Starting phenix.real_space_refine on Thu Sep 18 19:12:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5x6o_6708/09_2025/5x6o_6708.cif Found real_map, /net/cci-nas-00/data/ceres_data/5x6o_6708/09_2025/5x6o_6708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5x6o_6708/09_2025/5x6o_6708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5x6o_6708/09_2025/5x6o_6708.map" model { file = "/net/cci-nas-00/data/ceres_data/5x6o_6708/09_2025/5x6o_6708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5x6o_6708/09_2025/5x6o_6708.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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 70 5.16 5 C 12229 2.51 5 N 3377 2.21 5 O 3633 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19309 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 14240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1997, 14240 Classifications: {'peptide': 1997} Incomplete info: {'truncation_to_alanine': 584} Link IDs: {'PTRANS': 58, 'TRANS': 1938} Chain breaks: 26 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 2153 Unresolved non-hydrogen angles: 2755 Unresolved non-hydrogen dihedrals: 1829 Unresolved non-hydrogen chiralities: 195 Planarities with less than four sites: {'TYR:plan': 30, 'GLN:plan1': 17, 'PHE:plan': 31, 'GLU:plan': 39, 'ASP:plan': 28, 'ASN:plan1': 39, 'TRP:plan': 11, 'ARG:plan': 28, 'HIS:plan': 14} Unresolved non-hydrogen planarities: 1130 Chain: "G" Number of atoms: 5069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5069 Classifications: {'peptide': 704} Incomplete info: {'truncation_to_alanine': 210} Link IDs: {'PTRANS': 25, 'TRANS': 678} Chain breaks: 12 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 669 Unresolved non-hydrogen angles: 834 Unresolved non-hydrogen dihedrals: 528 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'ARG:plan': 10, 'GLU:plan': 21, 'PHE:plan': 4, 'ASP:plan': 15, 'GLN:plan1': 14, 'ASN:plan1': 15, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 316 Time building chain proxies: 4.76, per 1000 atoms: 0.25 Number of scatterers: 19309 At special positions: 0 Unit cell: (144.45, 128.25, 175.5, 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 70 16.00 O 3633 8.00 N 3377 7.00 C 12229 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 493 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 5242 Ramachandran restraints generated. 2621 Oldfield, 0 Emsley, 2621 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5236 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 1 sheets defined 70.2% alpha, 0.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'C' and resid 237 through 254 removed outlier: 4.077A pdb=" N LEU C 241 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE C 244 " --> pdb=" O GLN C 240 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 247 " --> pdb=" O TYR C 243 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N CYS C 252 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG C 254 " --> pdb=" O TYR C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 285 removed outlier: 4.076A pdb=" N LEU C 271 " --> pdb=" O CYS C 267 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N THR C 276 " --> pdb=" O LYS C 272 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N THR C 277 " --> pdb=" O PHE C 273 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN C 284 " --> pdb=" O HIS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 307 removed outlier: 3.933A pdb=" N TYR C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 305 " --> pdb=" O ARG C 301 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS C 306 " --> pdb=" O LEU C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 319 removed outlier: 4.200A pdb=" N HIS C 318 " --> pdb=" O CYS C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 324 removed outlier: 3.811A pdb=" N GLN C 323 " --> pdb=" O PRO C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 355 removed outlier: 4.388A pdb=" N VAL C 346 " --> pdb=" O ALA C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 379 removed outlier: 3.690A pdb=" N SER C 378 " --> pdb=" O PRO C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 397 removed outlier: 3.710A pdb=" N LYS C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 421 removed outlier: 4.003A pdb=" N VAL C 417 " --> pdb=" O LEU C 413 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 449 removed outlier: 3.620A pdb=" N VAL C 441 " --> pdb=" O ASN C 437 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN C 444 " --> pdb=" O SER C 440 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR C 445 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR C 449 " --> pdb=" O THR C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 470 removed outlier: 4.029A pdb=" N TRP C 458 " --> pdb=" O ARG C 454 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 460 " --> pdb=" O THR C 456 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 461 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY C 463 " --> pdb=" O THR C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 473 No H-bonds generated for 'chain 'C' and resid 471 through 473' Processing helix chain 'C' and resid 490 through 495 removed outlier: 3.688A pdb=" N ILE C 495 " --> pdb=" O HIS C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 504 removed outlier: 3.523A pdb=" N ARG C 504 " --> pdb=" O PRO C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 527 removed outlier: 4.006A pdb=" N ASN C 525 " --> pdb=" O ILE C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 554 Processing helix chain 'C' and resid 568 through 579 Processing helix chain 'C' and resid 581 through 590 removed outlier: 4.003A pdb=" N ARG C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 597 removed outlier: 3.753A pdb=" N PHE C 595 " --> pdb=" O ILE C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 618 removed outlier: 4.241A pdb=" N LEU C 611 " --> pdb=" O HIS C 607 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN C 618 " --> pdb=" O PHE C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 removed outlier: 3.534A pdb=" N THR C 632 " --> pdb=" O VAL C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 639 through 655 removed outlier: 3.537A pdb=" N ASP C 644 " --> pdb=" O ASN C 640 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 648 " --> pdb=" O ASP C 644 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN C 655 " --> pdb=" O ILE C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 658 through 677 removed outlier: 3.935A pdb=" N ILE C 663 " --> pdb=" O TYR C 659 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N MET C 664 " --> pdb=" O SER C 660 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE C 669 " --> pdb=" O MET C 665 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS C 670 " --> pdb=" O THR C 666 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS C 674 " --> pdb=" O LYS C 670 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 685 removed outlier: 3.502A pdb=" N SER C 685 " --> pdb=" O TYR C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 699 removed outlier: 3.813A pdb=" N ARG C 693 " --> pdb=" O PRO C 689 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN C 694 " --> pdb=" O VAL C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 700 through 702 No H-bonds generated for 'chain 'C' and resid 700 through 702' Processing helix chain 'C' and resid 704 through 714 removed outlier: 3.742A pdb=" N GLU C 711 " --> pdb=" O GLN C 707 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU C 712 " --> pdb=" O ASN C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 733 removed outlier: 6.003A pdb=" N ARG C 726 " --> pdb=" O ASP C 722 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR C 727 " --> pdb=" O ILE C 723 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE C 728 " --> pdb=" O PHE C 724 " (cutoff:3.500A) Proline residue: C 730 - end of helix removed outlier: 3.867A pdb=" N ILE C 733 " --> pdb=" O ILE C 729 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 750 removed outlier: 3.693A pdb=" N CYS C 749 " --> pdb=" O ALA C 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 768 removed outlier: 3.753A pdb=" N VAL C 761 " --> pdb=" O ASN C 757 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN C 762 " --> pdb=" O GLN C 758 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS C 765 " --> pdb=" O VAL C 761 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER C 768 " --> pdb=" O LEU C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 780 Processing helix chain 'C' and resid 783 through 792 Processing helix chain 'C' and resid 803 through 807 Processing helix chain 'C' and resid 813 through 819 removed outlier: 3.885A pdb=" N THR C 817 " --> pdb=" O LEU C 813 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS C 818 " --> pdb=" O ALA C 814 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 819 " --> pdb=" O GLU C 815 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 813 through 819' Processing helix chain 'C' and resid 820 through 822 No H-bonds generated for 'chain 'C' and resid 820 through 822' Processing helix chain 'C' and resid 831 through 844 removed outlier: 3.833A pdb=" N ASN C 835 " --> pdb=" O SER C 831 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 838 " --> pdb=" O ALA C 834 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 841 " --> pdb=" O ILE C 837 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE C 843 " --> pdb=" O CYS C 839 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU C 844 " --> pdb=" O SER C 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 851 Processing helix chain 'C' and resid 853 through 859 removed outlier: 4.470A pdb=" N LYS C 859 " --> pdb=" O GLY C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 892 removed outlier: 3.614A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLN C 873 " --> pdb=" O GLU C 869 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS C 874 " --> pdb=" O GLN C 870 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU C 881 " --> pdb=" O GLN C 877 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLY C 882 " --> pdb=" O ASP C 878 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE C 884 " --> pdb=" O ILE C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 916 removed outlier: 4.168A pdb=" N ILE C 914 " --> pdb=" O ILE C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 924 Processing helix chain 'C' and resid 925 through 938 removed outlier: 3.529A pdb=" N ILE C 931 " --> pdb=" O ALA C 927 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY C 936 " --> pdb=" O CYS C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 941 No H-bonds generated for 'chain 'C' and resid 939 through 941' Processing helix chain 'C' and resid 942 through 956 removed outlier: 3.659A pdb=" N LEU C 952 " --> pdb=" O ARG C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 976 removed outlier: 3.850A pdb=" N PHE C 972 " --> pdb=" O SER C 968 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE C 973 " --> pdb=" O LEU C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 980 Processing helix chain 'C' and resid 982 through 998 removed outlier: 3.513A pdb=" N ASN C 986 " --> pdb=" O GLY C 982 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR C 994 " --> pdb=" O SER C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 1007 through 1017 removed outlier: 4.382A pdb=" N THR C1011 " --> pdb=" O LYS C1007 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU C1012 " --> pdb=" O PRO C1008 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C1013 " --> pdb=" O TYR C1009 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C1014 " --> pdb=" O THR C1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1021 Processing helix chain 'C' and resid 1029 through 1040 removed outlier: 3.713A pdb=" N SER C1038 " --> pdb=" O ASN C1034 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR C1039 " --> pdb=" O LYS C1035 " (cutoff:3.500A) Processing helix chain 'C' and resid 1042 through 1050 removed outlier: 3.690A pdb=" N ALA C1047 " --> pdb=" O ILE C1043 " (cutoff:3.500A) Processing