Starting phenix.real_space_refine on Fri Apr 12 16:40:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pbl_17586/04_2024/8pbl_17586_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pbl_17586/04_2024/8pbl_17586.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pbl_17586/04_2024/8pbl_17586_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pbl_17586/04_2024/8pbl_17586_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pbl_17586/04_2024/8pbl_17586_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pbl_17586/04_2024/8pbl_17586.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pbl_17586/04_2024/8pbl_17586.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pbl_17586/04_2024/8pbl_17586_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pbl_17586/04_2024/8pbl_17586_updated.pdb" } resolution = 2.87 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= 0.000 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 67 5.49 5 Mg 1 5.21 5 S 107 5.16 5 C 16239 2.51 5 N 4656 2.21 5 O 5189 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 963": "OE1" <-> "OE2" Residue "F ARG 1246": "NH1" <-> "NH2" Residue "G GLU 1168": "OE1" <-> "OE2" 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: 26261 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 557 Classifications: {'DNA': 27} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "B" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 563 Unusual residues: {'TTD': 1} Classifications: {'DNA': 26, 'undetermined': 1} Modifications used: {'5*END': 1} Link IDs: {'p': 1, 'rna3p': 24, None: 1} Not linked: pdbres=" DA B 13 " pdbres="TTD B 14 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "D" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1779 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 219} Chain: "E" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1695 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 211} Chain breaks: 1 Chain: "F" Number of atoms: 10427 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1319, 10406 Classifications: {'peptide': 1319} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1263} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 1319, 10406 Classifications: {'peptide': 1319} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1263} Chain breaks: 1 bond proxies already assigned to first conformer: 10548 Chain: "G" Number of atoms: 10352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1330, 10352 Classifications: {'peptide': 1330} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1274} Chain breaks: 3 Chain: "H" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "R" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 303 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 11} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15470 SG CYS G 70 103.056 13.437 75.687 1.00257.96 S ATOM 15484 SG CYS G 72 99.724 11.670 74.736 1.00254.70 S ATOM 15592 SG CYS G 85 102.977 10.902 72.896 1.00276.94 S ATOM 15616 SG CYS G 88 101.170 14.176 72.399 1.00245.22 S ATOM 21304 SG CYS G 814 138.677 69.289 80.507 1.00129.60 S ATOM 21869 SG CYS G 888 134.966 68.156 79.696 1.00124.36 S ATOM 21920 SG CYS G 895 136.452 68.074 83.119 1.00128.74 S ATOM 21941 SG CYS G 898 135.525 71.350 81.493 1.00134.06 S Time building chain proxies: 18.52, per 1000 atoms: 0.71 Number of scatterers: 26261 At special positions: 0 Unit cell: (158.424, 132.02, 168.756, 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 107 16.00 P 67 15.00 Mg 1 11.99 O 5189 8.00 N 4656 7.00 C 16239 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.41 Conformation dependent library (CDL) restraints added in 6.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G1501 " pdb="ZN ZN G1501 " - pdb=" SG CYS G 88 " pdb="ZN ZN G1501 " - pdb=" SG CYS G 85 " pdb="ZN ZN G1501 " - pdb=" SG CYS G 72 " pdb="ZN ZN G1501 " - pdb=" SG CYS G 70 " pdb=" ZN G1502 " pdb="ZN ZN G1502 " - pdb=" SG CYS G 895 " pdb="ZN ZN G1502 " - pdb=" SG CYS G 898 " pdb="ZN ZN G1502 " - pdb=" SG CYS G 888 " pdb="ZN ZN G1502 " - pdb=" SG CYS G 814 " Number of angles added : 12 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5860 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 94 helices and 29 sheets defined 31.9% alpha, 11.2% beta 25 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 13.75 Creating SS restraints... Processing helix chain 'D' and resid 35 through 50 Processing helix chain 'D' and resid 78 through 86 Processing helix chain 'D' and resid 112 through 114 No H-bonds generated for 'chain 'D' and resid 112 through 114' Processing helix chain 'D' and resid 213 through 232 removed outlier: 3.984A pdb=" N ALA D 230 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE D 231 " --> pdb=" O GLN D 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 49 Processing helix chain 'E' and resid 78 through 87 removed outlier: 