Starting phenix.real_space_refine (version: dev) on Thu Feb 23 04:01:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x6o_6708/02_2023/5x6o_6708.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x6o_6708/02_2023/5x6o_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x6o_6708/02_2023/5x6o_6708.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x6o_6708/02_2023/5x6o_6708.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x6o_6708/02_2023/5x6o_6708.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x6o_6708/02_2023/5x6o_6708.pdb" } 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "C ARG 416": "NH1" <-> "NH2" Residue "C ARG 504": "NH1" <-> "NH2" Residue "C ARG 549": "NH1" <-> "NH2" Residue "C ARG 582": "NH1" <-> "NH2" Residue "C ARG 585": "NH1" <-> "NH2" Residue "C ARG 662": "NH1" <-> "NH2" Residue "C ARG 897": "NH1" <-> "NH2" Residue "C ARG 1412": "NH1" <-> "NH2" Residue "C ARG 1422": "NH1" <-> "NH2" Residue "C ARG 1498": "NH1" <-> "NH2" Residue "C ARG 1655": "NH1" <-> "NH2" Residue "C ARG 1717": "NH1" <-> "NH2" Residue "C ARG 1737": "NH1" <-> "NH2" Residue "C ASP 2179": "OD1" <-> "OD2" Residue "C ARG 2293": "NH1" <-> "NH2" Residue "G ARG 197": "NH1" <-> "NH2" Residue "G ARG 228": "NH1" <-> "NH2" Residue "G ARG 260": "NH1" <-> "NH2" Residue "G ARG 269": "NH1" <-> "NH2" Residue "G ARG 310": "NH1" <-> "NH2" Residue "G ARG 331": "NH1" <-> "NH2" Residue "G ARG 377": "NH1" <-> "NH2" Residue "G ARG 451": "NH1" <-> "NH2" Residue "G ARG 664": "NH1" <-> "NH2" Residue "G ARG 704": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/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: {'GLN:plan1': 17, 'HIS:plan': 14, 'TYR:plan': 30, 'ASN:plan1': 39, 'TRP:plan': 11, 'ASP:plan': 28, 'PHE:plan': 31, 'GLU:plan': 39, 'ARG:plan': 28} 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: {'GLN:plan1': 14, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 15, 'ASP:plan': 15, 'PHE:plan': 4, 'GLU:plan': 21, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 316 Time building chain proxies: 11.31, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 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: 7.87 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 1.48 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: 6.42 Time building geometry restraints manager: 8.48 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: 98.79 - 105.85: 242 105.85 - 112.90: 10863 112.90 - 119.96: 6773 119.96 - 127.01: 8564 127.01 - 134.07: 151 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 2.440 nonbonded pdb=" O SER C2285 " pdb=" OG1 THR C2288 " model vdw 2.038 2.440 nonbonded pdb=" O LEU C1570 " pdb=" ND2 ASN C1574 " model vdw 2.082 2.520 ... (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 ========== 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 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. 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: 0.710 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: 5.490 Check model and map are aligned: 0.300 Process input model: 50.210 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.180 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 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 19568 Z= 0.463 Angle : 1.010 11.550 26593 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 : 21.05 Ramachandran Plot: Outliers : 2.17 % Allowed : 15.76 % Favored : 82.07 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 *********************** 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 fitting. rotamer outliers: 28 poor density : 385 time to evaluate : 2.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 12 residues processed: 408 average time/residue: 0.3466 time to fit residues: 209.8682 Evaluate side-chains 214 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 202 time to evaluate : 2.289 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2222 time to fit residues: 7.8143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 227 optimal weight: 10.0000 chunk 203 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 210 optimal weight: 0.0470 chunk 81 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 244 optimal weight: 0.8980 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 270 GLN ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 ASN C 835 ASN C 877 GLN C 879 ASN C 885 GLN C 928 GLN ** C1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1423 GLN C1480 GLN C1625 HIS ** C2134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2229 ASN C2314 HIS ** C2325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2349 GLN ** G 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 GLN G 305 GLN ** G 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 416 ASN G 481 HIS G 494 ASN G 606 HIS G 678 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.088 19568 Z= 0.234 Angle : 0.775 10.686 26593 Z= 0.407 Chirality : 0.044 0.301 3218 Planarity : 0.005 0.080 3431 Dihedral : 6.227 34.378 2818 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 1.41 % Allowed : 8.81 % Favored : 89.77 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.15), residues: 2621 helix: -1.86 (0.11), residues: 1563 sheet: -4.61 (0.65), residues: 26 loop : -2.88 (0.19), residues: 1032 *********************** 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 324 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 284 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 20 residues processed: 310 average time/residue: 0.2859 time to fit residues: 141.3512 Evaluate side-chains 230 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 210 time to evaluate : 2.249 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1786 time to fit residues: 10.1213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 135 optimal weight: 7.9990 chunk 75 optimal weight: 0.7980 chunk 203 optimal weight: 6.9990 chunk 166 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 chunk 264 optimal weight: 0.7980 chunk 217 optimal weight: 0.0370 chunk 242 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 196 optimal weight: 0.0570 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 HIS ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 877 GLN C 879 ASN C 885 GLN C 928 GLN ** C1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1177 GLN ** C2325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 194 ASN G 481 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 19568 Z= 0.178 Angle : 0.684 11.271 26593 Z= 0.350 Chirality : 0.041 0.269 3218 Planarity : 0.004 0.066 3431 Dihedral : 5.450 28.243 2818 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 1.26 % Allowed : 8.85 % Favored : 89.89 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.16), residues: 2621 helix: -0.76 (0.12), residues: 1615 sheet: -4.39 (0.72), residues: 26 loop : -2.63 (0.20), residues: 980 *********************** 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 313 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 279 time to evaluate : 2.