helix chain 'C' and resid 1056 through 1076 removed outlier: 3.782A pdb=" N LEU C1062 " --> pdb=" O ILE C1058 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG C1071 " --> pdb=" O VAL C1067 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR C1074 " --> pdb=" O ARG C1070 " (cutoff:3.500A) Processing helix chain 'C' and resid 1091 through 1105 removed outlier: 3.770A pdb=" N LEU C1095 " --> pdb=" O ILE C1091 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C1099 " --> pdb=" O LEU C1095 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS C1103 " --> pdb=" O LEU C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1122 removed outlier: 3.660A pdb=" N LYS C1115 " --> pdb=" O ASP C1111 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C1117 " --> pdb=" O CYS C1113 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE C1120 " --> pdb=" O CYS C1116 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C1121 " --> pdb=" O ALA C1117 " (cutoff:3.500A) Processing helix chain 'C' and resid 1148 through 1161 removed outlier: 3.612A pdb=" N LYS C1154 " --> pdb=" O VAL C1150 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE C1155 " --> pdb=" O GLN C1151 " (cutoff:3.500A) Processing helix chain 'C' and resid 1164 through 1169 Processing helix chain 'C' and resid 1175 through 1189 removed outlier: 4.129A pdb=" N PHE C1179 " --> pdb=" O SER C1175 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA C1181 " --> pdb=" O GLN C1177 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU C1182 " --> pdb=" O LEU C1178 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL C1183 " --> pdb=" O PHE C1179 " (cutoff:3.500A) Processing helix chain 'C' and resid 1193 through 1199 Processing helix chain 'C' and resid 1216 through 1221 removed outlier: 4.036A pdb=" N SER C1220 " --> pdb=" O PHE C1216 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS C1221 " --> pdb=" O ASN C1217 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1216 through 1221' Processing helix chain 'C' and resid 1243 through 1250 Processing helix chain 'C' and resid 1253 through 1260 removed outlier: 4.081A pdb=" N TRP C1257 " --> pdb=" O GLY C1253 " (cutoff:3.500A) Processing helix chain 'C' and resid 1260 through 1268 Processing helix chain 'C' and resid 1273 through 1276 removed outlier: 3.679A pdb=" N LEU C1276 " --> pdb=" O ASN C1273 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1273 through 1276' Processing helix chain 'C' and resid 1277 through 1283 removed outlier: 3.685A pdb=" N ILE C1283 " --> pdb=" O PHE C1279 " (cutoff:3.500A) Processing helix chain 'C' and resid 1290 through 1305 removed outlier: 3.597A pdb=" N LEU C1294 " --> pdb=" O LEU C1290 " (cutoff:3.500A) Proline residue: C1296 - end of helix removed outlier: 3.724A pdb=" N ILE C1302 " --> pdb=" O ILE C1298 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ILE C1303 " --> pdb=" O SER C1299 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C1305 " --> pdb=" O ASP C1301 " (cutoff:3.500A) Processing helix chain 'C' and resid 1312 through 1327 removed outlier: 3.976A pdb=" N LEU C1316 " --> pdb=" O TYR C1312 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY C1318 " --> pdb=" O ASP C1314 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE C1319 " --> pdb=" O ILE C1315 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C1320 " --> pdb=" O LEU C1316 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE C1321 " --> pdb=" O ASN C1317 " (cutoff:3.500A) Processing helix chain 'C' and resid 1334 through 1368 removed outlier: 3.643A pdb=" N GLN C1338 " --> pdb=" O MET C1334 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG C1343 " --> pdb=" O VAL C1339 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET C1344 " --> pdb=" O ASP C1340 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL C1352 " --> pdb=" O SER C1348 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE C1353 " --> pdb=" O ILE C1349 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR C1367 " --> pdb=" O PHE C1363 " (cutoff:3.500A) Processing helix chain 'C' and resid 1377 through 1390 removed outlier: 4.049A pdb=" N THR C1381 " --> pdb=" O LYS C1377 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU C1390 " --> pdb=" O LEU C1386 " (cutoff:3.500A) Processing helix chain 'C' and resid 1395 through 1406 Processing helix chain 'C' and resid 1409 through 1423 removed outlier: 3.531A pdb=" N TYR C1416 " --> pdb=" O ARG C1412 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU C1417 " --> pdb=" O SER C1413 " (cutoff:3.500A) Processing helix chain 'C' and resid 1427 through 1446 removed outlier: 3.593A pdb=" N LEU C1435 " --> pdb=" O ASN C1431 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS C1436 " --> pdb=" O GLY C1432 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C1440 " --> pdb=" O LYS C1436 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY C1446 " --> pdb=" O TYR C1442 " (cutoff:3.500A) Processing helix chain 'C' and resid 1447 through 1458 removed outlier: 4.058A pdb=" N LEU C1451 " --> pdb=" O ASP C1447 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE C1458 " --> pdb=" O VAL C1454 " (cutoff:3.500A) Processing helix chain 'C' and resid 1462 through 1469 removed outlier: 3.902A pdb=" N LYS C1466 " --> pdb=" O ASN C1462 " (cutoff:3.500A) Processing helix chain 'C' and resid 1470 through 1474 removed outlier: 3.733A pdb=" N GLU C1474 " --> pdb=" O GLN C1471 " (cutoff:3.500A) Processing helix chain 'C' and resid 1475 through 1489 removed outlier: 3.669A pdb=" N ALA C1479 " --> pdb=" O ASN C1475 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN C1484 " --> pdb=" O GLN C1480 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL C1485 " --> pdb=" O ASP C1481 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU C1486 " --> pdb=" O CYS C1482 " (cutoff:3.500A) Processing helix chain 'C' and resid 1494 through 1506 Processing helix chain 'C' and resid 1508 through 1513 removed outlier: 4.238A pdb=" N ILE C1512 " --> pdb=" O LEU C1508 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE C1513 " --> pdb=" O TYR C1509 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1508 through 1513' Processing helix chain 'C' and resid 1532 through 1546 removed outlier: 4.248A pdb=" N SER C1536 " --> pdb=" O LYS C1532 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE C1537 " --> pdb=" O GLU C1533 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU C1540 " --> pdb=" O SER C1536 " (cutoff:3.500A) Processing helix chain 'C' and resid 1547 through 1560 removed outlier: 3.856A pdb=" N ASN C1553 " --> pdb=" O GLN C1549 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TRP C1554 " --> pdb=" O THR C1550 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N SER C1560 " --> pdb=" O GLU C1556 " (cutoff:3.500A) Processing helix chain 'C' and resid 1566 through 1584 removed outlier: 3.700A pdb=" N LEU C1570 " --> pdb=" O ASP C1566 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU C1571 " --> pdb=" O ARG C1567 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C1575 " --> pdb=" O LEU C1571 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA C1581 " --> pdb=" O LYS C1577 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C1583 " --> pdb=" O LEU C1579 " (cutoff:3.500A) Processing helix chain 'C' and resid 1586 through 1602 removed outlier: 3.512A pdb=" N LYS C1592 " --> pdb=" O LEU C1588 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU C1600 " --> pdb=" O ASN C1596 " (cutoff:3.500A) Processing helix chain 'C' and resid 1614 through 1616 No H-bonds generated for 'chain 'C' and resid 1614 through 1616' Processing helix chain 'C' and resid 1617 through 1634 removed outlier: 3.907A pdb=" N LYS C1623 " --> pdb=" O ASN C1619 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU C1627 " --> pdb=" O LYS C1623 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR C1628 " --> pdb=" O LEU C1624 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP C1629 " --> pdb=" O HIS C1625 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C1634 " --> pdb=" O LEU C1630 " (cutoff:3.500A) Processing helix chain 'C' and resid 1641 through 1653 removed outlier: 3.867A pdb=" N THR C1647 " --> pdb=" O LYS C1643 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE C1648 " --> pdb=" O SER C1644 " (cutoff:3.500A) Processing helix chain 'C' and resid 1654 through 1657 Processing helix chain 'C' and resid 1659 through 1677 removed outlier: 3.563A pdb=" N ASN C1663 " --> pdb=" O ASP C1659 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE C1666 " --> pdb=" O PRO C1662 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU C1676 " --> pdb=" O SER C1672 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS C1677 " --> pdb=" O PHE C1673 " (cutoff:3.500A) Processing helix chain 'C' and resid 1679 through 1700 removed outlier: 3.518A pdb=" N ALA C1684 " --> pdb=" O GLU C1680 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP C1685 " --> pdb=" O GLN C1681 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS C1688 " --> pdb=" O ALA C1684 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE C1690 " --> pdb=" O LEU C1686 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE C1691 " --> pdb=" O GLY C1687 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN C1699 " --> pdb=" O GLN C1695 " (cutoff:3.500A) Processing helix chain 'C' and resid 1702 through 1713 removed outlier: 3.952A pdb=" N ALA C1706 " --> pdb=" O ARG C1702 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU C1708 " --> pdb=" O ASP C1704 " (cutoff:3.500A) Processing helix chain 'C' and resid 1718 through 1732 removed outlier: 4.182A pdb=" N GLU C1722 " --> pdb=" O LEU C1718 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU C1723 " --> pdb=" O PRO C1719 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS C1731 " --> pdb=" O GLU C1727 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN C1732 " --> pdb=" O ILE C1728 " (cutoff:3.500A) Processing helix chain 'C' and resid 1734 through 1750 removed outlier: 4.181A pdb=" N ALA C1738 " --> pdb=" O GLU C1734 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE C1741 " --> pdb=" O ARG C1737 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL C1742 " --> pdb=" O ALA C1738 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU C1747 " --> pdb=" O GLN C1743 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN C1750 " --> pdb=" O HIS C1746 " (cutoff:3.500A) Processing helix chain 'C' and resid 1758 through 1774 removed outlier: 3.609A pdb=" N LEU C1764 " --> pdb=" O ARG C1760 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU C1773 " --> pdb=" O GLU C1769 " (cutoff:3.500A) Processing helix chain 'C' and resid 1778 through 1790 removed outlier: 4.498A pdb=" N ILE C1783 " --> pdb=" O SER C1779 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS C1784 " --> pdb=" O GLU C1780 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN C1785 " --> pdb=" O GLN C1781 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR C1786 " --> pdb=" O ILE C1782 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP C1788 " --> pdb=" O LYS C1784 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE C1789 " --> pdb=" O GLN C1785 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE C1790 " --> pdb=" O TYR C1786 " (cutoff:3.500A) Processing helix chain 'C' and resid 1791 through 1793 No H-bonds generated for 'chain 'C' and resid 1791 through 1793' Processing helix chain 'C' and resid 1798 through 1813 removed outlier: 3.577A pdb=" N SER C1802 " --> pdb=" O LYS C1798 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLY C1804 " --> pdb=" O TYR C1800 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU C1811 " --> pdb=" O TYR C1807 " (cutoff:3.500A) Processing helix chain 'C' and resid 1814 through 1814 No H-bonds generated for 'chain 'C' and resid 1814 through 1814' Processing helix chain 'C' and resid 1823 through 1827 Processing helix chain 'C' and resid 1828 through 1841 removed outlier: 4.691A pdb=" N LEU C1835 " --> pdb=" O SER C1831 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA C1836 " --> pdb=" O TYR C1832 