Starting phenix.real_space_refine on Fri Apr 12 17:08:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i24_35131/04_2024/8i24_35131.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i24_35131/04_2024/8i24_35131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i24_35131/04_2024/8i24_35131.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i24_35131/04_2024/8i24_35131.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i24_35131/04_2024/8i24_35131.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i24_35131/04_2024/8i24_35131.pdb" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 110 5.49 5 Mg 1 5.21 5 S 79 5.16 5 C 16294 2.51 5 N 4589 2.21 5 O 5246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 5": "OE1" <-> "OE2" Residue "B GLU 124": "OE1" <-> "OE2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "C TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 359": "OE1" <-> "OE2" Residue "C GLU 400": "OE1" <-> "OE2" Residue "C GLU 605": "OE1" <-> "OE2" Residue "C GLU 786": "OE1" <-> "OE2" Residue "C GLU 812": "OE1" <-> "OE2" Residue "C GLU 1135": "OE1" <-> "OE2" Residue "D PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D GLU 419": "OE1" <-> "OE2" Residue "D PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 491": "OE1" <-> "OE2" Residue "D GLU 609": "OE1" <-> "OE2" Residue "D GLU 768": "OE1" <-> "OE2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "F GLU 21": "OE1" <-> "OE2" Residue "F GLU 36": "OE1" <-> "OE2" Residue "F GLU 82": "OE1" <-> "OE2" Residue "F TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 26321 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1775 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 11, 'TRANS': 217} Chain: "A" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1753 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 11, 'TRANS': 214} Chain: "C" Number of atoms: 9121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9121 Classifications: {'peptide': 1164} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 54, 'TRANS': 1109} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 8969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1152, 8969 Classifications: {'peptide': 1152} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 47, 'TRANS': 1104} Chain breaks: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "E" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 497 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "F" Number of atoms: 1940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1940 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 5, 'TRANS': 227} Chain: "O" Number of atoms: 1199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1199 Classifications: {'DNA': 58} Link IDs: {'rna3p': 57} Chain: "P" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1064 Classifications: {'DNA': 52} Link IDs: {'rna3p': 51} Chain breaks: 3 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18879 SG CYS D 817 110.155 61.027 85.810 1.00 36.83 S ATOM 19449 SG CYS D 891 106.876 60.711 87.594 1.00 31.90 S ATOM 19503 SG CYS D 898 107.208 62.776 84.361 1.00 29.86 S ATOM 19523 SG CYS D 901 107.184 59.036 84.210 1.00 29.57 S ATOM 13083 SG CYS D 83 79.097 103.867 128.741 1.00 65.67 S ATOM 13099 SG CYS D 85 77.379 104.629 131.900 1.00 67.09 S ATOM 13209 SG CYS D 98 81.230 104.240 132.156 1.00 67.73 S ATOM 13234 SG CYS D 101 79.622 101.325 131.245 1.00 62.68 S Time building chain proxies: 13.54, per 1000 atoms: 0.51 Number of scatterers: 26321 At special positions: 0 Unit cell: (135.2, 167.44, 177.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 79 16.00 P 110 15.00 Mg 1 11.99 O 5246 8.00 N 4589 7.00 C 16294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 10.46 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1201 " pdb="ZN ZN D1201 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1201 " - pdb=" SG CYS D 891 " pdb="ZN ZN D1201 " - pdb=" SG CYS D 817 " pdb="ZN ZN D1201 " - pdb=" SG CYS D 901 " pdb=" ZN D1202 " pdb="ZN ZN D1202 " - pdb=" SG CYS D 101 " pdb="ZN ZN D1202 " - pdb=" SG CYS D 83 " pdb="ZN ZN D1202 " - pdb=" SG CYS D 98 " pdb="ZN ZN D1202 " - pdb=" SG CYS D 85 " Number of angles added : 12 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5678 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 44 sheets defined 40.8% alpha, 15.8% beta 24 base pairs and 87 stacking pairs defined. Time for finding SS restraints: 8.74 Creating SS restraints... Processing helix chain 'B' and resid 31 through 47 removed outlier: 3.880A pdb=" N THR B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 83 Processing helix chain 'B' and resid 205 through 221 removed outlier: 3.590A pdb=" N ILE B 210 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER B 211 " --> pdb=" O ASP B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 232 removed outlier: 3.532A pdb=" N ILE B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER B 228 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASP B 229 " --> pdb=" O ILE B 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 18 No H-bonds generated for 'chain 'A' and resid 16 through 18' Processing helix chain 'A' and resid 31 through 47 removed outlier: 3.728A pdb=" N THR A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 205 through 226 removed outlier: 3.961A pdb=" N SER A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE A 224 " --> pdb=" O HIS A 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 50 removed outlier: 3.684A pdb=" N LYS C 32 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N PHE C 43 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LYS C 44 " --> pdb=" O LYS C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 83 Processing helix chain 'C' and resid 190 through 196 removed outlier: 4.007A pdb=" N LEU C 194 " --> pdb=" O PRO C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 210 Processing helix chain 'C' and resid 213 through 223 removed outlier: 3.670A pdb=" N LEU C 217 " --> pdb=" O ASP C 213 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR C 219 " --> pdb=" O ARG C 215 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 240 removed outlier: 3.877A pdb=" N GLY C 231 " --> pdb=" O THR C 227 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG C 240 " --> pdb=" O TYR C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 259 Processing helix chain 'C' and resid 267 through 278 Processing helix chain 'C' and resid 279 through 284 removed outlier: 3.581A pdb=" N ILE C 284 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 316 Processing helix chain 'C' and resid 364 through 373 Processing helix chain 'C' and resid 377 through 393 removed outlier: 3.903A pdb=" N ILE C 381 " --> pdb=" O GLY C 377 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS C 382 " --> pdb=" O ASP C 378 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN C 386 " --> pdb=" O LYS C 382 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU C 387 " --> pdb=" O LYS C 383 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ASP C 390 " --> pdb=" O GLN C 386 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASP C 391 " --> pdb=" O GLU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 413 removed outlier: 3.801A pdb=" N ILE C 402 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE C 403 " --> pdb=" O LYS C 399 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER C 413 " --> pdb=" O ILE C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 456 Processing helix chain 'C' and resid 465 through 470 removed outlier: 3.578A pdb=" N LEU C 469 " --> pdb=" O THR C 465 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE C 470 " --> pdb=" O PRO C 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 465 through 470' Processing helix chain 'C' and resid 472 through 485 Processing helix chain 'C' and resid 496 through 505 Processing helix chain 'C' and resid 528 through 532 