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 7 residues processed: 304 average time/residue: 0.3004 time to fit residues: 144.7566 Evaluate side-chains 232 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 225 time to evaluate : 2.144 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1782 time to fit residues: 5.4553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 241 optimal weight: 2.9990 chunk 183 optimal weight: 0.5980 chunk 127 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 245 optimal weight: 8.9990 chunk 260 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 232 optimal weight: 4.9990 chunk 70 optimal weight: 0.0770 overall best weight: 1.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 HIS ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 ASN ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 GLN ** C1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1177 GLN C2089 GLN ** C2325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 481 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 19568 Z= 0.186 Angle : 0.662 11.065 26593 Z= 0.340 Chirality : 0.041 0.273 3218 Planarity : 0.004 0.056 3431 Dihedral : 5.193 27.384 2818 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 1.26 % Allowed : 9.19 % Favored : 89.55 % Rotamer Outliers : 2.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.16), residues: 2621 helix: -0.28 (0.13), residues: 1620 sheet: -4.39 (0.71), residues: 26 loop : -2.61 (0.20), residues: 975 *********************** 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 291 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 247 time to evaluate : 2.487 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 23 residues processed: 275 average time/residue: 0.2743 time to fit residues: 123.5471 Evaluate side-chains 230 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 207 time to evaluate : 2.292 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2164 time to fit residues: 11.9820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 216 optimal weight: 7.9990 chunk 147 optimal weight: 0.8980 chunk 3 optimal weight: 0.0030 chunk 193 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 221 optimal weight: 5.9990 chunk 179 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 233 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 678 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.057 19568 Z= 0.162 Angle : 0.645 12.034 26593 Z= 0.324 Chirality : 0.040 0.317 3218 Planarity : 0.004 0.053 3431 Dihedral : 4.902 21.884 2818 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 1.22 % Allowed : 9.00 % Favored : 89.77 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.17), residues: 2621 helix: 0.04 (0.13), residues: 1639 sheet: -4.31 (0.74), residues: 26 loop : -2.51 (0.21), residues: 956 *********************** 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 279 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 246 time to evaluate : 2.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 12 residues processed: 272 average time/residue: 0.2892 time to fit residues: 128.5856 Evaluate side-chains 227 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 215 time to evaluate : 2.539 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1897 time to fit residues: 7.6530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 87 optimal weight: 8.9990 chunk 234 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 152 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 260 optimal weight: 6.9990 chunk 216 optimal weight: 10.0000 chunk 120 optimal weight: 0.1980 chunk 21 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2134 ASN ** G 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 678 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 19568 Z= 0.242 Angle : 0.669 12.185 26593 Z= 0.342 Chirality : 0.042 0.300 3218 Planarity : 0.004 0.052 3431 Dihedral : 4.969 23.037 2818 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 1.26 % Allowed : 9.58 % Favored : 89.16 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.17), residues: 2621 helix: 0.12 (0.13), residues: 1638 sheet: -4.19 (0.78), residues: 26 loop : -2.60 (0.20), residues: 957 *********************** 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 253 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 223 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 242 average time/residue: 0.2940 time to fit residues: 116.1649 Evaluate side-chains 229 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 211 time to evaluate : 2.266 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1828 time to fit residues: 9.2820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 250 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 190 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 219 optimal weight: 0.0570 chunk 145 optimal weight: 10.0000 chunk 259 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 chunk 158 optimal weight: 40.0000 chunk 119 optimal weight: 7.9990 overall best weight: 1.