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE C1837 " --> pdb=" O PHE C1833 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C1838 " --> pdb=" O LEU C1834 " (cutoff:3.500A) Processing helix chain 'C' and resid 1846 through 1865 removed outlier: 3.605A pdb=" N LYS C1850 " --> pdb=" O GLU C1846 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL C1851 " --> pdb=" O ASN C1847 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ILE C1852 " --> pdb=" O LEU C1848 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP C1857 " --> pdb=" O THR C1853 " (cutoff:3.500A) Processing helix chain 'C' and resid 1870 through 1881 removed outlier: 3.508A pdb=" N ILE C1881 " --> pdb=" O ALA C1877 " (cutoff:3.500A) Processing helix chain 'C' and resid 1881 through 1891 removed outlier: 4.350A pdb=" N VAL C1885 " --> pdb=" O ILE C1881 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU C1886 " --> pdb=" O CYS C1882 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN C1890 " --> pdb=" O GLU C1886 " (cutoff:3.500A) Processing helix chain 'C' and resid 1895 through 1901 removed outlier: 4.443A pdb=" N PHE C1899 " --> pdb=" O TYR C1895 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL C1900 " --> pdb=" O ILE C1896 " (cutoff:3.500A) Processing helix chain 'C' and resid 1901 through 1907 removed outlier: 3.939A pdb=" N LEU C1905 " --> pdb=" O LEU C1901 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER C1906 " --> pdb=" O THR C1902 " (cutoff:3.500A) Processing helix chain 'C' and resid 1919 through 1928 removed outlier: 4.171A pdb=" N LEU C1923 " --> pdb=" O ILE C1919 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU C1924 " --> pdb=" O MET C1920 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER C1925 " --> pdb=" O HIS C1921 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU C1926 " --> pdb=" O ILE C1922 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C1927 " --> pdb=" O LEU C1923 " (cutoff:3.500A) Processing helix chain 'C' and resid 1928 through 1934 Processing helix chain 'C' and resid 1934 through 1950 removed outlier: 3.656A pdb=" N THR C1939 " --> pdb=" O LEU C1935 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA C1940 " --> pdb=" O TRP C1936 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N SER C1947 " --> pdb=" O ASN C1943 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS C1948 " --> pdb=" O SER C1944 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG C1949 " --> pdb=" O ASN C1945 " (cutoff:3.500A) Processing helix chain 'C' and resid 1956 through 1973 Proline residue: C1967 - end of helix Processing helix chain 'C' and resid 1982 through 2001 removed outlier: 4.511A pdb=" N ASP C1988 " --> pdb=" O VAL C1984 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL C1989 " --> pdb=" O CYS C1985 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS C1990 " --> pdb=" O LEU C1986 " (cutoff:3.500A) Processing helix chain 'C' and resid 2040 through 2045 removed outlier: 3.861A pdb=" N VAL C2043 " --> pdb=" O PHE C2040 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL C2044 " --> pdb=" O ARG C2041 " (cutoff:3.500A) Processing helix chain 'C' and resid 2083 through 2085 No H-bonds generated for 'chain 'C' and resid 2083 through 2085' Processing helix chain 'C' and resid 2086 through 2103 removed outlier: 3.632A pdb=" N TYR C2090 " --> pdb=" O GLN C2086 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C2094 " --> pdb=" O TYR C2090 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP C2098 " --> pdb=" O ALA C2094 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER C2102 " --> pdb=" O ASP C2098 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS C2103 " --> pdb=" O PHE C2099 " (cutoff:3.500A) Processing helix chain 'C' and resid 2107 through 2111 Processing helix chain 'C' and resid 2137 through 2148 removed outlier: 3.996A pdb=" N ILE C2141 " --> pdb=" O THR C2137 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS C2145 " --> pdb=" O ILE C2141 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TYR C2146 " --> pdb=" O LEU C2142 " (cutoff:3.500A) Processing helix chain 'C' and resid 2156 through 2164 removed outlier: 3.828A pdb=" N ASP C2160 " --> pdb=" O LYS C2156 " (cutoff:3.500A) Processing helix chain 'C' and resid 2173 through 2179 Processing helix chain 'C' and resid 2184 through 2191 removed outlier: 3.978A pdb=" N TRP C2188 " --> pdb=" O ILE C2184 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE C2189 " --> pdb=" O LEU C2185 " (cutoff:3.500A) Processing helix chain 'C' and resid 2195 through 2209 removed outlier: 3.536A pdb=" N ASN C2201 " --> pdb=" O ILE C2197 " (cutoff:3.500A) Processing helix chain 'C' and resid 2210 through 2221 removed outlier: 4.467A pdb=" N VAL C2216 " --> pdb=" O VAL C2212 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N HIS C2218 " --> pdb=" O ALA C2214 " (cutoff:3.500A) Processing helix chain 'C' and resid 2265 through 2271 removed outlier: 3.763A pdb=" N LEU C2269 " --> pdb=" O THR C2265 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP C2270 " --> pdb=" O PRO C2266 " (cutoff:3.500A) Processing helix chain 'C' and resid 2278 through 2296 removed outlier: 3.727A pdb=" N LYS C2283 " --> pdb=" O GLY C2279 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL C2287 " --> pdb=" O LYS C2283 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG C2293 " --> pdb=" O LEU C2289 " (cutoff:3.500A) Processing helix chain 'C' and resid 2296 through 2302 removed outlier: 3.701A pdb=" N MET C2300 " --> pdb=" O GLU C2296 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL C2302 " --> pdb=" O ALA C2298 " (cutoff:3.500A) Processing helix chain 'C' and resid 2304 through 2310 removed outlier: 3.677A pdb=" N TYR C2308 " --> pdb=" O GLU C2304 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG C2310 " --> pdb=" O ILE C2306 " (cutoff:3.500A) Processing helix chain 'C' and resid 2317 through 2319 No H-bonds generated for 'chain 'C' and resid 2317 through 2319' Processing helix chain 'C' and resid 2320 through 2329 removed outlier: 3.902A pdb=" N ARG C2324 " --> pdb=" O LEU C2320 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE C2327 " --> pdb=" O LEU C2323 " (cutoff:3.500A) Processing helix chain 'C' and resid 2341 through 2353 removed outlier: 3.703A pdb=" N LEU C2347 " --> pdb=" O GLN C2343 " (cutoff:3.500A) Processing helix chain 'C' and resid 2354 through 2359 Processing helix chain 'C' and resid 2361 through 2365 Processing helix chain 'G' and resid 4 through 16 Processing helix chain 'G' and resid 25 through 37 removed outlier: 3.594A pdb=" N GLN G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Proline residue: G 32 - end of helix Processing helix chain 'G' and resid 42 through 57 removed outlier: 5.029A pdb=" N VAL G 48 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N THR G 49 " --> pdb=" O THR G 45 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR G 50 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR G 51 " --> pdb=" O GLU G 47 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU G 53 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN G 54 " --> pdb=" O THR G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 80 removed outlier: 3.859A pdb=" N GLU G 74 " --> pdb=" O LYS G 70 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER G 76 " --> pdb=" O GLN G 72 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N MET G 77 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 100 removed outlier: 4.232A pdb=" N ASN G 94 " --> pdb=" O GLU G 90 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL G 98 " --> pdb=" O ASN G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 103 No H-bonds generated for 'chain 'G' and resid 101 through 103' Processing helix chain 'G' and resid 105 through 105 No H-bonds generated for 'chain 'G' and resid 105 through 105' Processing helix chain 'G' and resid 106 through 125 removed outlier: 3.708A pdb=" N LEU G 111 " --> pdb=" O HIS G 107 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA G 112 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU G 114 " --> pdb=" O GLU G 110 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS G 115 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU G 118 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN G 119 " --> pdb=" O LYS G 115 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU G 122 " --> pdb=" O LEU G 118 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS G 125 " --> pdb=" O LEU G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 151 removed outlier: 3.824A pdb=" N THR G 150 " --> pdb=" O PRO G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 189 removed outlier: 4.144A pdb=" N SER G 182 " --> pdb=" O LYS G 178 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU G 185 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS G 187 " --> pdb=" O ASP G 183 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS G 188 " --> pdb=" O ASN G 184 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN G 189 " --> pdb=" O LEU G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 213 removed outlier: 3.554A pdb=" N GLU G 208 " --> pdb=" O SER G 204 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE G 210 " --> pdb=" O PHE G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 265 removed outlier: 3.502A pdb=" N SER G 256 " --> pdb=" O LYS G 252 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR G 264 " --> pdb=" O ARG G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 266 through 287 removed outlier: 4.017A pdb=" N ILE G 271 " --> pdb=" O LEU G 267 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASP G 272 " --> pdb=" O ASP G 268 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP G 277 " --> pdb=" O THR G 273 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL G 280 " --> pdb=" O GLU G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 308 removed outlier: 4.373A pdb=" N PHE G 298 " --> pdb=" O LEU G 294 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA G 301 " --> pdb=" O PRO G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 333 removed outlier: 3.852A pdb=" N ARG G 331 " --> pdb=" O CYS G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 355 through 380 removed outlier: 3.685A pdb=" N ILE G 360 " --> pdb=" O GLN G 356 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP G 361 " --> pdb=" O TYR G 357 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE G 364 " --> pdb=" O ILE G 360 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE G 365 " --> pdb=" O ASP G 361 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU G 373 " --> pdb=" O PHE G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 391 removed outlier: 4.389A pdb=" N PHE G 390 " --> pdb=" O THR G 386 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE G 391 " --> pdb=" O TYR G 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 386 through 391' Processing helix chain 'G' and resid 392 through 407 removed outlier: 3.880A pdb=" N PHE G 401 " --> pdb=" O LYS G 397 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL G 402 " --> pdb=" O SER G 398 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU G 405 " --> pdb=" O PHE G 401 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 434 removed outlier: 3.622A pdb=" N ILE G 418 " --> pdb=" O MET G 414 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE G 419 " --> pdb=" O VAL G 415 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N SER G 420 " --> pdb=" O ASN G 416 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL G 424 " --> pdb=" O SER G 420 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL G 425 " --> pdb=" O ALA G 421 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR G 429 " --> pdb=" O VAL G 425 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU G 433 " --> pdb=" O THR G 429 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN G 434 " --> pdb=" O SER G 430 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 443 Processing helix chain 'G' and resid 446 through 456 Processing helix chain 'G' and resid 457 through 462 removed outlier: 4.024A pdb=" N