removed outlier: 3.782A pdb=" N TYR C 532 " --> pdb=" O HIS C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 648 Processing helix chain 'C' and resid 655 through 666 Processing helix chain 'C' and resid 684 through 693 removed outlier: 4.001A pdb=" N GLY C 693 " --> pdb=" O ALA C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 798 Processing helix chain 'C' and resid 831 through 835 removed outlier: 3.527A pdb=" N ALA C 834 " --> pdb=" O SER C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 879 Processing helix chain 'C' and resid 974 through 979 removed outlier: 4.201A pdb=" N SER C 978 " --> pdb=" O LEU C 974 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG C 979 " --> pdb=" O GLY C 975 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 974 through 979' Processing helix chain 'C' and resid 982 through 998 Processing helix chain 'C' and resid 1010 through 1021 Processing helix chain 'C' and resid 1057 through 1061 removed outlier: 3.787A pdb=" N ASP C1060 " --> pdb=" O LEU C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1090 through 1101 Processing helix chain 'C' and resid 1102 through 1112 removed outlier: 3.663A pdb=" N LEU C1106 " --> pdb=" O ALA C1102 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN C1107 " --> pdb=" O ALA C1103 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1130 removed outlier: 3.870A pdb=" N VAL C1121 " --> pdb=" O VAL C1117 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1152 removed outlier: 3.769A pdb=" N LYS C1143 " --> pdb=" O PRO C1139 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 46 Processing helix chain 'D' and resid 107 through 113 removed outlier: 3.748A pdb=" N VAL D 110 " --> pdb=" O ARG D 107 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG D 112 " --> pdb=" O LYS D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 130 Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 174 through 186 Processing helix chain 'D' and resid 194 through 203 removed outlier: 3.556A pdb=" N VAL D 198 " --> pdb=" O GLY D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 219 removed outlier: 3.544A pdb=" N LEU D 210 " --> pdb=" O ASN D 206 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS D 219 " --> pdb=" O ARG D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 241 removed outlier: 4.105A pdb=" N VAL D 227 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG D 228 " --> pdb=" O GLN D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 248 Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 275 through 297 removed outlier: 3.668A pdb=" N ASP D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP D 296 " --> pdb=" O LYS D 292 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 320 Processing helix chain 'D' and resid 339 through 343 Processing helix chain 'D' and resid 348 through 353 Processing helix chain 'D' and resid 382 through 389 Processing helix chain 'D' and resid 389 through 401 Processing helix chain 'D' and resid 405 through 415 removed outlier: 3.831A pdb=" N ALA D 409 " --> pdb=" O ASN D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 420 through 428 removed outlier: 3.571A pdb=" N LEU D 424 " --> pdb=" O VAL D 420 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU D 426 " --> pdb=" O ASP D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 444 No H-bonds generated for 'chain 'D' and resid 442 through 444' Processing helix chain 'D' and resid 462 through 464 No H-bonds generated for 'chain 'D' and resid 462 through 464' Processing helix chain 'D' and resid 465 through 470 Processing helix chain 'D' and resid 485 through 495 Processing helix chain 'D' and resid 497 through 501 Processing helix chain 'D' and resid 516 through 527 Processing helix chain 'D' and resid 541 through 551 Processing helix chain 'D' and resid 581 through 587 Processing helix chain 'D' and resid 616 through 630 Processing helix chain 'D' and resid 633 through 654 removed outlier: 3.634A pdb=" N ILE D 637 " --> pdb=" O THR D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 662 removed outlier: 3.666A pdb=" N MET D 662 " --> pdb=" O ILE D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 685 Processing helix chain 'D' and resid 692 through 719 removed outlier: 3.673A pdb=" N LEU D 719 " --> pdb=" O LEU D 715 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 731 Processing helix chain 'D' and resid 736 through 745 removed outlier: 3.987A pdb=" N GLN D 742 " --> pdb=" O ASN D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 807 removed outlier: 3.982A pdb=" N HIS D 780 " --> pdb=" O PHE D 776 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY D 781 " --> pdb=" O ILE D 777 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA D 782 " --> pdb=" O SER D 778 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA D 790 " --> pdb=" O LEU D 786 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA D 794 " --> pdb=" O ALA D 790 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP D 795 " --> pdb=" O LEU D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 838 through 842 removed outlier: 3.679A pdb=" N ILE D 842 " --> pdb=" O SER D 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 879 Processing helix chain 'D' and resid 887 through 891 removed outlier: 3.811A pdb=" N CYS D 891 " --> pdb=" O VAL D 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 899 through 903 Processing helix chain 'D' and resid 917 through 928 removed outlier: 3.706A pdb=" N ILE D 921 " --> pdb=" O ALA D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 929 through 931 No H-bonds generated for 'chain 'D' and resid 929 through 931' Processing helix chain 'D' and resid 951 through 961 Processing helix chain 'D' and resid 1028 through 1036 removed outlier: 3.544A pdb=" N ILE D1032 " --> pdb=" O ASN D1028 " (cutoff:3.500A) Processing helix chain 'D' and resid 1038 through 1056 removed outlier: 3.608A pdb=" N VAL D1046 " --> pdb=" O GLN D1042 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN D1056 " --> pdb=" O VAL D1052 " (cutoff:3.500A) Processing helix chain 'D' and resid 1061 through 1072 removed outlier: 4.024A pdb=" N ILE D1065 " --> pdb=" O ASN D1061 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL D1067 " --> pdb=" O LYS D1063 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE D1068 " --> pdb=" O HIS D1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 1094 through 1107 removed outlier: 3.575A pdb=" N GLU D1098 " --> pdb=" O VAL D1094 " (cutoff:3.500A) Processing helix chain 'D' and resid 1120 through 1127 Processing helix chain 'D' and resid 1130 through 1138 removed outlier: 3.691A pdb=" N ALA D1134 " --> pdb=" O SER D1130 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN D1138 " --> pdb=" O ALA D1134 " (cutoff:3.500A) Processing helix chain 'D' and resid 1139 through 1151 removed outlier: 3.818A pdb=" N VAL D1143 " --> pdb=" O GLU D1139 " (cutoff:3.500A) Processing helix chain 'D' and resid 1158 through 1166 removed outlier: 3.700A pdb=" N ASN D1162 " --> pdb=" O GLY D1158 " (cutoff:3.500A) Processing helix chain 'D' and resid 1171 through 1174 Processing helix chain 'D' and resid 1175 through 1180 Processing helix chain 'E' and resid 15 through 21 removed outlier: 3.502A pdb=" N GLU E 21 " --> pdb=" O ASN E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 44 removed outlier: 3.859A pdb=" N VAL E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA E 44 " --> pdb=" O LEU E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 65 Processing helix chain 'F' and resid 15 through 28 removed outlier: 4.120A pdb=" N ILE F 19 " --> pdb=" O THR F 15 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE F 20 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS F 27 " --> pdb=" O LEU F 23 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA F 28 " --> pdb=" O ASN F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 53 