3.715A pdb=" N GLY E 87 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 227 removed outlier: 3.530A pdb=" N ILE E 217 " --> pdb=" O PRO E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 231 No H-bonds generated for 'chain 'E' and resid 229 through 231' Processing helix chain 'F' and resid 29 through 39 Processing helix chain 'F' and resid 48 through 56 removed outlier: 3.910A pdb=" N VAL F 56 " --> pdb=" O ALA F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 88 Processing helix chain 'F' and resid 206 through 212 Processing helix chain 'F' and resid 217 through 224 Processing helix chain 'F' and resid 271 through 277 removed outlier: 3.858A pdb=" N LEU F 277 " --> pdb=" O HIS F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 294 removed outlier: 3.985A pdb=" N ALA F 293 " --> pdb=" O VAL F 289 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY F 294 " --> pdb=" O GLU F 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 289 through 294' Processing helix chain 'F' and resid 319 through 327 Processing helix chain 'F' and resid 346 through 353 Processing helix chain 'F' and resid 359 through 370 Processing helix chain 'F' and resid 378 through 389 removed outlier: 3.646A pdb=" N PHE F 389 " --> pdb=" O PHE F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 408 Processing helix chain 'F' and resid 422 through 436 Processing helix chain 'F' and resid 456 through 481 removed outlier: 3.854A pdb=" N ALA F 474 " --> pdb=" O ARG F 470 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU F 477 " --> pdb=" O ARG F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 508 Processing helix chain 'F' and resid 520 through 528 Processing helix chain 'F' and resid 552 through 554 No H-bonds generated for 'chain 'F' and resid 552 through 554' Processing helix chain 'F' and resid 610 through 613 removed outlier: 3.670A pdb=" N ASN F 613 " --> pdb=" O GLU F 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 610 through 613' Processing helix chain 'F' and resid 671 through 673 No H-bonds generated for 'chain 'F' and resid 671 through 673' Processing helix chain 'F' and resid 676 through 688 removed outlier: 3.889A pdb=" N ARG F 687 " --> pdb=" O ALA F 683 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLN F 688 " --> pdb=" O ASN F 684 " (cutoff:3.500A) Processing helix chain 'F' and resid 705 through 711 Processing helix chain 'F' and resid 738 through 740 No H-bonds generated for 'chain 'F' and resid 738 through 740' Processing helix chain 'F' and resid 820 through 824 Processing helix chain 'F' and resid 859 through 863 Processing helix chain 'F' and resid 943 through 980 removed outlier: 4.246A pdb=" N GLU F 962 " --> pdb=" O LYS F 958 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLU F 963 " --> pdb=" O ASP F 959 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER F 973 " --> pdb=" O ALA F 969 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ARG F 974 " --> pdb=" O GLY F 970 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ILE F 975 " --> pdb=" O LEU F 971 " (cutoff:3.500A) Processing helix chain 'F' and resid 986 through 988 No H-bonds generated for 'chain 'F' and resid 986 through 988' Processing helix chain 'F' and resid 1009 through 1036 removed outlier: 3.735A pdb=" N GLN F1017 " --> pdb=" O GLN F1013 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR F1018 " --> pdb=" O LEU F1014 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASP F1019 " --> pdb=" O ALA F1015 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU F1020 " --> pdb=" O GLU F1016 " (cutoff:3.500A) Processing helix chain 'F' and resid 1100 through 1106 removed outlier: 3.526A pdb=" N VAL F1103 " --> pdb=" O PRO F1100 " (cutoff:3.500A) Proline residue: F1104 - end of helix No H-bonds generated for 'chain 'F' and resid 1100 through 1106' Processing helix chain 'F' and resid 1109 through 1133 removed outlier: 4.357A pdb=" N GLU F1114 " --> pdb=" O GLN F1111 " (cutoff:3.500A) Processing helix chain 'F' and resid 1138 through 1149 Processing helix chain 'F' and resid 1166 through 1175 Processing helix chain 'F' and resid 1192 through 1201 Processing helix chain 'F' and resid 1239 through 1242 No H-bonds generated for 'chain 'F' and resid 1239 through 1242' Processing helix chain 'F' and resid 1272 through 1280 Processing helix chain 'F' and resid 1284 through 1292 Processing helix chain 'F' and resid 1300 through 1309 removed outlier: 3.686A pdb=" N MET F1304 " --> pdb=" O GLY F1300 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR F1305 " --> pdb=" O ARG F1301 " (cutoff:3.500A) Processing helix chain 'F' and resid 1321 through 1333 removed outlier: 3.744A pdb=" N LEU F1333 " --> pdb=" O GLU F1329 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 33 Processing helix chain 'G' and resid 59 through 62 No H-bonds generated for 'chain 'G' and resid 