GLU G 462 " --> pdb=" O TYR G 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 502 through 506 removed outlier: 3.749A pdb=" N SER G 505 " --> pdb=" O GLY G 502 " (cutoff:3.500A) Processing helix chain 'G' and resid 536 through 547 removed outlier: 3.506A pdb=" N MET G 541 " --> pdb=" O ILE G 537 " (cutoff:3.500A) Processing helix chain 'G' and resid 548 through 550 No H-bonds generated for 'chain 'G' and resid 548 through 550' Processing helix chain 'G' and resid 551 through 564 removed outlier: 3.634A pdb=" N PHE G 556 " --> pdb=" O VAL G 552 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU G 557 " --> pdb=" O LEU G 553 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASN G 558 " --> pdb=" O ASN G 554 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR G 563 " --> pdb=" O LEU G 559 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY G 564 " --> pdb=" O LEU G 560 " (cutoff:3.500A) Processing helix chain 'G' and resid 567 through 572 removed outlier: 4.251A pdb=" N ASN G 571 " --> pdb=" O ALA G 567 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 593 removed outlier: 3.825A pdb=" N HIS G 577 " --> pdb=" O GLU G 573 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG G 584 " --> pdb=" O LYS G 580 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU G 585 " --> pdb=" O PHE G 581 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE G 590 " --> pdb=" O GLN G 586 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR G 593 " --> pdb=" O MET G 589 " (cutoff:3.500A) Processing helix chain 'G' and resid 600 through 622 removed outlier: 3.509A pdb=" N LEU G 612 " --> pdb=" O ILE G 608 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR G 613 " --> pdb=" O GLU G 609 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE G 614 " --> pdb=" O HIS G 610 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE G 615 " --> pdb=" O THR G 611 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS G 622 " --> pdb=" O LEU G 618 " (cutoff:3.500A) Processing helix chain 'G' and resid 634 through 647 removed outlier: 3.901A pdb=" N ILE G 639 " --> pdb=" O GLU G 635 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE G 645 " --> pdb=" O SER G 641 " (cutoff:3.500A) Processing helix chain 'G' and resid 648 through 651 Processing helix chain 'G' and resid 656 through 667 removed outlier: 3.676A pdb=" N MET G 660 " --> pdb=" O ASN G 656 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP G 662 " --> pdb=" O ARG G 658 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS G 663 " --> pdb=" O GLU G 659 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG G 664 " --> pdb=" O MET G 660 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N HIS G 665 " --> pdb=" O ARG G 661 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU G 666 " --> pdb=" O ASP G 662 " (cutoff:3.500A) Processing helix chain 'G' and resid 668 through 679 removed outlier: 4.283A pdb=" N ALA G 679 " --> pdb=" O ILE G 675 " (cutoff:3.500A) Processing helix chain 'G' and resid 693 through 710 removed outlier: 3.524A pdb=" N LEU G 697 " --> pdb=" O ILE G 693 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU G 701 " --> pdb=" O LEU G 697 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN G 702 " --> pdb=" O LYS G 698 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS G 703 " --> pdb=" O MET G 699 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE G 708 " --> pdb=" O ARG G 704 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET G 709 " --> pdb=" O THR G 705 " (cutoff:3.500A) Processing helix chain 'G' and resid 717 through 724 removed outlier: 3.924A pdb=" N ALA G 721 " --> pdb=" O PHE G 717 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE G 724 " --> pdb=" O MET G 720 " (cutoff:3.500A) Processing helix chain 'G' and resid 735 through 744 removed outlier: 4.264A pdb=" N SER G 740 " --> pdb=" O GLU G 736 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU G 741 " --> pdb=" O GLU G 737 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR G 742 " --> pdb=" O ALA G 738 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 236 through 238 916 hydrogen bonds defined for protein. 2700 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: 4.02 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3332 1.30 - 1.44: 4803 1.44 - 1.57: 11323 1.57 - 1.70: 1 1.70 - 1.84: 109 Bond restraints: 19568 Sorted by residual: bond pdb=" C TYR C1355 " pdb=" O TYR C1355 " ideal model delta sigma weight residual 1.237 1.171 0.066 1.16e-02 7.43e+03 3.22e+01 bond pdb=" C TYR C1254 " pdb=" O TYR C1254 " ideal model delta sigma weight residual 1.236 1.171 0.065 1.19e-02 7.06e+03 3.01e+01 bond pdb=" CA ILE C 845 " pdb=" C ILE C 845 " ideal model delta sigma weight residual 1.523 1.578 -0.055 1.27e-02 6.20e+03 1.91e+01 bond pdb=" N TYR C1254 " pdb=" CA TYR C1254 " ideal model delta sigma weight residual 1.459 1.415 0.044 1.24e-02 6.50e+03 1.23e+01 bond pdb=" C TYR C1297 " pdb=" O TYR C1297 " ideal model delta sigma weight residual 1.236 1.196 0.039 1.18e-02 7.18e+03 1.11e+01 ... (remaining 19563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 25634 2.31 - 4.62: 762 4.62 - 6.93: 135 6.93 - 9.24: 54 9.24 - 11.55: 8 Bond angle restraints: 26593 Sorted by residual: angle pdb=" N PRO C 385 " pdb=" CA PRO C 385 " pdb=" CB PRO C 385 " ideal model delta sigma weight residual 101.83 110.00 -8.17 8.40e-01 1.42e+00 9.47e+01 angle pdb=" N PRO C2018 " pdb=" CA PRO C2018 " pdb=" CB PRO C2018 " ideal model delta sigma weight residual 103.25 111.52 -8.27 1.05e+00 9.07e-01 6.21e+01 angle pdb=" N PRO G 146 " pdb=" CA PRO G 146 " pdb=" CB PRO G 146 " ideal model delta sigma weight residual 103.08 110.66 -7.58 9.70e-01 1.06e+00 6.10e+01 angle pdb=" N PRO G 160 " pdb=" CA PRO G 160 " pdb=" CB PRO G 160 " ideal model delta sigma weight residual 103.25 111.34 -8.09 1.05e+00 9.07e-01 5.93e+01 angle pdb=" N PRO C 356 " pdb=" CA PRO C 356 " pdb=" CB PRO C 356 " ideal model delta sigma weight residual 103.25 111.18 -7.93 1.05e+00 9.07e-01 5.71e+01 ... (remaining 26588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 11355 17.75 - 35.49: 346 35.49 - 53.24: 78 53.24 - 70.99: 18 70.99 - 88.73: 22 Dihedral angle restraints: 11819 sinusoidal: 3849 harmonic: 7970 Sorted by residual: dihedral pdb=" CA LEU G 444 " pdb=" C LEU G 444 " pdb=" N ILE G 445 " pdb=" CA ILE G 445 " ideal model delta harmonic sigma weight residual 180.00 151.34 28.66 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA PHE G 686 " pdb=" C PHE G 686 " pdb=" N GLU G 687 " pdb=" CA GLU G 687 " ideal model delta harmonic sigma weight residual 180.00 151.39 28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA SER C 656 " pdb=" C SER C 656 " pdb=" N ASP C 657 " pdb=" CA ASP C 657 " ideal model delta harmonic sigma weight residual -180.00 -151.75 -28.25 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 11816 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3008 0.098 - 0.196: 165 0.196 - 0.295: 35 0.295 - 0.393: 6 0.393 - 0.491: 4 Chirality restraints: 3218 Sorted by residual: chirality pdb=" CA PRO G 160 " pdb=" N PRO G 160 " pdb=" C PRO G 160 " pdb=" CB PRO G 160 " both_signs ideal model delta sigma weight residual False 2.72 2.23 0.49 2.00e-01 2.50e+01 6.03e+00 chirality pdb=" CA ASN G 194 " pdb=" N ASN G 194 " pdb=" C ASN G 194 " pdb=" CB ASN G 194 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.93e+00 chirality pdb=" CA PRO G 171 " pdb=" N PRO G 171 " pdb=" C PRO G 171 " pdb=" CB PRO G 171 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.65e+00 ... (remaining 3215 not shown) Planarity restraints: 3431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C2195 " 0.058 5.00e-02 4.00e+02 8.79e-02 1.24e+01 pdb=" N PRO C2196 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO C2196 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C2196 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR C2174 " 0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C TYR C2174 " -0.057 2.00e-02 2.50e+03 pdb=" O TYR C2174 " 0.022 2.00e-02 2.50e+03 pdb=" N MET C2175 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C1297 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.41e+00 pdb=" C TYR C1297 " -0.050 2.00e-02 2.50e+03 pdb=" O TYR C1297 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE C1298 " 0.017 2.00e-02 2.50e+03 ... (remaining 3428 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 139 2.47 - 3.08: 16589 3.08 - 3.69: 27283 3.69 - 4.29: 39462 4.29 - 4.90: 59799 Nonbonded interactions: 143272 Sorted by model distance: nonbonded pdb=" O GLY C1124 " pdb=" CG2 VAL C1125 " model vdw 1.863 3.460 nonbonded pdb=" CG1 VAL C2167 " pdb=" N ASP C2168 " model vdw 2.033 3.540 nonbonded pdb=" O LEU G 638 " pdb=" OG SER G 641 " model vdw 2.034 3.040 nonbonded pdb=" O SER C2285 " pdb=" OG1 THR C2288 " model vdw 2.038 3.040 nonbonded pdb=" O LEU C1570 " pdb=" ND2 ASN C1574 " model vdw 2.082 3.120 ... (remaining 143267 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.350 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 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 : 0.007 0.075 19569 Z= 0.346 Angle : 1.011 11.550 26595 Z= 0.612 Chirality : 0.059 0.491 3218 Planarity : 0.005 0.088 3431 Dihedral : 11.258 88.733 6580 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 2.17 % Allowed : 15.76 % Favored : 82.07 % Rotamer: Outliers : 1.64 % Allowed : 2.29 % Favored : 96.07 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.44 (0.12), residues: 2621 helix: -3.96 (0.08), residues: 1361 sheet: -4.59 (0.61), residues: 26 loop : -3.09 (0.16), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 582 TYR 0.030 0.003 TYR G 539 PHE 0.040 0.003 PHE C1410 TRP 0.026 0.003 TRP C1534 HIS 0.018 0.002 HIS C2241 Details of bonding type rmsd covalent geometry : bond 0.00700 (19568) covalent geometry : angle 1.01046 (26593) SS BOND : bond 0.01035 ( 1) SS BOND : angle 2.52805 ( 2) hydrogen bonds : bond 0.33692 ( 916) hydrogen bonds : angle 11.03078 ( 2700) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5242 Ramachandran restraints generated. 2621 Oldfield, 0 Emsley, 2621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5242 Ramachandran restraints generated. 2621 Oldfield, 0 Emsley, 2621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 385 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 681 TYR cc_start: 0.7553 (t80) cc_final: 0.7301 (t80) REVERT: C 1138 TYR cc_start: 0.3990 (OUTLIER) cc_final: 0.3374 (p90) REVERT: G 196 ASN cc_start: 0.6347 (OUTLIER) cc_final: 0.6043 (t0) REVERT: G 224 GLU cc_start: 0.8237 (tp30) cc_final: 0.7956 (tp30) REVERT: G 541 MET cc_start: 0.8858 (tpp) cc_final: 0.8368 (tpp) REVERT: G 544 TRP cc_start: 0.8431 (t-100) cc_final: 0.8221 (t-100) outliers start: 28 outliers final: 12 residues processed: 408 average time/residue: 0.1726 time to fit residues: 104.9847 Evaluate side-chains 216 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 202 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 1126 LEU Chi-restraints excluded: chain C residue 1138 TYR Chi-restraints excluded: chain C residue 2179 ASP Chi-restraints excluded: chain C residue 2209 SER Chi-restraints excluded: chain C residue 2246 CYS Chi-restraints excluded: chain C residue 2265 THR Chi-restraints excluded: chain C residue 2357 LEU Chi-restraints excluded: chain G residue 196 ASN Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 287 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.0170 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 overall best weight: 1.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 270 GLN ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 633 GLN C 640 ASN C 835 ASN C 877 GLN C 885 GLN ** C 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1049 ASN C1185 GLN C1423 GLN C1480 GLN C1625 HIS C2229 ASN C2314 HIS ** C2325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2349 GLN G 334 HIS G 481 HIS G 494 ASN G 606 HIS G 678 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.108191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.092428 restraints weight = 67219.