removed outlier: 4.470A pdb=" N GLU F 35 " --> pdb=" O ASP F 31 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU F 36 " --> pdb=" O SER F 32 " (cutoff:3.500A) Proline residue: F 43 - end of helix Processing helix chain 'F' and resid 62 through 79 removed outlier: 3.979A pdb=" N SER F 66 " --> pdb=" O SER F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 107 removed outlier: 4.110A pdb=" N PHE F 90 " --> pdb=" O ASN F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 110 No H-bonds generated for 'chain 'F' and resid 108 through 110' Processing helix chain 'F' and resid 116 through 118 No H-bonds generated for 'chain 'F' and resid 116 through 118' Processing helix chain 'F' and resid 122 through 129 removed outlier: 3.710A pdb=" N GLU F 126 " --> pdb=" O ASP F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 157 removed outlier: 4.289A pdb=" N SER F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU F 153 " --> pdb=" O LEU F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 167 Processing helix chain 'F' and resid 171 through 189 removed outlier: 4.171A pdb=" N LEU F 177 " --> pdb=" O ASP F 173 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU F 178 " --> pdb=" O SER F 174 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP F 189 " --> pdb=" O ILE F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 197 Processing helix chain 'F' and resid 203 through 211 Processing helix chain 'F' and resid 214 through 232 removed outlier: 5.106A pdb=" N LYS F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N TYR F 223 " --> pdb=" O ARG F 219 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG F 232 " --> pdb=" O SER F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 245 removed outlier: 4.120A pdb=" N LYS F 239 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLU F 240 " --> pdb=" O GLU F 236 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 9 through 14 removed outlier: 6.708A pdb=" N LYS B 22 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N CYS B 14 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N TYR B 20 " --> pdb=" O CYS B 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY B 21 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ASP B 192 " --> pdb=" O PRO B 27 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LYS B 193 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL B 180 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR B 195 " --> pdb=" O TYR B 178 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR B 178 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N GLU B 197 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL B 176 " --> pdb=" O GLU B 197 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TRP B 199 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 112 through 113 removed outlier: 3.666A pdb=" N ALA B 101 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 136 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N TYR B 137 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ILE B 58 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLU B 139 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE B 56 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR B 141 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 87 through 88 removed outlier: 3.961A pdb=" N ASN B 88 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 108 removed outlier: 3.594A pdb=" N ALA B 128 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 149 Processing sheet with id=AA6, first strand: chain 'A' and resid 10 through 14 removed outlier: 5.700A pdb=" N CYS A 11 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL A 24 " --> pdb=" O CYS A 11 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL A 13 " --> pdb=" O LYS A 22 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 21 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASP A 192 " --> pdb=" O PRO A 27 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS A 175 " --> pdb=" O TRP A 199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 96 through 101 removed outlier: 6.038A pdb=" N GLU A 139 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE A 56 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR A 141 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP A 143 " --> pdb=" O ALA A 52 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA A 52 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 87 through 88 removed outlier: 3.793A pdb=" N ASN A 88 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 106 through 108 removed outlier: 7.189A pdb=" N VAL A 107 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.714A pdb=" N MET C 13 " --> pdb=" O ALA C1002 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 61 through 68 removed outlier: 3.831A pdb=" N ILE C 61 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL C 65 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LYS C 94 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N TYR C 67 " --> pdb=" O LYS C 92 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LYS C 92 " --> pdb=" O TYR C 67 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY C 113 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL C 93 " --> pdb=" O PHE C 111 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE C 111 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N VAL C 95 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N GLU C 109 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N LEU C 97 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLU C 107 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 124 through 126 Processing sheet with id=AB4, first strand: chain 'C' and resid 428 through 431 removed outlier: 3.563A pdb=" N SER C 135 " --> pdb=" O ARG C 506 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 142 through 149 removed outlier: 3.569A pdb=" N ALA C 146 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 169 through 173 removed outlier: 3.583A pdb=" N GLU C 170 " --> pdb=" O ARG C 182 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 288 through 289 removed outlier: 3.693A pdb=" N ILE C 288 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 341 through 342 removed outlier: 3.550A pdb=" N LYS C 362 " --> pdb=" O VAL C 342 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 557 through 558 removed outlier: 6.691A pdb=" N ILE C 564 " --> pdb=" O LEU C 586 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU C 586 " --> pdb=" O ILE C 564 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N THR C 566 " --> pdb=" O VAL C 584 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL C 584 " --> pdb=" O THR C 566 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TYR C 568 " --> pdb=" O GLU C 582 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU C 582 " --> pdb=" O TYR C 568 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS C 570 " --> pdb=" O THR C 580 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 557 through 558 Processing sheet with id=AC2, first strand: chain 'C' and resid 614 through 618 removed outlier: 4.107A pdb=" N VAL C 614 " --> pdb=" O VAL C 625 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 625 " --> pdb=" O VAL C 614 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 623 " --> pdb=" O CYS C 616 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 696 through 697 removed outlier: 7.289A pdb=" N ILE C 696 " --> pdb=" O ILE C 756 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 756 " --> pdb=" O ILE C 696 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 703 through 707 removed outlier: 7.027A pdb=" N ILE C 713 " --> pdb=" O GLU C 705 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL C 707 " --> pdb=" O GLU C 711 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLU C 711 " --> pdb=" O VAL C 707 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 728 through 