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 ASN ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 633 GLN ** C1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 241 ASN ** G 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 678 GLN ** G 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 19568 Z= 0.178 Angle : 0.650 13.182 26593 Z= 0.326 Chirality : 0.041 0.266 3218 Planarity : 0.004 0.053 3431 Dihedral : 4.810 22.149 2818 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 1.30 % Allowed : 9.04 % Favored : 89.66 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.17), residues: 2621 helix: 0.27 (0.13), residues: 1648 sheet: -4.17 (0.85), residues: 24 loop : -2.49 (0.21), residues: 949 *********************** 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 251 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 233 time to evaluate : 2.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 246 average time/residue: 0.2961 time to fit residues: 119.0612 Evaluate side-chains 223 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 212 time to evaluate : 2.376 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1829 time to fit residues: 7.3812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 160 optimal weight: 30.0000 chunk 103 optimal weight: 4.9990 chunk 154 optimal weight: 20.0000 chunk 78 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 chunk 164 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 203 optimal weight: 9.9990 chunk 235 optimal weight: 0.1980 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1645 ASN C1681 GLN C2218 HIS G 213 HIS G 305 GLN G 334 HIS ** G 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 678 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 19568 Z= 0.336 Angle : 0.754 14.180 26593 Z= 0.385 Chirality : 0.044 0.335 3218 Planarity : 0.004 0.053 3431 Dihedral : 5.270 24.568 2818 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 1.26 % Allowed : 10.68 % Favored : 88.06 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.17), residues: 2621 helix: -0.07 (0.13), residues: 1663 sheet: -4.22 (0.86), residues: 24 loop : -2.73 (0.21), residues: 934 *********************** 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 225 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 204 time to evaluate : 2.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 216 average time/residue: 0.2843 time to fit residues: 100.0199 Evaluate side-chains 214 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 200 time to evaluate : 2.174 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1740 time to fit residues: 7.5506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 248 optimal weight: 4.9990 chunk 226 optimal weight: 0.9990 chunk 241 optimal weight: 0.9980 chunk 145 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 218 optimal weight: 0.9990 chunk 228 optimal weight: 0.7980 chunk 240 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1645 ASN ** G 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 19568 Z= 0.169 Angle : 0.672 14.624 26593 Z= 0.334 Chirality : 0.040 0.217 3218 Planarity : 0.004 0.053 3431 Dihedral : 4.838 23.378 2818 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 1.26 % Allowed : 9.46 % Favored : 89.28 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.17), residues: 2621 helix: 0.26 (0.13), residues: 1663 sheet: -4.26 (0.85), residues: 24 loop : -2.57 (0.21), residues: 934 *********************** 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 234 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 225 time to evaluate : 2.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 231 average time/residue: 0.2956 time to fit residues: 110.9014 Evaluate side-chains 213 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 208 time to evaluate : 2.400 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2029 time to fit residues: 5.9806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 255 optimal weight: 6.9990 chunk 155 optimal weight: 20.0000 chunk 121 optimal weight: 0.5980 chunk 177 optimal weight: 0.0470 chunk 267 optimal weight: 9.9990 chunk 246 optimal weight: 2.9990 chunk 213 optimal weight: 30.0000 chunk 22 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 130 optimal weight: 0.4980 chunk 169 optimal weight: 50.0000 overall best weight: 1.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 19568 Z= 0.167 Angle : 0.674 16.807 26593 Z= 0.333 Chirality : 0.041 0.368 3218 Planarity : 0.004 0.052 3431 Dihedral : 4.641 22.911 2818 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 1.26 % Allowed : 9.27 % Favored : 89.47 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.17), residues: 2621 helix: 0.45 (0.13), residues: 1660 sheet: -4.14 (0.87), residues: 24 loop : -2.45 (0.22), residues: 937 ********************** 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 240 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 238 time to evaluate : 2.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 239 average time/residue: 0.2926 time to fit residues: 113.5509 Evaluate side-chains 209 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 2.132 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 227 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 196 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 213 optimal weight: 30.0000 chunk 89 optimal weight: 0.0970 chunk 219 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 187 optimal weight: 0.1980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1049 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 = 0.3774 r_free = 0.3774 target = 0.111252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.096719 restraints weight = 67500.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.097796 restraints weight = 41416.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.098636 restraints weight = 26916.013| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.053 19568 Z= 0.156 Angle : 0.673 16.359 26593 Z= 0.331 Chirality : 0.040 0.292 3218 Planarity : 0.004 0.051 3431 Dihedral : 4.493 22.036 2818 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 1.30 % Allowed : 8.36 % Favored : 90.35 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.17), residues: 2621 helix: 0.60 (0.13), residues: 1642 sheet: -4.20 (0.85), residues: 24 loop : -2.38 (0.21), residues: 955 =============================================================================== Job complete usr+sys time: 3295.86 seconds wall clock time: 60 minutes 55.15 seconds (3655.15 seconds total)