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.094265 restraints weight = 38714.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.095484 restraints weight = 25995.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.096296 restraints weight = 19481.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.096806 restraints weight = 15947.187| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 19569 Z= 0.179 Angle : 0.799 10.539 26595 Z= 0.420 Chirality : 0.045 0.299 3218 Planarity : 0.005 0.079 3431 Dihedral : 6.797 50.743 2841 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 1.41 % Allowed : 8.58 % Favored : 90.00 % Rotamer: Outliers : 2.64 % Allowed : 10.45 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -3.41 (0.15), residues: 2621 helix: -1.84 (0.11), residues: 1575 sheet: -4.72 (0.61), residues: 26 loop : -2.73 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 905 TYR 0.023 0.002 TYR C1806 PHE 0.037 0.002 PHE G 399 TRP 0.018 0.002 TRP C 950 HIS 0.010 0.002 HIS C 529 Details of bonding type rmsd covalent geometry : bond 0.00356 (19568) covalent geometry : angle 0.79872 (26593) SS BOND : bond 0.00773 ( 1) SS BOND : angle 2.10965 ( 2) hydrogen bonds : bond 0.06370 ( 916) hydrogen bonds : angle 6.07813 ( 2700) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5242 Ramachandran restraints generated. 2621 Oldfield, 0 Emsley, 2621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5242 Ramachandran restraints generated. 2621 Oldfield, 0 Emsley, 2621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 286 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 295 MET cc_start: 0.7699 (ptp) cc_final: 0.7109 (ptm) REVERT: C 547 LEU cc_start: 0.9054 (tp) cc_final: 0.8834 (tp) REVERT: C 549 ARG cc_start: 0.9106 (mtt-85) cc_final: 0.8282 (mmm-85) REVERT: C 627 LEU cc_start: 0.8608 (tp) cc_final: 0.8401 (tp) REVERT: C 681 TYR cc_start: 0.8100 (t80) cc_final: 0.7369 (t80) REVERT: C 885 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7857 (tp40) REVERT: C 1135 ARG cc_start: 0.7766 (mmm-85) cc_final: 0.7490 (mmm-85) REVERT: C 1290 LEU cc_start: 0.9094 (tp) cc_final: 0.8863 (pt) REVERT: C 1345 CYS cc_start: 0.8842 (m) cc_final: 0.8556 (m) REVERT: C 2131 MET cc_start: 0.7075 (mmm) cc_final: 0.6390 (tmm) REVERT: C 2191 GLU cc_start: 0.8469 (pp20) cc_final: 0.8032 (pp20) REVERT: C 2232 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.7911 (pt) REVERT: C 2359 LYS cc_start: 0.9052 (pptt) cc_final: 0.8799 (pptt) REVERT: G 198 ILE cc_start: 0.5667 (OUTLIER) cc_final: 0.5312 (mm) REVERT: G 348 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8795 (pp) REVERT: G 377 ARG cc_start: 0.8386 (tpp-160) cc_final: 0.8130 (tmt170) REVERT: G 482 MET cc_start: 0.8905 (tmm) cc_final: 0.8547 (tmm) REVERT: G 509 TYR cc_start: 0.7482 (t80) cc_final: 0.7210 (t80) REVERT: G 541 MET cc_start: 0.9024 (tpp) cc_final: 0.8334 (tpp) REVERT: G 544 TRP cc_start: 0.8360 (t-100) cc_final: 0.7799 (t-100) REVERT: G 636 SER cc_start: 0.8691 (OUTLIER) cc_final: 0.8299 (p) outliers start: 45 outliers final: 19 residues processed: 319 average time/residue: 0.1410 time to fit residues: 71.0745 Evaluate side-chains 240 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 1291 SER Chi-restraints excluded: chain C residue 1356 CYS Chi-restraints excluded: chain C residue 1714 LEU Chi-restraints excluded: chain C residue 1755 VAL Chi-restraints excluded: chain C residue 1771 LEU Chi-restraints excluded: chain C residue 2091 MET Chi-restraints excluded: chain C residue 2179 ASP Chi-restraints excluded: chain C residue 2209 SER Chi-restraints excluded: chain C residue 2232 LEU Chi-restraints excluded: chain C residue 2246 CYS Chi-restraints excluded: chain C residue 2280 THR Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain G residue 196 ASN Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 348 LEU Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 525 ILE Chi-restraints excluded: chain G residue 636 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 160 optimal weight: 30.0000 chunk 43 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 165 optimal weight: 20.0000 chunk 183 optimal weight: 0.0030 chunk 130 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 186 optimal weight: 0.0030 chunk 19 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 overall best weight: 0.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 877 GLN C1049 ASN ** C2325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 GLN G 481 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.110255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.094887 restraints weight = 67146.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.096628 restraints weight = 39364.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.097819 restraints weight = 26840.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.098523 restraints weight = 20283.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.099130 restraints weight = 16830.098| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 19569 Z= 0.137 Angle : 0.689 10.268 26595 Z= 0.357 Chirality : 0.042 0.270 3218 Planarity : 0.004 0.066 3431 Dihedral : 5.823 53.618 2828 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 1.26 % Allowed : 8.89 % Favored : 89.85 % Rotamer: Outliers : 3.17 % Allowed : 12.21 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.19 (0.16), residues: 2621 helix: -0.71 (0.12), residues: 1607 sheet: -4.58 (0.67), residues: 26 loop : -2.53 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1652 TYR 0.026 0.001 TYR C1806 PHE 0.026 0.002 PHE G 399 TRP 0.009 0.001 TRP C 950 HIS 0.006 0.001 HIS C 553 Details of bonding type rmsd covalent geometry : bond 0.00276 (19568) covalent geometry : angle 0.68861 (26593) SS BOND : bond 0.00697 ( 1) SS BOND : angle 1.87618 ( 2) hydrogen bonds : bond 0.04651 ( 916) hydrogen bonds : angle 5.05052 ( 2700) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5242 Ramachandran restraints generated. 2621 Oldfield, 0 Emsley, 2621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5242 Ramachandran restraints generated. 2621 Oldfield, 0 Emsley, 2621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 296 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 583 TYR cc_start: 0.7888 (t80) cc_final: 0.7362 (t80) REVERT: C 669 ILE cc_start: 0.9456 (OUTLIER) cc_final: 0.9221 (mt) REVERT: C 1135 ARG cc_start: 0.7705 (mmm-85) cc_final: 0.7409 (mmm-85) REVERT: C 1290 LEU cc_start: 0.9161 (tp) cc_final: 0.8891 (pt) REVERT: C 1345 CYS cc_start: 0.8789 (m) cc_final: 0.8508 (m) REVERT: C 1444 GLU cc_start: 0.8322 (tp30) cc_final: 0.7703 (tp30) REVERT: C 1477 LYS cc_start: 0.8414 (mttp) cc_final: 0.8117 (mptt) REVERT: C 1737 ARG cc_start: 0.7340 (mtt180) cc_final: 0.6856 (ttt180) REVERT: C 1788 ASP cc_start: 0.7025 (m-30) cc_final: 0.6588 (t70) REVERT: C 2131 MET cc_start: 0.7049 (mmm) cc_final: 0.6562 (tmm) REVERT: C 2232 LEU cc_start: 0.8464 (tt) cc_final: 0.7949 (pt) REVERT: C 2292 MET cc_start: 0.7130 (tmm) cc_final: 0.6813 (tmm) REVERT: G 198 ILE cc_start: 0.5496 (OUTLIER) cc_final: 0.5122 (mm) REVERT: G 348 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8902 (pp) REVERT: G 377 ARG cc_start: 0.8467 (tpp-160) cc_final: 0.7837 (tmt170) REVERT: G 482 MET cc_start: 0.8992 (tmm) cc_final: 0.8563 (tmm) REVERT: G 489 PHE cc_start: 0.7813 (m-10) cc_final: 0.7314 (m-10) REVERT: G 494 ASN cc_start: 0.8311 (m-40) cc_final: 0.7697 (p0) REVERT: G 541 MET cc_start: 0.9038 (tpp) cc_final: 0.8328 (tpp) REVERT: G 636 SER cc_start: 0.8805 (OUTLIER) cc_final: 0.8373 (p) REVERT: G 708 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8229 (mt) outliers start: 54 outliers final: 25 residues processed: 337 average time/residue: 0.1309 time to fit residues: 70.9339 Evaluate side-chains 256 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 226 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain C residue 888 SER Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 932 CYS Chi-restraints excluded: chain C residue 1183 VAL Chi-restraints excluded: chain C residue 1714 LEU Chi-restraints excluded: chain C residue 1755 VAL Chi-restraints excluded: chain C residue 2091 MET Chi-restraints excluded: chain C residue 2105 ILE Chi-restraints excluded: chain C residue 2179 ASP Chi-restraints excluded: chain C residue 2246 CYS Chi-restraints excluded: chain C residue 2280 THR Chi-restraints excluded: chain C residue 2323 LEU Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2337 VAL Chi-restraints excluded: chain C residue 2344 THR Chi-restraints excluded: chain G residue 196 ASN Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 348 LEU Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 525 ILE Chi-restraints excluded: chain G residue 550 ASP Chi-restraints excluded: chain G residue 588 LEU Chi-restraints excluded: chain G residue 636 SER Chi-restraints excluded: chain G residue 708 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 216 optimal weight: 20.0000 chunk 209 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 210 optimal weight: 0.0370 chunk 212 optimal weight: 5.9990 chunk 151 optimal weight: 20.0000 chunk 206 optimal weight: 0.9990 chunk 241 optimal weight: 3.9990 chunk 189 optimal weight: 0.4980 chunk 115 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 overall best weight: 2.3064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 HIS ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 885 GLN C 928 GLN ** C2325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 196 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.108604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.093982 restraints weight = 67948.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.095458 restraints weight = 40805.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.095738 restraints weight = 25959.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.096123 restraints weight = 24523.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.096288 restraints weight = 21699.207| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19569 Z= 0.152 Angle : 0.689 12.135 26595 Z= 0.354 Chirality : 0.042 0.284 3218 Planarity : 0.004 0.055 3431 Dihedral : 5.688 58.519 2827 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 1.22 % Allowed : 9.12 % Favored : 89.66 % Rotamer: Outliers : 3.58 % Allowed : 14.20 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.16), residues: 2621 helix: -0.36 (0.13), residues: 1623 sheet: -4.63 (0.65), residues: 26 loop : -2.58 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1652 TYR 0.026 0.001 TYR G 509 PHE 0.029 0.002 PHE G 399 TRP 0.010 0.001 TRP G 544 HIS 0.005 0.001 HIS C 529 Details of bonding type rmsd covalent geometry : bond 0.00329 (19568) covalent geometry : angle 0.68860 (26593) SS BOND : bond 0.00502 ( 1) SS BOND : angle 1.97380 ( 2) hydrogen bonds : bond 0.04265 ( 916) hydrogen bonds : angle 4.90045 ( 2700) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5242 Ramachandran restraints generated. 2621 Oldfield, 0 Emsley, 2621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5242 Ramachandran restraints generated. 