731 Processing sheet with id=AC6, first strand: chain 'C' and resid 762 through 763 Processing sheet with id=AC7, first strand: chain 'C' and resid 939 through 940 removed outlier: 4.898A pdb=" N THR C1045 " --> pdb=" O PHE C 777 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 773 " --> pdb=" O MET C1049 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N ILE C 969 " --> pdb=" O ASN C 772 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU C 774 " --> pdb=" O ILE C 969 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU C 971 " --> pdb=" O LEU C 774 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLY C 776 " --> pdb=" O LEU C 971 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 790 " --> pdb=" O VAL C 970 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ILE C 789 " --> pdb=" O ARG C 951 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N LEU C 953 " --> pdb=" O ILE C 789 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE C 791 " --> pdb=" O LEU C 953 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 939 through 940 Processing sheet with id=AC9, first strand: chain 'C' and resid 819 through 820 removed outlier: 3.527A pdb=" N THR C 816 " --> pdb=" O GLY C 819 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS C 921 " --> pdb=" O ALA C 813 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP C 815 " --> pdb=" O VAL C 919 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL C 919 " --> pdb=" O ASP C 815 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP C 903 " --> pdb=" O TYR C 926 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ALA C 928 " --> pdb=" O VAL C 901 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL C 901 " --> pdb=" O ALA C 928 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N LYS C 930 " --> pdb=" O GLY C 899 " (cutoff:3.500A) removed outlier: 9.177A pdb=" N GLY C 899 " --> pdb=" O LYS C 930 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 855 through 857 removed outlier: 7.173A pdb=" N LEU C 891 " --> pdb=" O LEU C 856 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 860 through 862 Processing sheet with id=AD3, first strand: chain 'C' and resid 1063 through 1065 removed outlier: 7.454A pdb=" N LEU D 459 " --> pdb=" O ARG D 364 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL D 366 " --> pdb=" O LEU D 459 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LEU D 461 " --> pdb=" O VAL D 366 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL D 368 " --> pdb=" O LEU D 461 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1087 through 1089 removed outlier: 3.785A pdb=" N GLN C1087 " --> pdb=" O VAL D 359 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1154 through 1157 Processing sheet with id=AD6, first strand: chain 'D' and resid 47 through 50 removed outlier: 7.578A pdb=" N HIS D 117 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU D 50 " --> pdb=" O HIS D 117 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N GLU D 119 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N LEU D 120 " --> pdb=" O PRO D 255 " (cutoff:3.500A) removed outlier: 10.818A pdb=" N ALA D 122 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL D 253 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 57 through 58 removed outlier: 4.276A pdb=" N LYS D 63 " --> pdb=" O ASN D 58 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 172 through 173 removed outlier: 7.220A pdb=" N ARG D 190 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 264 through 266 removed outlier: 6.438A pdb=" N PHE D 272 " --> pdb=" O TYR F 113 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 538 through 539 removed outlier: 3.677A pdb=" N VAL D 562 " --> pdb=" O ILE D 577 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS D 575 " --> pdb=" O MET D 564 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG D 566 " --> pdb=" O LYS D 573 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 812 through 814 Processing sheet with id=AE3, first strand: chain 'D' and resid 823 through 825 removed outlier: 4.148A pdb=" N VAL D 883 " --> pdb=" O VAL D 825 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 828 through 829 removed outlier: 6.976A pdb=" N ILE D 828 " --> pdb=" O ILE D 835 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 851 through 852 removed outlier: 7.238A pdb=" N ILE D 851 " --> pdb=" O ILE D 860 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 980 through 981 removed outlier: 3.857A pdb=" N GLU D 987 " --> pdb=" O ILE D1002 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1091 through 1093 removed outlier: 7.216A pdb=" N VAL D1113 " --> pdb=" O GLU D1079 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1183 through 1184 removed outlier: 3.688A pdb=" N THR E 69 " --> pdb=" O SER D1184 " (cutoff:3.500A) 942 hydrogen bonds defined for protein. 2688 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 87 stacking parallelities Total time for adding SS restraints: 13.66 Time building geometry restraints manager: 11.16 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: 4287 1.30 - 1.43: 6672 1.43 - 1.56: 15662 1.56 - 1.68: 215 1.68 - 1.81: 136 Bond restraints: 26972 Sorted by residual: bond pdb=" CA GLU F 218 " pdb=" C GLU F 218 " ideal model delta sigma weight residual 1.524 1.438 0.087 1.24e-02 6.50e+03 4.87e+01 bond pdb=" C ILE F 217 " pdb=" N GLU F 218 " ideal model delta sigma weight residual 1.334 1.258 0.076 1.23e-02 6.61e+03 3.85e+01 bond pdb=" C ARG F 215 " pdb=" O ARG F 215 " ideal model delta sigma weight residual 1.236 1.308 -0.073 1.28e-02 6.10e+03 3.21e+01 bond pdb=" CA ILE F 217 " pdb=" C ILE F 217 " ideal model delta sigma weight residual 1.523 1.443 0.080 1.42e-02 4.96e+03 3.14e+01 bond pdb=" N GLU F 218 " pdb=" CA GLU F 218 " ideal model delta sigma weight residual 1.459 1.397 0.062 1.17e-02 7.31e+03 2.78e+01 ... (remaining 26967 not shown) Histogram of bond angle deviations from ideal: 98.21 - 105.36: 892 105.36 - 112.52: 14226 112.52 - 119.68: 9235 119.68 - 126.84: 12005 126.84 - 134.00: 529 Bond angle restraints: 36887 Sorted by residual: angle pdb=" N LYS C 353 " pdb=" CA LYS C 353 " pdb=" C LYS C 353 " ideal model delta sigma weight residual 111.28 122.68 -11.40 1.09e+00 8.42e-01 1.09e+02 angle pdb=" N LYS C 345 " pdb=" CA LYS C 345 " pdb=" C LYS C 345 " ideal model delta sigma weight residual 111.36 120.89 -9.53 1.09e+00 8.42e-01 7.64e+01 angle pdb=" N PRO C 352 " pdb=" CA PRO C 352 " pdb=" C PRO C 352 " ideal model delta sigma weight residual 114.80 104.87 9.93 1.42e+00 4.96e-01 4.89e+01 angle pdb=" C ASP C 351 " pdb=" N PRO C 352 " pdb=" CA PRO C 352 " ideal model delta sigma weight residual 120.89 113.08 7.81 1.21e+00 6.83e-01 4.16e+01 angle pdb=" N ASP E 24 " pdb=" CA ASP E 24 " pdb=" C ASP E 24 " ideal model delta sigma weight residual 110.56 121.27 -10.71 1.94e+00 2.66e-01 3.05e+01 ... (remaining 36882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.55: 14302 21.55 - 43.11: 1490 43.11 - 64.66: 475 64.66 - 86.21: 38 86.21 - 107.76: 6 Dihedral angle restraints: 16311 sinusoidal: 7479 harmonic: 8832 Sorted by residual: dihedral pdb=" CA SER C1114 " pdb=" C SER C1114 " pdb=" N ASP C1115 " pdb=" CA ASP C1115 " ideal model delta harmonic sigma weight residual -180.00 -159.21 -20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ASN D 717 " pdb=" C ASN D 717 " pdb=" N ASN D 718 " pdb=" CA ASN D 718 " ideal model delta harmonic sigma weight residual 180.00 -161.75 -18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ALA C 870 " pdb=" C ALA C 870 " pdb=" N GLU C 871 " pdb=" CA GLU C 871 " ideal model delta harmonic sigma weight residual -180.00 -161.89 -18.11 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 16308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 3967 0.097 - 0.195: 230 0.195 - 0.292: 12 0.292 - 0.390: 2 0.390 - 0.487: 4 Chirality restraints: 4215 Sorted by residual: chirality