( 6) link_BETA1-6 : bond 0.00453 ( 1) link_BETA1-6 : angle 1.74187 ( 3) link_NAG-ASN : bond 0.00449 ( 5) link_NAG-ASN : angle 5.88924 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7931 (mp) REVERT: A 336 MET cc_start: 0.8706 (mmm) cc_final: 0.8336 (mmp) REVERT: A 1137 ARG cc_start: 0.8417 (ttt90) cc_final: 0.7694 (ttp-110) REVERT: A 1163 MET cc_start: 0.7313 (ptp) cc_final: 0.7106 (ptp) REVERT: A 1237 ASP cc_start: 0.7703 (m-30) cc_final: 0.7445 (m-30) REVERT: A 1263 LEU cc_start: 0.8420 (tt) cc_final: 0.8181 (mt) REVERT: A 1277 ARG cc_start: 0.8275 (mtp180) cc_final: 0.8018 (ptp-170) REVERT: A 1283 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7104 (mmt-90) REVERT: A 1418 TYR cc_start: 0.8566 (m-80) cc_final: 0.8228 (m-80) REVERT: A 1461 GLN cc_start: 0.8019 (mt0) cc_final: 0.7651 (tt0) REVERT: C 65 ARG cc_start: 0.6304 (OUTLIER) cc_final: 0.5667 (ppt-90) outliers start: 22 outliers final: 13 residues processed: 149 average time/residue: 0.4855 time to fit residues: 78.9813 Evaluate side-chains 148 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 925 LEU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1204 TYR Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain A residue 1283 ARG Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 65 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 8 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 82 optimal weight: 0.0000 chunk 14 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 ASN A1028 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.156224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.119925 restraints weight = 12674.636| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.54 r_work: 0.3251 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10891 Z= 0.115 Angle : 0.628 16.568 14847 Z= 0.297 Chirality : 0.043 0.360 1714 Planarity : 0.004 0.063 1812 Dihedral : 9.940 120.183 1612 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.76 % Favored : 93.08 % Rotamer: Outliers : 1.82 % Allowed : 16.73 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.24), residues: 1301 helix: 1.41 (0.18), residues: 870 sheet: -2.17 (1.02), residues: 22 loop : -1.63 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1131 TYR 0.018 0.001 TYR A 578 PHE 0.014 0.001 PHE A 301 TRP 0.008 0.001 TRP A1355 HIS 0.004 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00252 (10873) covalent geometry : angle 0.59117 (14802) SS BOND : bond 0.00169 ( 9) SS BOND : angle 0.79526 ( 18) hydrogen bonds : bond 0.03968 ( 605) hydrogen bonds : angle 3.74031 ( 1725) link_BETA1-3 : bond 0.00809 ( 1) link_BETA1-3 : angle 2.23054 ( 3) link_BETA1-4 : bond 0.00122 ( 2) link_BETA1-4 : angle 5.30350 ( 6) link_BETA1-6 : bond 0.00732 ( 1) link_BETA1-6 : angle 2.07450 ( 3) link_NAG-ASN : bond 0.00529 ( 5) link_NAG-ASN : angle 5.60497 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8032 (mp) REVERT: A 336 MET cc_start: 0.8620 (mmm) cc_final: 0.8240 (mmp) REVERT: A 1137 ARG cc_start: 0.8397 (ttt90) cc_final: 0.7675 (ttp-110) REVERT: A 1163 MET cc_start: 0.7184 (ptp) cc_final: 0.6976 (ptp) REVERT: A 1237 ASP cc_start: 0.7654 (m-30) cc_final: 0.7396 (m-30) REVERT: A 1263 LEU cc_start: 0.8369 (tt) cc_final: 0.8139 (mt) REVERT: A 1277 ARG cc_start: 0.8204 (mtp180) cc_final: 0.7991 (ptp-170) REVERT: A 1418 TYR cc_start: 0.8523 (m-80) cc_final: 0.8246 (m-80) REVERT: A 1461 GLN cc_start: 0.7965 (mt0) cc_final: 0.7604 (tt0) REVERT: C 65 ARG cc_start: 0.6325 (OUTLIER) cc_final: 0.5592 (ppt-90) outliers start: 20 outliers final: 14 residues processed: 145 average time/residue: 0.4931 time to fit residues: 77.9468 Evaluate side-chains 143 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 925 LEU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1204 TYR Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 65 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 125 optimal weight: 5.9990 chunk 80 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 ASN A 643 ASN A1028 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.155328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.119854 restraints weight = 12753.719| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.53 r_work: 0.3258 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10891 Z= 0.130 Angle : 0.644 16.828 14847 Z= 0.305 Chirality : 0.043 0.375 1714 Planarity : 0.004 0.062 1812 Dihedral : 9.813 123.172 1612 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.84 % Favored : 93.01 % Rotamer: Outliers : 1.64 % Allowed : 17.09 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.24), residues: 1301 helix: 1.37 (0.18), residues: 868 sheet: -2.13 (1.02), residues: 22 loop : -1.62 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1131 TYR 0.017 0.001 TYR A 578 PHE 0.013 0.001 PHE A 301 TRP 0.007 0.001 TRP A1355 HIS 0.004 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00300 (10873) covalent geometry : angle 0.60757 (14802) SS BOND : bond 0.00201 ( 9) SS BOND : angle 0.83570 ( 18) hydrogen bonds : bond 0.04237 ( 605) hydrogen bonds : angle 3.76934 ( 1725) link_BETA1-3 : bond 0.00853 ( 1) link_BETA1-3 : angle 2.43528 ( 3) link_BETA1-4 : bond 0.00089 ( 2) link_BETA1-4 : angle 5.18290 ( 6) link_BETA1-6 : bond 0.00582 ( 1) link_BETA1-6 : angle 1.93309 ( 3) link_NAG-ASN : bond 0.00489 ( 5) link_NAG-ASN : angle 5.67730 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3834.19 seconds wall clock time: 65 minutes 51.25 seconds (3951.25 seconds total)