2621 Oldfield, 0 Emsley, 2621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 234 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 544 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8839 (mt) REVERT: C 1135 ARG cc_start: 0.7974 (mmm-85) cc_final: 0.7569 (mmm-85) REVERT: C 1290 LEU cc_start: 0.9176 (tp) cc_final: 0.8862 (pt) REVERT: C 1345 CYS cc_start: 0.8922 (m) cc_final: 0.8631 (m) REVERT: C 1444 GLU cc_start: 0.8547 (tp30) cc_final: 0.8214 (tp30) REVERT: C 1477 LYS cc_start: 0.8416 (mttp) cc_final: 0.8014 (mtmm) REVERT: C 1737 ARG cc_start: 0.7341 (mtt180) cc_final: 0.6740 (ttt180) REVERT: C 1788 ASP cc_start: 0.7348 (m-30) cc_final: 0.6833 (t70) REVERT: C 2131 MET cc_start: 0.7101 (mmm) cc_final: 0.6574 (tmm) REVERT: C 2215 MET cc_start: 0.7580 (ttm) cc_final: 0.7221 (ptm) REVERT: C 2232 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.7954 (pt) REVERT: C 2292 MET cc_start: 0.6926 (tmm) cc_final: 0.6479 (tmm) REVERT: G 198 ILE cc_start: 0.6051 (OUTLIER) cc_final: 0.5751 (mm) REVERT: G 348 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8817 (pp) REVERT: G 377 ARG cc_start: 0.8494 (tpp-160) cc_final: 0.8171 (tpp80) REVERT: G 482 MET cc_start: 0.9006 (tmm) cc_final: 0.8507 (tmm) REVERT: G 494 ASN cc_start: 0.8344 (m-40) cc_final: 0.7605 (p0) REVERT: G 541 MET cc_start: 0.9027 (tpp) cc_final: 0.8367 (tpp) REVERT: G 636 SER cc_start: 0.8753 (OUTLIER) cc_final: 0.8333 (p) REVERT: G 646 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8554 (tt) outliers start: 61 outliers final: 31 residues processed: 273 average time/residue: 0.1214 time to fit residues: 55.0105 Evaluate side-chains 245 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 888 SER Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 932 CYS Chi-restraints excluded: chain C residue 1183 VAL Chi-restraints excluded: chain C residue 1579 LEU Chi-restraints excluded: chain C residue 1714 LEU Chi-restraints excluded: chain C residue 1755 VAL Chi-restraints excluded: chain C residue 2091 MET Chi-restraints excluded: chain C residue 2105 ILE Chi-restraints excluded: chain C residue 2179 ASP Chi-restraints excluded: chain C residue 2232 LEU Chi-restraints excluded: chain C residue 2280 THR Chi-restraints excluded: chain C residue 2323 LEU Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2337 VAL Chi-restraints excluded: chain C residue 2344 THR Chi-restraints excluded: chain G residue 196 ASN Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 348 LEU Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 479 THR Chi-restraints excluded: chain G residue 508 ILE Chi-restraints excluded: chain G residue 525 ILE Chi-restraints excluded: chain G residue 550 ASP Chi-restraints excluded: chain G residue 575 LEU Chi-restraints excluded: chain G residue 588 LEU Chi-restraints excluded: chain G residue 636 SER Chi-restraints excluded: chain G residue 646 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 105 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 180 optimal weight: 0.0050 chunk 193 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 53 optimal weight: 0.0670 chunk 229 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 264 optimal weight: 10.0000 overall best weight: 0.5534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 525 ASN ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.111057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.095510 restraints weight = 67481.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.097320 restraints weight = 39295.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.098535 restraints weight = 26425.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.099353 restraints weight = 19822.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.099854 restraints weight = 16202.164| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 19569 Z= 0.119 Angle : 0.655 10.225 26595 Z= 0.332 Chirality : 0.041 0.351 3218 Planarity : 0.003 0.052 3431 Dihedral : 5.321 59.810 2826 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 1.22 % Allowed : 8.28 % Favored : 90.50 % Rotamer: Outliers : 2.88 % Allowed : 14.85 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.17), residues: 2621 helix: -0.03 (0.13), residues: 1643 sheet: -4.49 (0.73), residues: 24 loop : -2.42 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 512 TYR 0.017 0.001 TYR C1806 PHE 0.022 0.001 PHE C2099 TRP 0.009 0.001 TRP G 544 HIS 0.004 0.001 HIS G 382 Details of bonding type rmsd covalent geometry : bond 0.00235 (19568) covalent geometry : angle 0.65491 (26593) SS BOND : bond 0.00513 ( 1) SS BOND : angle 1.45475 ( 2) hydrogen bonds : bond 0.03677 ( 916) hydrogen bonds : angle 4.49348 ( 2700) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5242 Ramachandran restraints generated. 2621 Oldfield, 0 Emsley, 2621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5242 Ramachandran restraints generated. 2621 Oldfield, 0 Emsley, 2621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 272 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 323 GLN cc_start: 0.6647 (tp40) cc_final: 0.6189 (mt0) REVERT: C 506 ASN cc_start: 0.8766 (t0) cc_final: 0.8563 (p0) REVERT: C 544 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8805 (mt) REVERT: C 583 TYR cc_start: 0.7780 (t80) cc_final: 0.7365 (t80) REVERT: C 1290 LEU cc_start: 0.9144 (tp) cc_final: 0.8851 (pt) REVERT: C 1477 LYS cc_start: 0.8297 (mttp) cc_final: 0.7974 (mtmm) REVERT: C 1481 ASP cc_start: 0.8559 (m-30) cc_final: 0.8279 (p0) REVERT: C 1711 MET cc_start: 0.7459 (tmm) cc_final: 0.6851 (tpt) REVERT: C 1737 ARG cc_start: 0.7279 (mtt180) cc_final: 0.6675 (ttt180) REVERT: C 1788 ASP cc_start: 0.7152 (m-30) cc_final: 0.6682 (t70) REVERT: C 2131 MET cc_start: 0.6907 (mmm) cc_final: 0.6659 (mmm) REVERT: C 2186 TYR cc_start: 0.8522 (p90) cc_final: 0.8010 (p90) REVERT: C 2215 MET cc_start: 0.7478 (ttm) cc_final: 0.7140 (ptm) REVERT: C 2232 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.7962 (pt) REVERT: C 2235 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7499 (pp30) REVERT: G 198 ILE cc_start: 0.6301 (OUTLIER) cc_final: 0.5989 (mm) REVERT: G 348 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8720 (pp) REVERT: G 377 ARG cc_start: 0.8381 (tpp-160) cc_final: 0.8005 (tpp80) REVERT: G 434 ASN cc_start: 0.7210 (m-40) cc_final: 0.6927 (m-40) REVERT: G 481 HIS cc_start: 0.7790 (p90) cc_final: 0.7220 (p90) REVERT: G 482 MET cc_start: 0.8998 (tmm) cc_final: 0.8584 (tmm) REVERT: G 494 ASN cc_start: 0.8296 (m-40) cc_final: 0.7653 (p0) REVERT: G 541 MET cc_start: 0.9037 (tpp) cc_final: 0.8410 (tpp) REVERT: G 555 ILE cc_start: 0.8935 (mt) cc_final: 0.8642 (mm) REVERT: G 646 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8412 (tt) REVERT: G 709 MET cc_start: 0.7569 (ppp) cc_final: 0.6560 (ppp) outliers start: 49 outliers final: 31 residues processed: 304 average time/residue: 0.1292 time to fit residues: 65.2881 Evaluate side-chains 269 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 232 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 932 CYS Chi-restraints excluded: chain C residue 1120 ILE Chi-restraints excluded: chain C residue 1183 VAL Chi-restraints excluded: chain C residue 1579 LEU Chi-restraints excluded: chain C residue 1714 LEU Chi-restraints excluded: chain C residue 2091 MET Chi-restraints excluded: chain C residue 2100 LEU Chi-restraints excluded: chain C residue 2105 ILE Chi-restraints excluded: chain C residue 2179 ASP Chi-restraints excluded: chain C residue 2232 LEU Chi-restraints excluded: chain C residue 2235 GLN Chi-restraints excluded: chain C residue 2280 THR Chi-restraints excluded: chain C residue 2323 LEU Chi-restraints excluded: chain C residue 2337 VAL Chi-restraints excluded: chain C residue 2344 THR Chi-restraints excluded: chain G residue 196 ASN Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 348 LEU Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 508 ILE Chi-restraints excluded: chain G residue 525 ILE Chi-restraints excluded: chain G residue 550 ASP Chi-restraints excluded: chain G residue 588 LEU Chi-restraints excluded: chain G residue 589 MET Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain G residue 674 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 108 optimal weight: 7.9990 chunk 256 optimal weight: 0.3980 chunk 220 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 259 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 238 optimal weight: 6.9990 chunk 131 optimal weight: 0.0070 chunk 228 optimal weight: 0.8980 overall best weight: 1.8602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1060 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.109851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.094191 restraints weight = 68051.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.095954 restraints weight = 39620.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.097142 restraints weight = 26904.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.097951 restraints weight = 20392.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.098510 restraints weight = 16691.422| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19569 Z= 0.133 Angle : 0.661 11.705 26595 Z= 0.335 Chirality : 0.042 0.297 3218 Planarity : 0.004 0.053 3431 Dihedral : 5.242 58.865 2826 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 1.26 % Allowed : 8.66 % Favored : 90.08 % Rotamer: Outliers : 3.70 % Allowed : 16.73 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.17), residues: 2621 helix: 0.13 (0.13), residues: 1651 sheet: -4.34 (0.81), residues: 24 loop : -2.41 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1652 TYR 0.016 0.001 TYR C1806 PHE 0.025 0.001 PHE C 706 TRP 0.011 0.001 TRP G 544 HIS 0.003 0.001 HIS C 529 Details of bonding type rmsd covalent geometry : bond 0.00287 (19568) covalent geometry : angle 0.66103 (26593) SS BOND : bond 0.00446 ( 1) SS BOND : angle 1.65350 ( 2) hydrogen bonds : bond 0.03649 ( 916) hydrogen bonds : angle 4.47672 ( 2700) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5242 Ramachandran restraints generated. 2621 Oldfield, 0 Emsley, 2621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5242 Ramachandran restraints generated. 2621 Oldfield, 0 Emsley, 2621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 237 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 323 GLN cc_start: 0.5933 (tp40) cc_final: 0.5676 (mt0) REVERT: C 506 ASN cc_start: 0.8761 (t0) cc_final: 0.8556 (p0) REVERT: C 544 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8707 (mt) REVERT: C 575 LYS cc_start: 0.8345 (tppt) cc_final: 0.8123 (tppt) REVERT: C 579 ASN cc_start: 0.7598 (t0) cc_final: 0.7218 (t0) REVERT: C 583 TYR cc_start: 0.7910 (t80) cc_final: 0.7511 (t80) REVERT: C 932 CYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7893 (p) REVERT: C 1075 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7857 (mp0) REVERT: C 1135 ARG cc_start: 0.7726 (mmm-85) cc_final: 0.7359 (mmm-85) REVERT: C 1290 LEU cc_start: 0.9150 (tp) cc_final: 0.8849 (pt) REVERT: C 1477 LYS cc_start: 0.8376 (mttp) cc_final: 0.8106 (mtmm) REVERT: C 1711 MET cc_start: 0.7473 (tmm) cc_final: 0.6877 (tpt) REVERT: C 1737 ARG cc_start: 0.7274 (mtt180) cc_final: 0.6665 (ttt180) REVERT: C 1788 ASP cc_start: 0.7196 (m-30) cc_final: 0.6781 (t70) REVERT: C 2131 MET cc_start: 0.6927 (mmm) cc_final: 0.6668 (mmm) REVERT: C 2232 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7912 (pt) REVERT: G 224 GLU cc_start: 0.8228 (tp30) cc_final: 0.7955 (tp30) REVERT: G 270 PHE cc_start: 0.8489 (t80) cc_final: 0.8240 (t80) REVERT: G 348 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8710 (pp) REVERT: G 377 ARG cc_start: 0.8396 (tpp-160) cc_final: 0.8007 (tpp80) REVERT: G 482 MET cc_start: 0.8955 (tmm) cc_final: 0.8510 (tmm) REVERT: G 541 MET cc_start: 0.8998 (tpp) cc_final: 0.8656 (tpp) REVERT: G 646 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8516 (tt) outliers start: 63 outliers final: 40 residues processed: 278 average time/residue: 0.1316 time to fit residues: 59.7757 Evaluate side-chains 265 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 219 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 888 SER Chi-restraints excluded: chain C residue 932 CYS Chi-restraints excluded: chain C residue 942 VAL Chi-restraints excluded: chain C residue 1075 GLU Chi-restraints excluded: chain C residue 1175 SER Chi-restraints excluded: chain C residue 1183 VAL Chi-restraints excluded: chain C residue 1579 LEU Chi-restraints excluded: chain C residue 1714 LEU Chi-restraints excluded: chain C residue 1771 LEU Chi-restraints excluded: chain C residue 2091 MET Chi-restraints excluded: chain C residue 2100 LEU Chi-restraints excluded: chain C residue 2101 LEU Chi-restraints excluded: chain C residue 2105 ILE Chi-restraints excluded: chain C residue 2179 ASP Chi-restraints excluded: chain C residue 2232 LEU Chi-restraints excluded: chain C residue 2280 THR Chi-restraints excluded: chain C residue 2323 LEU Chi-restraints excluded: chain C residue 2336 LEU Chi-restraints excluded: chain C residue 2337 VAL Chi-restraints excluded: chain C residue 2344 THR Chi-restraints excluded: chain G residue 196 ASN Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 288 HIS Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 348 LEU Chi-restraints excluded: chain G residue 361 ASP Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 479 THR Chi-restraints excluded: chain G residue 508 ILE Chi-restraints excluded: chain G residue 525 ILE Chi-restraints excluded: chain G residue 588 LEU Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain G residue 674 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 265 optimal weight: 0.9980 chunk 176 optimal weight: 0.3980 chunk 175 optimal weight: 8.9990 chunk 202 optimal weight: 10.0000 chunk 52 optimal weight: 30.0000 chunk 132 optimal weight: 0.9980 chunk 20 optimal weight: 20.0000 chunk 41 optimal weight: 0.9990 chunk 213 optimal weight: 30.0000 chunk 72 optimal weight: 4.9990 chunk 56 optimal weight: 20.