pdb=" C3' DT O 55 " pdb=" C4' DT O 55 " pdb=" O3' DT O 55 " pdb=" C2' DT O 55 " both_signs ideal model delta sigma weight residual False -2.66 -2.17 -0.49 2.00e-01 2.50e+01 5.93e+00 chirality pdb=" CA ASP E 24 " pdb=" N ASP E 24 " pdb=" C ASP E 24 " pdb=" CB ASP E 24 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" CA ASN D 28 " pdb=" N ASN D 28 " pdb=" C ASN D 28 " pdb=" CB ASN D 28 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.33e+00 ... (remaining 4212 not shown) Planarity restraints: 4386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 601 " 0.076 5.00e-02 4.00e+02 1.17e-01 2.19e+01 pdb=" N PRO D 602 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO D 602 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO D 602 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 819 " -0.062 5.00e-02 4.00e+02 9.49e-02 1.44e+01 pdb=" N PRO C 820 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO C 820 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 820 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 351 " 0.049 5.00e-02 4.00e+02 7.52e-02 9.04e+00 pdb=" N PRO C 352 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO C 352 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 352 " 0.045 5.00e-02 4.00e+02 ... (remaining 4383 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 230 2.60 - 3.18: 21028 3.18 - 3.75: 40543 3.75 - 4.33: 56967 4.33 - 4.90: 91811 Nonbonded interactions: 210579 Sorted by model distance: nonbonded pdb=" OD1 ASP D 474 " pdb="MG MG D1203 " model vdw 2.029 2.170 nonbonded pdb=" OD2 ASP D 474 " pdb="MG MG D1203 " model vdw 2.068 2.170 nonbonded pdb=" OG1 THR A 189 " pdb=" OE2 GLU D 455 " model vdw 2.202 2.440 nonbonded pdb=" OD2 ASP C 718 " pdb=" NZ LYS C 720 " model vdw 2.203 2.520 nonbonded pdb=" O SER C 140 " pdb=" OH TYR C 144 " model vdw 2.209 2.440 ... (remaining 210574 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 4 through 229) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.270 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 82.800 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 26972 Z= 0.221 Angle : 0.605 11.402 36887 Z= 0.348 Chirality : 0.048 0.487 4215 Planarity : 0.004 0.117 4386 Dihedral : 18.263 107.764 10633 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.91 % Allowed : 0.76 % Favored : 98.33 % 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: -0.46 (0.15), residues: 3054 helix: 0.35 (0.16), residues: 1113 sheet: 0.24 (0.31), residues: 311 loop : -0.84 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 999 HIS 0.005 0.001 HIS F 84 PHE 0.012 0.001 PHE C 491 TYR 0.013 0.001 TYR D 649 ARG 0.009 0.000 ARG F 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 575 time to evaluate : 2.869 Fit side-chains revert: symmetry clash REVERT: B 226 ASP cc_start: 0.7770 (m-30) cc_final: 0.7397 (m-30) REVERT: A 17 ASP cc_start: 0.7489 (t0) cc_final: 0.7250 (t0) REVERT: C 362 LYS cc_start: 0.7061 (mmpt) cc_final: 0.6722 (mmpt) REVERT: C 963 ASP cc_start: 0.8131 (p0) cc_final: 0.7916 (p0) REVERT: D 412 MET cc_start: 0.8238 (mtp) cc_final: 0.7943 (mtp) REVERT: D 706 GLU cc_start: 0.6647 (mm-30) cc_final: 0.6268 (mm-30) REVERT: D 788 ASP cc_start: 0.7428 (m-30) cc_final: 0.7054 (m-30) REVERT: F 26 ILE cc_start: 0.7811 (mm) cc_final: 0.7499 (mm) REVERT: F 110 LYS cc_start: 0.8610 (mmpt) cc_final: 0.8292 (mmmt) REVERT: F 219 ARG cc_start: 0.5956 (OUTLIER) cc_final: 0.4934 (ptp90) outliers start: 24 outliers final: 5 residues processed: 595 average time/residue: 0.4270 time to fit residues: 384.8645 Evaluate side-chains 514 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 508 time to evaluate : 3.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain F residue 219 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 4.9990 chunk 237 optimal weight: 0.5980 chunk 132 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 160 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 246 optimal weight: 0.0770 chunk 95 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 285 optimal weight: 6.9990 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 ASN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 GLN C 784 ASN D 736 ASN E 61 ASN ** E 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26972 Z= 0.222 Angle : 0.536 10.046 36887 Z= 0.289 Chirality : 0.043 0.226 4215 Planarity : 0.004 0.064 4386 Dihedral : 18.315 94.294 4590 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.75 % Allowed : 9.28 % Favored : 88.97 % 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: -0.31 (0.15), residues: 3054 helix: 0.58 (0.16), residues: 1132 sheet: 0.29 (0.31), residues: 320 loop : -0.86 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 999 HIS 0.005 0.001 HIS F 84 PHE 0.017 0.001 PHE C 491 TYR 0.014 0.001 TYR D 649 ARG 0.005 0.000 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 542 time to evaluate : 2.987 Fit side-chains revert: symmetry clash REVERT: B 46 SER cc_start: 0.8587 (OUTLIER) cc_final: 0.8335 (t) REVERT: B 88 ASN cc_start: 0.8668 (p0) cc_final: 0.8424 (p0) REVERT: B 226 ASP cc_start: 0.7668 (m-30) cc_final: 0.7327 (m-30) REVERT: A 17 ASP cc_start: 0.7503 (t0) cc_final: 0.7224 (t0) REVERT: C 112 MET cc_start: 0.8126 (mtt) cc_final: 0.7717 (mtt) REVERT: C 362 LYS cc_start: 0.7131 (mmpt) cc_final: 0.6857 (mmpt) REVERT: C 367 MET cc_start: 0.6700 (mmp) cc_final: 0.6298 (mmp) REVERT: C 963 ASP cc_start: 0.8172 (p0) cc_final: 0.7951 (p0) REVERT: D 237 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7344 (mt-10) REVERT: D 412 MET cc_start: 0.8248 (mtp) cc_final: 0.8005 (mtp) REVERT: D 671 TYR cc_start: 0.6703 (m-10) cc_final: 0.6301 (m-10) REVERT: D 706 GLU cc_start: 0.6658 (mm-30) cc_final: 0.6283 (mm-30) REVERT: D 788 ASP cc_start: 0.7451 (m-30) cc_final: 0.7059 (m-30) REVERT: E 51 GLU cc_start: 0.6464 (OUTLIER) cc_final: 0.6115 (pm20) REVERT: F 110 LYS cc_start: 0.8516 (mmpt) cc_final: 0.8175 (mmmt) outliers start: 46 outliers final: 30 residues processed: 568 average time/residue: 0.4390 time to fit residues: 380.7531 Evaluate side-chains 547 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 515 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 920 ASN Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 990 VAL Chi-restraints excluded: chain D residue 1096 ASP Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1115 LYS Chi-restraints excluded: chain D residue 1128 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 219 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 158 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 237 optimal weight: 0.3980 chunk 194 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 285 optimal weight: 6.9990 chunk 308 optimal weight: 3.9990 chunk 254 optimal weight: 5.9990 chunk 283 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 GLN ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN E 61 ASN E 66 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 26972 Z= 0.393 Angle : 0.616 10.020 36887 Z= 0.329 Chirality : 0.046 0.178 4215 Planarity : 0.005 0.067 4386 Dihedral : 18.378 100.259 4587 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.47 % Allowed : 13.38 % Favored : 84.14 % 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: -0.65 (0.15), residues: 3054 helix: 0.25 (0.15), residues: 1138 sheet: 0.17 (0.29), residues: 344 loop : -1.05 (0.14), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 999 HIS 0.006 0.001 HIS F 84 PHE 0.022 0.002 PHE F 72 TYR 0.017 0.001 TYR D 649 ARG 0.006 0.001 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 513 time to evaluate : 2.739 Fit side-chains REVERT: B 191 TYR cc_start: 0.5905 (p90) cc_final: 0.4538 (p90) REVERT: A 17 ASP cc_start: 0.7583 (t0) cc_final: 0.7256 (t0) REVERT: C 362 LYS cc_start: 0.7085 (mmpt) cc_final: 0.6761 (mmpt) REVERT: C 367 MET cc_start: 0.6748 (mmp) cc_final: 0.6363 (mmp) REVERT: D 153 TYR