59 through 62' Processing helix chain 'G' and resid 95 through 97 No H-bonds generated for 'chain 'G' and resid 95 through 97' Processing helix chain 'G' and resid 115 through 118 No H-bonds generated for 'chain 'G' and resid 115 through 118' Processing helix chain 'G' and resid 123 through 127 Processing helix chain 'G' and resid 132 through 139 Processing helix chain 'G' and resid 162 through 171 removed outlier: 3.888A pdb=" N GLU G 171 " --> pdb=" O ASP G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 191 Processing helix chain 'G' and resid 194 through 206 Processing helix chain 'G' and resid 211 through 230 Processing helix chain 'G' and resid 234 through 237 removed outlier: 3.723A pdb=" N MET G 237 " --> pdb=" O PRO G 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 234 through 237' Processing helix chain 'G' and resid 247 through 250 Processing helix chain 'G' and resid 264 through 284 Processing helix chain 'G' and resid 289 through 307 Processing helix chain 'G' and resid 337 through 341 Processing helix chain 'G' and resid 370 through 387 Proline residue: G 379 - end of helix Processing helix chain 'G' and resid 394 through 403 Processing helix chain 'G' and resid 406 through 416 Processing helix chain 'G' and resid 431 through 433 No H-bonds generated for 'chain 'G' and resid 431 through 433' Processing helix chain 'G' and resid 451 through 454 removed outlier: 3.647A pdb=" N CYS G 454 " --> pdb=" O PRO G 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 451 through 454' Processing helix chain 'G' and resid 474 through 482 Processing helix chain 'G' and resid 505 through 514 Processing helix chain 'G' and resid 530 through 538 Processing helix chain 'G' and resid 574 through 581 removed outlier: 3.736A pdb=" N MET G 581 " --> pdb=" O ALA G 577 " (cutoff:3.500A) Processing helix chain 'G' and resid 589 through 591 No H-bonds generated for 'chain 'G' and resid 589 through 591' Processing helix chain 'G' and resid 598 through 611 Processing helix chain 'G' and resid 614 through 635 Processing helix chain 'G' and resid 650 through 669 Processing helix chain 'G' and resid 675 through 698 Processing helix chain 'G' and resid 721 through 728 Processing helix chain 'G' and resid 734 through 741 Processing helix chain 'G' and resid 769 through 804 removed outlier: 3.506A pdb=" N HIS G 777 " --> pdb=" O PHE G 773 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY G 778 " --> pdb=" O ILE G 774 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA G 791 " --> pdb=" O ALA G 787 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN G 792 " --> pdb=" O LEU G 788 " (cutoff:3.500A) Processing helix chain 'G' and resid 835 through 839 Processing helix chain 'G' and resid 866 through 875 Processing helix chain 'G' and resid 915 through 929 Proline residue: G 926 - end of helix removed outlier: 4.474A pdb=" N GLN G 929 " --> pdb=" O GLU G 925 " (cutoff:3.500A) Processing helix chain 'G' and resid 1137 through 1145 Processing helix chain 'G' and resid 1218 through 1223 Processing helix chain 'G' and resid 1226 through 1244 removed outlier: 3.802A pdb=" N GLN G1244 " --> pdb=" O VAL G1240 " (cutoff:3.500A) Processing helix chain 'G' and resid 1250 through 1261 Processing helix chain 'G' and resid 1282 through 1294 Processing helix chain 'G' and resid 1309 through 1314 Processing helix chain 'G' and resid 1319 through 1325 Processing helix chain 'G' and resid 1328 through 1338 Processing helix chain 'G' and resid 1347 through 1352 Processing helix chain 'G' and resid 1360 through 1372 removed outlier: 4.453A pdb=" N ALA G1364 " --> pdb=" O THR G1361 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG G1372 " --> pdb=" O ARG G1369 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 13 removed outlier: 3.621A pdb=" N ILE H 13 " --> pdb=" O VAL H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 32 Processing helix chain 'H' and resid 46 through 56 Processing helix chain 'H' and resid 61 through 73 Processing sheet with id= A, first strand: chain 'D' and resid 12 through 18 removed outlier: 6.451A pdb=" N THR D 27 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE D 16 " --> pdb=" O LYS D 25 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LYS D 25 " --> pdb=" O ILE D 16 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLN D 18 " --> pdb=" O HIS D 23 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N HIS D 23 " --> pdb=" O GLN D 18 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 90 through 92 Processing sheet with id= C, first strand: chain 'D' and resid 97 through 105 removed outlier: 3.592A pdb=" N GLU D 58 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLN D 147 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL D 56 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY D 149 " --> pdb=" O CYS D 54 