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 678 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.109937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.094347 restraints weight = 67823.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.096103 restraints weight = 39308.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.097296 restraints weight = 26678.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.098130 restraints weight = 20143.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.098514 restraints weight = 16406.761| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19569 Z= 0.126 Angle : 0.653 10.790 26595 Z= 0.331 Chirality : 0.041 0.324 3218 Planarity : 0.004 0.048 3431 Dihedral : 5.169 58.882 2826 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 1.26 % Allowed : 8.74 % Favored : 90.00 % Rotamer: Outliers : 3.35 % Allowed : 17.25 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.17), residues: 2621 helix: 0.25 (0.13), residues: 1660 sheet: -4.19 (0.85), residues: 24 loop : -2.42 (0.21), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1717 TYR 0.014 0.001 TYR C1807 PHE 0.023 0.001 PHE C2099 TRP 0.011 0.001 TRP G 544 HIS 0.003 0.001 HIS G 288 Details of bonding type rmsd covalent geometry : bond 0.00271 (19568) covalent geometry : angle 0.65301 (26593) SS BOND : bond 0.00410 ( 1) SS BOND : angle 1.49116 ( 2) hydrogen bonds : bond 0.03517 ( 916) hydrogen bonds : angle 4.38641 ( 2700) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5242 Ramachandran restraints generated. 2621 Oldfield, 0 Emsley, 2621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5242 Ramachandran restraints generated. 2621 Oldfield, 0 Emsley, 2621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 240 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 544 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8726 (mt) REVERT: C 575 LYS cc_start: 0.8365 (tppt) cc_final: 0.8131 (tppt) REVERT: C 579 ASN cc_start: 0.7584 (t0) cc_final: 0.7181 (t0) REVERT: C 583 TYR cc_start: 0.8014 (t80) cc_final: 0.7618 (t80) REVERT: C 932 CYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7879 (p) REVERT: C 940 LYS cc_start: 0.8745 (mttm) cc_final: 0.8497 (tptp) REVERT: C 1075 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7865 (mp0) REVERT: C 1135 ARG cc_start: 0.7682 (mmm-85) cc_final: 0.7308 (mmm-85) REVERT: C 1290 LEU cc_start: 0.9137 (tp) cc_final: 0.8844 (pt) REVERT: C 1444 GLU cc_start: 0.8460 (tp30) cc_final: 0.8246 (tp30) REVERT: C 1711 MET cc_start: 0.7127 (tmm) cc_final: 0.6520 (tpt) REVERT: C 1737 ARG cc_start: 0.7237 (mtt180) cc_final: 0.6661 (ttt180) REVERT: C 1788 ASP cc_start: 0.7237 (m-30) cc_final: 0.6843 (t70) REVERT: C 2131 MET cc_start: 0.6885 (mmm) cc_final: 0.6619 (mmm) REVERT: C 2218 HIS cc_start: 0.7041 (OUTLIER) cc_final: 0.6825 (m-70) REVERT: C 2232 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7831 (pt) REVERT: C 2235 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7493 (pp30) REVERT: G 224 GLU cc_start: 0.8164 (tp30) cc_final: 0.7899 (tp30) REVERT: G 270 PHE cc_start: 0.8483 (t80) cc_final: 0.8207 (t80) REVERT: G 348 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8692 (pp) REVERT: G 377 ARG cc_start: 0.8379 (tpp-160) cc_final: 0.7972 (tpp80) REVERT: G 482 MET cc_start: 0.8888 (tmm) cc_final: 0.8486 (tmm) REVERT: G 541 MET cc_start: 0.8955 (tpp) cc_final: 0.8583 (tpp) REVERT: G 636 SER cc_start: 0.8794 (OUTLIER) cc_final: 0.8415 (p) REVERT: G 646 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8534 (tt) outliers start: 57 outliers final: 39 residues processed: 278 average time/residue: 0.1305 time to fit residues: 59.5759 Evaluate side-chains 265 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 217 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 888 SER Chi-restraints excluded: chain C residue 932 CYS Chi-restraints excluded: chain C residue 942 VAL Chi-restraints excluded: chain C residue 1075 GLU Chi-restraints excluded: chain C residue 1175 SER Chi-restraints excluded: chain C residue 1183 VAL Chi-restraints excluded: chain C residue 1714 LEU Chi-restraints excluded: chain C residue 1724 GLU Chi-restraints excluded: chain C residue 1771 LEU Chi-restraints excluded: chain C residue 2091 MET Chi-restraints excluded: chain C residue 2100 LEU Chi-restraints excluded: chain C residue 2105 ILE Chi-restraints excluded: chain C residue 2179 ASP Chi-restraints excluded: chain C residue 2218 HIS Chi-restraints excluded: chain C residue 2232 LEU Chi-restraints excluded: chain C residue 2235 GLN Chi-restraints excluded: chain C residue 2280 THR Chi-restraints excluded: chain C residue 2323 LEU Chi-restraints excluded: chain C residue 2336 LEU Chi-restraints excluded: chain C residue 2337 VAL Chi-restraints excluded: chain C residue 2344 THR Chi-restraints excluded: chain G residue 196 ASN Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 288 HIS Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 348 LEU Chi-restraints excluded: chain G residue 361 ASP Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 508 ILE Chi-restraints excluded: chain G residue 525 ILE Chi-restraints excluded: chain G residue 550 ASP Chi-restraints excluded: chain G residue 588 LEU Chi-restraints excluded: chain G residue 636 SER Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain G residue 674 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 159 optimal weight: 40.0000 chunk 185 optimal weight: 0.9990 chunk 246 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 207 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 218 optimal weight: 0.2980 chunk 263 optimal weight: 0.2980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.110128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.094568 restraints weight = 67550.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.096258 restraints weight = 39119.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.097424 restraints weight = 26779.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.098272 restraints weight = 20426.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.098764 restraints weight = 16545.008| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19569 Z= 0.125 Angle : 0.663 11.210 26595 Z= 0.332 Chirality : 0.041 0.308 3218 Planarity : 0.004 0.047 3431 Dihedral : 5.099 59.153 2826 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 1.30 % Allowed : 8.81 % Favored : 89.89 % Rotamer: Outliers : 3.29 % Allowed : 18.60 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.17), residues: 2621 helix: 0.36 (0.13), residues: 1658 sheet: -4.25 (0.86), residues: 24 loop : -2.40 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1717 TYR 0.014 0.001 TYR C1009 PHE 0.026 0.001 PHE C1293 TRP 0.013 0.001 TRP G 544 HIS 0.003 0.001 HIS G 288 Details of bonding type rmsd covalent geometry : bond 0.00269 (19568) covalent geometry : angle 0.66241 (26593) SS BOND : bond 0.00416 ( 1) SS BOND : angle 1.44293 ( 2) hydrogen bonds : bond 0.03415 ( 916) hydrogen bonds : angle 4.34340 ( 2700) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5242 Ramachandran restraints generated. 2621 Oldfield, 0 Emsley, 2621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5242 Ramachandran restraints generated. 2621 Oldfield, 0 Emsley, 2621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 239 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 309 ASN cc_start: 0.8629 (t0) cc_final: 0.8349 (t0) REVERT: C 544 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8785 (mt) REVERT: C 583 TYR cc_start: 0.7993 (t80) cc_final: 0.7582 (t80) REVERT: C 710 ILE cc_start: 0.9082 (tp) cc_final: 0.8851 (pt) REVERT: C 897 ARG cc_start: 0.7644 (mtm-85) cc_final: 0.7185 (mmm-85) REVERT: C 932 CYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7893 (p) REVERT: C 1075 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7846 (mp0) REVERT: C 1135 ARG cc_start: 0.7629 (mmm-85) cc_final: 0.7277 (mmm-85) REVERT: C 1290 LEU cc_start: 0.9095 (tp) cc_final: 0.8803 (pt) REVERT: C 1344 MET cc_start: 0.9338 (ttp) cc_final: 0.8934 (ttp) REVERT: C 1444 GLU cc_start: 0.8510 (tp30) cc_final: 0.8244 (tp30) REVERT: C 1711 MET cc_start: 0.7150 (tmm) cc_final: 0.6544 (tpt) REVERT: C 1737 ARG cc_start: 0.7362 (mtt180) cc_final: 0.6620 (ttt180) REVERT: C 1788 ASP cc_start: 0.7157 (m-30) cc_final: 0.6777 (t70) REVERT: C 2131 MET cc_start: 0.6865 (mmm) cc_final: 0.6619 (mmm) REVERT: C 2218 HIS cc_start: 0.7027 (OUTLIER) cc_final: 0.6736 (m-70) REVERT: C 2232 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7806 (pt) REVERT: C 2235 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7461 (pp30) REVERT: G 224 GLU cc_start: 0.8134 (tp30) cc_final: 0.7867 (tp30) REVERT: G 270 PHE cc_start: 0.8474 (t80) cc_final: 0.8168 (t80) REVERT: G 303 MET cc_start: 0.8269 (mtp) cc_final: 0.8049 (ttt) REVERT: G 348 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8724 (pp) REVERT: G 377 ARG cc_start: 0.8408 (tpp-160) cc_final: 0.8007 (tpp80) REVERT: G 482 MET cc_start: 0.8943 (tmm) cc_final: 0.8533 (tmm) REVERT: G 541 MET cc_start: 0.8956 (tpp) cc_final: 0.8580 (tpp) REVERT: G 560 LEU cc_start: 0.7982 (mm) cc_final: 0.7679 (mm) REVERT: G 646 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8532 (tt) REVERT: G 709 MET cc_start: 0.7719 (ppp) cc_final: 0.7314 (ppp) outliers start: 56 outliers final: 40 residues processed: 278 average time/residue: 0.1305 time to fit residues: 59.4902 Evaluate side-chains 271 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 223 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 932 CYS Chi-restraints excluded: chain C residue 942 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1011 THR Chi-restraints excluded: chain C residue 1075 GLU Chi-restraints excluded: chain C residue 1120 ILE Chi-restraints excluded: chain C residue 1175 SER Chi-restraints excluded: chain C residue 1183 VAL Chi-restraints excluded: chain C residue 1356 CYS Chi-restraints excluded: chain C residue 1714 LEU Chi-restraints excluded: chain C residue 1724 GLU Chi-restraints excluded: chain C residue 2091 MET Chi-restraints excluded: chain C residue 2100 LEU Chi-restraints excluded: chain C residue 2105 ILE Chi-restraints excluded: chain C residue 2135 VAL Chi-restraints excluded: chain C residue 2179 ASP Chi-restraints excluded: chain C residue 2218 HIS Chi-restraints excluded: chain C residue 2232 LEU Chi-restraints excluded: chain C residue 2235 GLN Chi-restraints excluded: chain C residue 2280 THR Chi-restraints excluded: chain C residue 2323 LEU Chi-restraints excluded: chain C residue 2336 LEU Chi-restraints excluded: chain C residue 2337 VAL Chi-restraints excluded: chain C residue 2344 THR Chi-restraints excluded: chain G residue 196 ASN Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 288 HIS Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 348 LEU Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 525 ILE Chi-restraints excluded: chain G residue 550 ASP Chi-restraints excluded: chain G residue 588 LEU Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain G residue 674 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 209 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 19 optimal weight: 0.4980 chunk 213 optimal weight: 20.0000 chunk 94 optimal weight: 9.9990 chunk 264 optimal weight: 9.9990 chunk 84 optimal weight: 0.0270 chunk 67 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 overall best weight: 3.9044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 618 GLN ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1645 ASN C2089 GLN G 213 HIS G 334 HIS G 678 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.107042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.092048 restraints weight = 68835.