cc_start: 0.7733 (m-10) cc_final: 0.7302 (m-10) REVERT: D 237 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7361 (mt-10) REVERT: D 671 TYR cc_start: 0.6962 (m-10) cc_final: 0.6465 (m-10) REVERT: D 706 GLU cc_start: 0.6708 (mm-30) cc_final: 0.6293 (mm-30) REVERT: D 788 ASP cc_start: 0.7498 (m-30) cc_final: 0.7076 (m-30) REVERT: D 866 MET cc_start: 0.8550 (tpp) cc_final: 0.8339 (ttm) REVERT: D 1099 GLU cc_start: 0.7176 (tm-30) cc_final: 0.6694 (pt0) REVERT: F 35 GLU cc_start: 0.7423 (mp0) cc_final: 0.6790 (mp0) outliers start: 65 outliers final: 47 residues processed: 554 average time/residue: 0.4425 time to fit residues: 370.3491 Evaluate side-chains 538 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 491 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 722 ASP Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 920 ASN Chi-restraints excluded: chain C residue 978 SER Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 916 GLU Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 990 VAL Chi-restraints excluded: chain D residue 1096 ASP Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1128 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 219 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 282 optimal weight: 8.9990 chunk 214 optimal weight: 0.9990 chunk 148 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 191 optimal weight: 0.5980 chunk 286 optimal weight: 2.9990 chunk 303 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 chunk 271 optimal weight: 0.9980 chunk 81 optimal weight: 0.0670 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 639 GLN E 61 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26972 Z= 0.170 Angle : 0.501 10.203 36887 Z= 0.271 Chirality : 0.042 0.198 4215 Planarity : 0.004 0.056 4386 Dihedral : 18.123 95.054 4587 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.13 % Allowed : 15.29 % Favored : 82.59 % 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: -0.34 (0.15), residues: 3054 helix: 0.58 (0.16), residues: 1136 sheet: 0.32 (0.30), residues: 333 loop : -0.92 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 999 HIS 0.004 0.001 HIS F 84 PHE 0.021 0.001 PHE F 72 TYR 0.015 0.001 TYR D 649 ARG 0.005 0.000 ARG F 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 537 time to evaluate : 2.500 Fit side-chains revert: symmetry clash REVERT: A 17 ASP cc_start: 0.7532 (t0) cc_final: 0.7202 (t0) REVERT: C 362 LYS cc_start: 0.7112 (mmpt) cc_final: 0.6843 (mmtt) REVERT: C 367 MET cc_start: 0.6606 (mmp) cc_final: 0.6205 (mmp) REVERT: C 799 ASP cc_start: 0.7899 (p0) cc_final: 0.7688 (p0) REVERT: D 237 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7321 (mt-10) REVERT: D 323 ARG cc_start: 0.7968 (mtp-110) cc_final: 0.7687 (mtp-110) REVERT: D 426 GLU cc_start: 0.7656 (mp0) cc_final: 0.7316 (mp0) REVERT: D 561 LYS cc_start: 0.8132 (mmtp) cc_final: 0.7778 (mppt) REVERT: D 671 TYR cc_start: 0.6833 (m-10) cc_final: 0.6401 (m-10) REVERT: D 706 GLU cc_start: 0.6608 (mm-30) cc_final: 0.6203 (mm-30) REVERT: D 788 ASP cc_start: 0.7454 (m-30) cc_final: 0.7054 (m-30) REVERT: D 894 GLU cc_start: 0.7254 (pt0) cc_final: 0.6462 (pt0) REVERT: D 895 TYR cc_start: 0.7412 (m-80) cc_final: 0.7055 (m-80) REVERT: D 1099 GLU cc_start: 0.7101 (tm-30) cc_final: 0.6642 (pt0) outliers start: 56 outliers final: 40 residues processed: 569 average time/residue: 0.4494 time to fit residues: 388.3695 Evaluate side-chains 556 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 516 time to evaluate : 3.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 220 HIS Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 722 ASP Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 920 ASN Chi-restraints excluded: chain C residue 945 ASN Chi-restraints excluded: chain C residue 978 SER Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 773 MET Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 990 VAL Chi-restraints excluded: chain D residue 1096 ASP Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 219 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 252 optimal weight: 0.9990 chunk 172 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 225 optimal weight: 8.9990 chunk 125 optimal weight: 3.9990 chunk 259 optimal weight: 0.9990 chunk 209 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 272 optimal weight: 0.0970 chunk 76 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 ASN C 639 GLN ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 26972 Z= 0.312 Angle : 0.559 10.178 36887 Z= 0.298 Chirality : 0.044 0.210 4215 Planarity : 0.004 0.062 4386 Dihedral : 18.181 98.637 4587 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.89 % Allowed : 16.43 % Favored : 80.68 % 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: -0.49 (0.15), residues: 3054 helix: 0.43 (0.15), residues: 1140 sheet: 0.21 (0.30), residues: 334 loop : -0.99 (0.14), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 999 HIS 0.005 0.001 HIS F 84 PHE 0.023 0.001 PHE F 72 TYR 0.016 0.001 TYR D 649 ARG 0.007 0.000 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 508 time to evaluate : 2.875 Fit side-chains revert: symmetry clash REVERT: A 17 ASP cc_start: 0.7573 (t0) cc_final: 0.7244 (t0) REVERT: A 140 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.6806 (mmp) REVERT: C 45 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6562 (pt0) REVERT: C 362 LYS cc_start: 0.7108 (mmpt) cc_final: 0.6833 (mmtt) REVERT: C 367 MET cc_start: 0.6783 (mmp) cc_final: 0.6356 (mmp) REVERT: D 237 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7402 (mt-10) REVERT: D 561 LYS cc_start: 0.8187 (mmtp) cc_final: 0.7836 (mppt) REVERT: D 671 TYR cc_start: 0.6859 (m-10) cc_final: 0.6384 (m-10) REVERT: D 706 GLU cc_start: 0.6662 (mm-30) cc_final: 0.6218 (mm-30) REVERT: D 788 ASP cc_start: 0.7535 (m-30) cc_final: 0.7105 (m-30) REVERT: D 866 MET cc_start: 0.8563 (tpp) cc_final: 0.8067 (tpp) outliers start: 76 outliers final: 59 residues processed: 556 average time/residue: 0.4365 time to fit residues: 369.9675 Evaluate side-chains 563 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 502 time to evaluate : 2.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 722 ASP Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 920 ASN Chi-restraints excluded: chain C residue 945 ASN Chi-restraints excluded: chain C residue 978 SER Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain C residue 1118 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 916 GLU Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 990 VAL Chi-restraints excluded: chain D residue 1096 ASP Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1128 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 219 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 102 optimal weight: 3.9990 chunk 273 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 178 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 303 optimal weight: 2.9990 chunk 252 optimal weight: 0.5980 chunk 140 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 159 optimal weight: 0.0170 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 639 GLN ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26972 Z= 0.169 Angle : 0.493 9.797 36887 Z= 0.265 Chirality : 0.042 0.179 4215 Planarity : 0.004 0.056 4386 Dihedral : 18.066 97.307 4587 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.43 % Allowed : 17.95 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.24 (0.15), residues: 3054 helix: 0.68 (0.16), residues: 1138 sheet: 0.33 (0.29), residues: 347 loop : -0.87 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 999 HIS 0.004 0.001 HIS F 84 PHE 0.023 0.001 PHE F 72 TYR 0.016 0.001 TYR D 649 ARG 0.007 0.000 ARG F 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 544 time to evaluate : 2.854 Fit side-chains revert: symmetry clash REVERT: A 17 ASP cc_start: 0.7535 (t0) cc_final: 0.7226 (t0) REVERT: A 108 LYS cc_start: 0.7563 (tppt) cc_final: 0.7349 (tppt) REVERT: C 45 GLU cc_start: 0.6835 (pt0) cc_final: 0.6544 (pt0) REVERT: C 362 LYS cc_start: 0.7058 (mmpt) cc_final: 0.6800 (mmtt) REVERT: C 367 MET cc_start: 0.6600 (mmp) cc_final: 0.6222 (mmp) REVERT: C 715 ARG cc_start: 0.7758 (ttm110) cc_final: 0.7452 (ttp80) REVERT: C 955 VAL cc_start: 0.8680 (t) cc_final: 0.8446 (m) REVERT: D 426 GLU cc_start: 0.7703 (mp0) cc_final: 0.7326 (mp0) REVERT: D 561 LYS cc_start: 0.8162 (mmtp) cc_final: 0.7835 (mppt) REVERT: D 671 TYR cc_start: 0.6828 (m-10) cc_final: 0.6388 (m-10) REVERT: D 706 GLU cc_start: 0.6600 (mm-30) cc_final: 0.6166 (mm-30) REVERT: D 788 ASP cc_start: 0.7423 (m-30) cc_final: 0.6997 (m-30) REVERT: D 866 MET cc_start: 0.8576 (tpp) cc_final: 0.8101 (tpp) REVERT: D 1099 GLU cc_start: 0.7066 (tm-30) cc_final: 0.6566 (pt0) outliers start: 64 outliers final: 52 residues processed: 584 average time/residue: 0.4465 time to fit residues: 398.0977 Evaluate side-chains 580 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 528 time to evaluate : 2.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 220 HIS Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 722 ASP Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 920 ASN Chi-restraints excluded: chain C residue 945 ASN Chi-restraints excluded: chain C residue 978 SER Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 773 MET Chi-restraints excluded: chain D residue 916 GLU Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 934 THR Chi-restraints excluded: chain D residue 990 VAL Chi-restraints excluded: chain D residue 1096 ASP Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 219 ARG Chi-restraints excluded: chain F residue 241 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 292 optimal weight: 0.3980 chunk 34 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 chunk 221 optimal weight: 0.7980 chunk 171 optimal weight: 0.9980 chunk 255 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 chunk 302 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 184 optimal weight: 4.9990 chunk 139 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 639 GLN ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26972 Z= 0.166 Angle : 0.490 9.744 36887 Z= 0.262 Chirality : 0.041 0.169 4215 Planarity : 0.004 0.057 4386 Dihedral : 18.035 96.235 4587 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.59 % Allowed : 18.59 % Favored : 78.82 % 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: -0.14 (0.15), residues: 3054 helix: 0.75 (0.16), residues: 1142 sheet: 0.41 (0.30), residues: 336 loop : -0.82 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 999 HIS 0.004 0.001 HIS F 84 PHE 0.026 0.001 PHE F 72 TYR 0.016 0.001 TYR D 649 ARG 0.008 0.000 ARG C 608 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 545 time to evaluate : 2.757 Fit side-chains revert: symmetry clash REVERT: A 17 ASP cc_start: 0.7522 (t0) cc_final: 0.7188 (t0) REVERT: A 108 LYS cc_start: 0.7470 (tppt) cc_final: 0.7236 (tppt) REVERT: A 140 MET cc_start: 0.7545 (mmp) cc_final: 0.6892 (mtp) REVERT: C 45 GLU cc_start: 0.6786 (pt0) cc_final: 0.6466 (pt0) REVERT: C 59 ASN cc_start: 0.6716 (p0) cc_final: 0.5373 (t0) REVERT: C 362 LYS cc_start: 0.7029 (mmpt) cc_final: 0.6766 (mmtt) REVERT: C 367 MET cc_start: 0.6638 (mmp) cc_final: 0.6270 (mmp) REVERT: C 400 GLU cc_start: 0.6932 (pm20) cc_final: 0.6712 (pm20) REVERT: C 715 ARG cc_start: 0.7774 (ttm110) cc_final: 0.7463 (ttp80) REVERT: C 955 VAL cc_start: 0.8665 (t) cc_final: 0.8440 (m) REVERT: D 426 GLU cc_start: 0.7712 (mp0) cc_final: 0.7338 (mp0) REVERT: D 561 LYS cc_start: 0.8145 (mmtp) cc_final: 0.7835 (mppt) REVERT: D 671 TYR cc_start: 0.6822 (m-10) cc_final: 0.6391 (m-10) REVERT: D 706 GLU cc_start: 0.6615 (mm-30) cc_final: 0.6181 (mm-30) REVERT: D 788 ASP cc_start: 0.7403 (m-30) cc_final: 0.6991 (m-30) REVERT: D 1095 PHE cc_start: 0.6232 (t80) cc_final: 0.5979 (t80) REVERT: D 1099 GLU cc_start: 0.7063 (tm-30) cc_final: 0.6579 (pt0) outliers start: 68 outliers final: 52 residues processed: 589 average time/residue: 0.4375 time to fit residues: 392.9604 Evaluate side-chains 581 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 529 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 920 ASN Chi-restraints excluded: chain C residue 945 ASN Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain C residue 1118 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 773 MET Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 934 THR Chi-restraints excluded: chain D residue 990 VAL Chi-restraints excluded: chain D residue 1096 ASP Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 219 ARG Chi-restraints excluded: chain F residue 241 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 187 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 chunk 180 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 chunk 192 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 237 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 639 GLN ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26972 Z= 0.264 Angle : 0.536 9.859 36887 Z= 0.285 Chirality : 0.043 0.185 4215 Planarity : 0.004 0.058 4386 Dihedral : 18.091 98.646 4587 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.62 % Allowed : 18.86 % Favored : 78.52 % 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: -0.34 (0.15), residues: 3054 helix: 0.56 (0.16), residues: 1148 sheet: 0.29 (0.30), residues: 334 loop : -0.91 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 999 HIS 0.005 0.001 HIS F 84 PHE 0.025 0.001 PHE F 72 TYR 0.016 0.001 TYR D 649 ARG 0.008 0.000 ARG F 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 518 time to evaluate : 2.888 Fit side-chains revert: symmetry clash REVERT: A 17 ASP cc_start: 0.7540 (t0) cc_final: 0.7218 (t0) REVERT: A 108 LYS cc_start: 0.7511 (tppt) cc_final: 0.7291 (tppt) REVERT: A 140 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.6938 (mtp) REVERT: C 45 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6505 (pt0) REVERT: C 59 ASN cc_start: 0.6877 (p0) cc_final: 0.5759 (t0) REVERT: C 194 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6877 (tt) REVERT: C 291 GLU cc_start: 0.6970 (tt0) cc_final: 0.6740 (pp20) REVERT: C 362 LYS cc_start: 0.7074 (mmpt) cc_final: 0.6798 (mmtt) REVERT: C 367 MET cc_start: 0.6662 (mmp) cc_final: 0.6305 (mmp) REVERT: C 715 ARG cc_start: 0.7767 (ttm110) cc_final: 0.7458 (ttp80) REVERT: C 955 VAL cc_start: 0.8687 (t) cc_final: 0.8466 (m) REVERT: D 237 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7559 (mt-10) REVERT: D 426 GLU cc_start: 0.7660 (mp0) cc_final: 0.7304 (mp0) REVERT: D 561 LYS cc_start: 0.8151 (mmtp) cc_final: 0.7842 (mppt) REVERT: D 671 TYR cc_start: 0.6750 (m-10) cc_final: 0.6274 (m-10) REVERT: D 706 GLU cc_start: 0.6643 (mm-30) cc_final: 0.6199 (mm-30) REVERT: D 788 ASP cc_start: 0.7468 (m-30) cc_final: 0.7050 (m-30) REVERT: D 866 MET cc_start: 0.8674 (tpp) cc_final: 0.8051 (tpp) REVERT: D 1099 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6577 (pt0) outliers start: 69 outliers final: 57 residues processed: 562 average time/residue: 0.4548 time to fit residues: 390.2907 Evaluate side-chains 576 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 514 time to evaluate : 2.