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.093217 restraints weight = 42696.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.094098 restraints weight = 27505.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.094298 restraints weight = 23799.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.094314 restraints weight = 22297.383| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19569 Z= 0.202 Angle : 0.729 11.602 26595 Z= 0.371 Chirality : 0.044 0.371 3218 Planarity : 0.004 0.049 3431 Dihedral : 5.393 58.914 2826 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 1.34 % Allowed : 9.81 % Favored : 88.86 % Rotamer: Outliers : 3.23 % Allowed : 19.60 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.17), residues: 2621 helix: 0.16 (0.13), residues: 1669 sheet: -4.18 (0.85), residues: 24 loop : -2.56 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1652 TYR 0.020 0.002 TYR C1009 PHE 0.027 0.002 PHE C1293 TRP 0.015 0.002 TRP G 544 HIS 0.006 0.001 HIS C 529 Details of bonding type rmsd covalent geometry : bond 0.00444 (19568) covalent geometry : angle 0.72856 (26593) SS BOND : bond 0.00406 ( 1) SS BOND : angle 2.12359 ( 2) hydrogen bonds : bond 0.03883 ( 916) hydrogen bonds : angle 4.65610 ( 2700) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5242 Ramachandran restraints generated. 2621 Oldfield, 0 Emsley, 2621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5242 Ramachandran restraints generated. 2621 Oldfield, 0 Emsley, 2621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 221 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 578 MET cc_start: 0.8562 (mmm) cc_final: 0.8362 (mmp) REVERT: C 583 TYR cc_start: 0.8009 (t80) cc_final: 0.7619 (t80) REVERT: C 897 ARG cc_start: 0.7849 (mtm-85) cc_final: 0.7195 (mmm-85) REVERT: C 1135 ARG cc_start: 0.7995 (mmm-85) cc_final: 0.7613 (mmm-85) REVERT: C 1290 LEU cc_start: 0.9152 (tp) cc_final: 0.8767 (pt) REVERT: C 1344 MET cc_start: 0.9355 (ttp) cc_final: 0.8934 (ttp) REVERT: C 1444 GLU cc_start: 0.8644 (tp30) cc_final: 0.8327 (tp30) REVERT: C 1737 ARG cc_start: 0.7662 (mtt180) cc_final: 0.6695 (ttt180) REVERT: C 1788 ASP cc_start: 0.7608 (m-30) cc_final: 0.7288 (t70) REVERT: C 2131 MET cc_start: 0.7115 (mmm) cc_final: 0.6799 (mmm) REVERT: C 2218 HIS cc_start: 0.6998 (OUTLIER) cc_final: 0.6770 (m-70) REVERT: C 2232 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.7719 (pt) REVERT: G 224 GLU cc_start: 0.8244 (tp30) cc_final: 0.7926 (tp30) REVERT: G 348 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8750 (pp) REVERT: G 377 ARG cc_start: 0.8505 (tpp-160) cc_final: 0.8133 (tpp80) REVERT: G 482 MET cc_start: 0.8978 (tmm) cc_final: 0.8420 (tmm) REVERT: G 541 MET cc_start: 0.9014 (tpp) cc_final: 0.8704 (tpp) REVERT: G 636 SER cc_start: 0.8571 (OUTLIER) cc_final: 0.8194 (p) REVERT: G 646 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8699 (tt) outliers start: 55 outliers final: 41 residues processed: 261 average time/residue: 0.1248 time to fit residues: 53.6747 Evaluate side-chains 263 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 217 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 888 SER Chi-restraints excluded: chain C residue 932 CYS Chi-restraints excluded: chain C residue 942 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1011 THR Chi-restraints excluded: chain C residue 1175 SER Chi-restraints excluded: chain C residue 1183 VAL Chi-restraints excluded: chain C residue 1356 CYS Chi-restraints excluded: chain C residue 1579 LEU Chi-restraints excluded: chain C residue 1714 LEU Chi-restraints excluded: chain C residue 2091 MET Chi-restraints excluded: chain C residue 2100 LEU Chi-restraints excluded: chain C residue 2101 LEU Chi-restraints excluded: chain C residue 2105 ILE Chi-restraints excluded: chain C residue 2135 VAL Chi-restraints excluded: chain C residue 2179 ASP Chi-restraints excluded: chain C residue 2218 HIS Chi-restraints excluded: chain C residue 2232 LEU Chi-restraints excluded: chain C residue 2280 THR Chi-restraints excluded: chain C residue 2323 LEU Chi-restraints excluded: chain C residue 2337 VAL Chi-restraints excluded: chain C residue 2344 THR Chi-restraints excluded: chain G residue 196 ASN Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 288 HIS Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 348 LEU Chi-restraints excluded: chain G residue 361 ASP Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 525 ILE Chi-restraints excluded: chain G residue 559 LEU Chi-restraints excluded: chain G residue 636 SER Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain G residue 674 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 266 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 268 optimal weight: 30.0000 chunk 75 optimal weight: 0.0570 chunk 262 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 235 optimal weight: 0.4980 chunk 153 optimal weight: 30.0000 chunk 119 optimal weight: 7.9990 overall best weight: 2.9104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1645 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.107862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.092960 restraints weight = 68761.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.094109 restraints weight = 41636.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.095141 restraints weight = 26946.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.095377 restraints weight = 23003.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.095549 restraints weight = 20570.599| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19569 Z= 0.161 Angle : 0.705 11.255 26595 Z= 0.355 Chirality : 0.043 0.310 3218 Planarity : 0.004 0.056 3431 Dihedral : 5.301 59.114 2824 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 1.30 % Allowed : 9.65 % Favored : 89.05 % Rotamer: Outliers : 2.93 % Allowed : 20.31 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.17), residues: 2621 helix: 0.21 (0.13), residues: 1672 sheet: -4.15 (0.84), residues: 24 loop : -2.57 (0.21), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 260 TYR 0.017 0.001 TYR C1009 PHE 0.034 0.002 PHE G 270 TRP 0.012 0.001 TRP G 544 HIS 0.006 0.001 HIS C 529 Details of bonding type rmsd covalent geometry : bond 0.00357 (19568) covalent geometry : angle 0.70467 (26593) SS BOND : bond 0.00444 ( 1) SS BOND : angle 1.94886 ( 2) hydrogen bonds : bond 0.03658 ( 916) hydrogen bonds : angle 4.56643 ( 2700) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5242 Ramachandran restraints generated. 2621 Oldfield, 0 Emsley, 2621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5242 Ramachandran restraints generated. 2621 Oldfield, 0 Emsley, 2621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 229 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 583 TYR cc_start: 0.8017 (t80) cc_final: 0.7666 (t80) REVERT: C 897 ARG cc_start: 0.7818 (mtm-85) cc_final: 0.7154 (mmm-85) REVERT: C 1135 ARG cc_start: 0.7948 (mmm-85) cc_final: 0.7575 (mmm-85) REVERT: C 1290 LEU cc_start: 0.9078 (tp) cc_final: 0.8721 (pt) REVERT: C 1305 LYS cc_start: 0.8095 (mmtt) cc_final: 0.7871 (pttp) REVERT: C 1344 MET cc_start: 0.9327 (ttp) cc_final: 0.8912 (ttp) REVERT: C 1444 GLU cc_start: 0.8584 (tp30) cc_final: 0.8320 (tp30) REVERT: C 1737 ARG cc_start: 0.7574 (mtt180) cc_final: 0.6658 (ttt180) REVERT: C 1788 ASP cc_start: 0.7354 (m-30) cc_final: 0.7031 (t70) REVERT: C 2131 MET cc_start: 0.7130 (mmm) cc_final: 0.6818 (mmm) REVERT: C 2218 HIS cc_start: 0.7032 (OUTLIER) cc_final: 0.6813 (m-70) REVERT: G 224 GLU cc_start: 0.8063 (tp30) cc_final: 0.7804 (tp30) REVERT: G 303 MET cc_start: 0.8201 (mtp) cc_final: 0.7997 (ttt) REVERT: G 348 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8867 (pp) REVERT: G 377 ARG cc_start: 0.8442 (tpp-160) cc_final: 0.8075 (tpp80) REVERT: G 482 MET cc_start: 0.8842 (tmm) cc_final: 0.8360 (tmm) REVERT: G 646 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8577 (tt) outliers start: 50 outliers final: 44 residues processed: 264 average time/residue: 0.1250 time to fit residues: 53.9166 Evaluate side-chains 269 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 222 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 888 SER Chi-restraints excluded: chain C residue 932 CYS Chi-restraints excluded: chain C residue 942 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1011 THR Chi-restraints excluded: chain C residue 1175 SER Chi-restraints excluded: chain C residue 1183 VAL Chi-restraints excluded: chain C residue 1356 CYS Chi-restraints excluded: chain C residue 1579 LEU Chi-restraints excluded: chain C residue 1714 LEU Chi-restraints excluded: chain C residue 2091 MET Chi-restraints excluded: chain C residue 2100 LEU Chi-restraints excluded: chain C residue 2101 LEU Chi-restraints excluded: chain C residue 2105 ILE Chi-restraints excluded: chain C residue 2135 VAL Chi-restraints excluded: chain C residue 2179 ASP Chi-restraints excluded: chain C residue 2218 HIS Chi-restraints excluded: chain C residue 2235 GLN Chi-restraints excluded: chain C residue 2246 CYS Chi-restraints excluded: chain C residue 2280 THR Chi-restraints excluded: chain C residue 2323 LEU Chi-restraints excluded: chain C residue 2337 VAL Chi-restraints excluded: chain C residue 2344 THR Chi-restraints excluded: chain G residue 196 ASN Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 288 HIS Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 348 LEU Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 417 VAL Chi-restraints excluded: chain G residue 479 THR Chi-restraints excluded: chain G residue 525 ILE Chi-restraints excluded: chain G residue 559 LEU Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain G residue 674 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 170 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 247 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 193 optimal weight: 0.9980 chunk 204 optimal weight: 20.0000 chunk 194 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1151 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.108476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.093601 restraints weight = 67792.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.095213 restraints weight = 39677.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.095900 restraints weight = 24921.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.096280 restraints weight = 22265.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.096478 restraints weight = 19607.651| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19569 Z= 0.143 Angle : 0.696 11.019 26595 Z= 0.348 Chirality : 0.042 0.364 3218 Planarity : 0.004 0.054 3431 Dihedral : 5.198 59.608 2824 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 1.30 % Allowed : 9.73 % Favored : 88.97 % Rotamer: Outliers : 2.82 % Allowed : 20.54 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.17), residues: 2621 helix: 0.30 (0.13), residues: 1676 sheet: -4.15 (0.84), residues: 24 loop : -2.58 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 585 TYR 0.016 0.001 TYR C1009 PHE 0.026 0.002 PHE C1293 TRP 0.025 0.001 TRP G 450 HIS 0.004 0.001 HIS C 529 Details of bonding type rmsd covalent geometry : bond 0.00316 (19568) covalent geometry : angle 0.69539 (26593) SS BOND : bond 0.00441 ( 1) SS BOND : angle 1.73354 ( 2) hydrogen bonds : bond 0.03525 ( 916) hydrogen bonds : angle 4.47272 ( 2700) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3072.30 seconds wall clock time: 54 minutes 0.23 seconds (3240.23 seconds total)