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 920 ASN Chi-restraints excluded: chain C residue 945 ASN Chi-restraints excluded: chain C residue 978 SER Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain C residue 1118 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 916 GLU Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 934 THR Chi-restraints excluded: chain D residue 990 VAL Chi-restraints excluded: chain D residue 1096 ASP Chi-restraints excluded: chain D residue 1099 GLU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 219 ARG Chi-restraints excluded: chain F residue 241 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 275 optimal weight: 3.9990 chunk 289 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 chunk 282 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 221 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 254 optimal weight: 5.9990 chunk 266 optimal weight: 0.7980 chunk 281 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 639 GLN ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26972 Z= 0.219 Angle : 0.521 11.993 36887 Z= 0.277 Chirality : 0.042 0.180 4215 Planarity : 0.004 0.058 4386 Dihedral : 18.068 98.809 4587 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.43 % Allowed : 19.62 % Favored : 77.95 % 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: -0.31 (0.15), residues: 3054 helix: 0.58 (0.16), residues: 1147 sheet: 0.29 (0.29), residues: 345 loop : -0.88 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 999 HIS 0.005 0.001 HIS F 84 PHE 0.024 0.001 PHE F 72 TYR 0.016 0.001 TYR D 649 ARG 0.009 0.000 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 520 time to evaluate : 2.868 Fit side-chains revert: symmetry clash REVERT: A 17 ASP cc_start: 0.7528 (t0) cc_final: 0.7207 (t0) REVERT: A 108 LYS cc_start: 0.7483 (tppt) cc_final: 0.7277 (tppt) REVERT: A 140 MET cc_start: 0.7540 (mmp) cc_final: 0.6894 (mtp) REVERT: C 45 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6479 (pt0) REVERT: C 59 ASN cc_start: 0.6833 (p0) cc_final: 0.5758 (t0) REVERT: C 362 LYS cc_start: 0.7037 (mmpt) cc_final: 0.6744 (mmtt) REVERT: C 367 MET cc_start: 0.6655 (mmp) cc_final: 0.6278 (mmp) REVERT: C 400 GLU cc_start: 0.6972 (pm20) cc_final: 0.6753 (pm20) REVERT: C 715 ARG cc_start: 0.7757 (ttm110) cc_final: 0.7453 (ttp80) REVERT: C 955 VAL cc_start: 0.8675 (t) cc_final: 0.8455 (m) REVERT: D 237 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7525 (mt-10) REVERT: D 561 LYS cc_start: 0.8158 (mmtp) cc_final: 0.7670 (mmmt) REVERT: D 671 TYR cc_start: 0.6742 (m-10) cc_final: 0.6269 (m-10) REVERT: D 706 GLU cc_start: 0.6633 (mm-30) cc_final: 0.6194 (mm-30) REVERT: D 788 ASP cc_start: 0.7456 (m-30) cc_final: 0.7056 (m-30) REVERT: D 866 MET cc_start: 0.8662 (tpp) cc_final: 0.8012 (tpp) REVERT: D 1095 PHE cc_start: 0.6278 (t80) cc_final: 0.6015 (t80) REVERT: D 1099 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6590 (pt0) outliers start: 64 outliers final: 57 residues processed: 558 average time/residue: 0.4546 time to fit residues: 383.9727 Evaluate side-chains 577 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 517 time to evaluate : 3.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 665 MET Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 920 ASN Chi-restraints excluded: chain C residue 945 ASN Chi-restraints excluded: chain C residue 978 SER Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain C residue 1118 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 877 LYS Chi-restraints excluded: chain D residue 916 GLU Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 934 THR Chi-restraints excluded: chain D residue 990 VAL Chi-restraints excluded: chain D residue 1096 ASP Chi-restraints excluded: chain D residue 1099 GLU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 219 ARG Chi-restraints excluded: chain F residue 241 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 185 optimal weight: 3.9990 chunk 298 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 207 optimal weight: 3.9990 chunk 312 optimal weight: 5.9990 chunk 287 optimal weight: 0.8980 chunk 249 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 192 optimal weight: 0.1980 chunk 152 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 639 GLN ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26972 Z= 0.225 Angle : 0.526 13.994 36887 Z= 0.279 Chirality : 0.043 0.230 4215 Planarity : 0.004 0.058 4386 Dihedral : 18.062 99.080 4587 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.59 % Allowed : 19.39 % Favored : 78.02 % 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: -0.31 (0.15), residues: 3054 helix: 0.58 (0.16), residues: 1148 sheet: 0.28 (0.29), residues: 345 loop : -0.89 (0.15), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 999 HIS 0.004 0.001 HIS F 84 PHE 0.025 0.001 PHE F 72 TYR 0.018 0.001 TYR D 895 ARG 0.010 0.000 ARG C 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 516 time to evaluate : 2.847 Fit side-chains revert: symmetry clash REVERT: A 17 ASP cc_start: 0.7533 (t0) cc_final: 0.7200 (t0) REVERT: A 108 LYS cc_start: 0.7473 (tppt) cc_final: 0.7263 (tppt) REVERT: C 45 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6522 (pt0) REVERT: C 59 ASN cc_start: 0.6795 (p0) cc_final: 0.5811 (t0) REVERT: C 362 LYS cc_start: 0.7039 (mmpt) cc_final: 0.6744 (mmtt) REVERT: C 367 MET cc_start: 0.6656 (mmp) cc_final: 0.6275 (mmp) REVERT: C 715 ARG cc_start: 0.7761 (ttm110) cc_final: 0.7458 (ttp80) REVERT: C 955 VAL cc_start: 0.8673 (t) cc_final: 0.8453 (m) REVERT: D 237 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7544 (mt-10) REVERT: D 426 GLU cc_start: 0.7674 (mp0) cc_final: 0.7337 (mp0) REVERT: D 561 LYS cc_start: 0.8158 (mmtp) cc_final: 0.7669 (mmmt) REVERT: D 671 TYR cc_start: 0.6742 (m-10) cc_final: 0.6275 (m-10) REVERT: D 706 GLU cc_start: 0.6605 (mm-30) cc_final: 0.6163 (mm-30) REVERT: D 788 ASP cc_start: 0.7454 (m-30) cc_final: 0.7052 (m-30) REVERT: D 866 MET cc_start: 0.8648 (tpp) cc_final: 0.8011 (tpp) REVERT: D 1095 PHE cc_start: 0.6277 (t80) cc_final: 0.6016 (t80) REVERT: D 1099 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6589 (pt0) REVERT: E 51 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.5926 (pm20) outliers start: 68 outliers final: 59 residues processed: 558 average time/residue: 0.4441 time to fit residues: 377.1626 Evaluate side-chains 577 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 514 time to evaluate : 2.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 665 MET Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 920 ASN Chi-restraints excluded: chain C residue 945 ASN Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain C residue 1118 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 877 LYS Chi-restraints excluded: chain D residue 916 GLU Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 934 THR Chi-restraints excluded: chain D residue 990 VAL Chi-restraints excluded: chain D residue 1096 ASP Chi-restraints excluded: chain D residue 1099 GLU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 219 ARG Chi-restraints excluded: chain F residue 241 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 2.9990 chunk 265 optimal weight: 0.3980 chunk 76 optimal weight: 10.0000 chunk 229 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 69 optimal weight: 5.9990 chunk 249 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 256 optimal weight: 0.0980 chunk 31 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 639 GLN ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.144366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.101534 restraints weight = 31775.448| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.58 r_work: 0.2794 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26972 Z= 0.201 Angle : 0.514 13.242 36887 Z= 0.273 Chirality : 0.042 0.178 4215 Planarity : 0.004 0.057 4386 Dihedral : 18.037 99.104 4587 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.32 % Allowed : 19.70 % Favored : 77.98 % 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: -0.26 (0.15), residues: 3054 helix: 0.61 (0.16), residues: 1149 sheet: 0.33 (0.30), residues: 345 loop : -0.86 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 999 HIS 0.004 0.001 HIS F 84 PHE 0.027 0.001 PHE F 72 TYR 0.016 0.001 TYR D 649 ARG 0.009 0.000 ARG F 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7265.65 seconds wall clock time: 132 minutes 22.11 seconds (7942.11 seconds total)