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N CYS D 54 " --> pdb=" O GLY D 149 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 108 through 111 Processing sheet with id= E, first strand: chain 'E' and resid 13 through 18 removed outlier: 3.654A pdb=" N ALA E 24 " --> pdb=" O MET E 205 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET E 205 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU E 28 " --> pdb=" O LEU E 201 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU E 201 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU E 198 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 90 through 92 Processing sheet with id= G, first strand: chain 'E' and resid 97 through 101 removed outlier: 4.646A pdb=" N ARG E 143 " --> pdb=" O GLU E 60 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU E 60 " --> pdb=" O ARG E 143 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU E 58 " --> pdb=" O LYS E 145 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLN E 147 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL E 56 " --> pdb=" O GLN E 147 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLY E 149 " --> pdb=" O CYS E 54 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N CYS E 54 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 136 through 138 Processing sheet with id= I, first strand: chain 'F' and resid 148 through 151 Processing sheet with id= J, first strand: chain 'F' and resid 154 through 158 Processing sheet with id= K, first strand: chain 'F' and resid 238 through 240 removed outlier: 3.514A pdb=" N ILE F 285 " --> pdb=" O MET F 239 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 529 through 531 Processing sheet with id= M, first strand: chain 'F' and resid 603 through 607 Processing sheet with id= N, first strand: chain 'F' and resid 634 through 637 Processing sheet with id= O, first strand: chain 'F' and resid 748 through 752 removed outlier: 5.436A pdb=" N LYS F 735 " --> pdb=" O VAL F 724 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL F 724 " --> pdb=" O LYS F 735 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 1226 through 1232 removed outlier: 4.424A pdb=" N THR F1226 " --> pdb=" O PHE F 804 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE F1096 " --> pdb=" O ALA F 803 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL F 818 " --> pdb=" O SER F1077 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE F1079 " --> pdb=" O VAL F 818 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 830 through 840 removed outlier: 3.836A pdb=" N LYS F1048 " --> pdb=" O SER F 840 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP F 930 " --> pdb=" O TYR F1053 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA F1055 " --> pdb=" O VAL F 928 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N VAL F 928 " --> pdb=" O ALA F1055 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 66 through 75 removed outlier: 7.161A pdb=" N LYS F 99 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N TYR F 73 " --> pdb=" O ARG F 97 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG F 97 " --> pdb=" O TYR F 73 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU F 75 " --> pdb=" O PRO F 95 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY F 125 " --> pdb=" O LEU F 96 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL F 98 " --> pdb=" O TYR F 123 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N TYR F 123 " --> pdb=" O VAL F 98 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU F 100 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLU F 121 " --> pdb=" O LEU F 100 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU F 102 " --> pdb=" O GLU F 119 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLU F 119 " --> pdb=" O LEU F 102 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ILE F 104 " --> pdb=" O ILE F 117 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE F 117 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 19 through 21 Processing sheet with id= T, first strand: chain 'G' and resid 241 through 244 removed outlier: 3.628A pdb=" N GLY G 103 " --> pdb=" O VAL G 244 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N HIS G 104 " --> pdb=" O PHE G 35 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU G 37 " --> pdb=" O HIS G 104 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLU G 106 " --> pdb=" O GLU G 37 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 350 through 354 Processing sheet with id= V, first strand: chain 'G' and resid 355 through 358 removed outlier: 5.914A pdb=" N ILE G 447 " --> pdb=" O THR G 356 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLY G 358 " --> pdb=" O ILE G 447 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LEU G 449 " --> pdb=" O GLY G 358 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'G' and resid 547 through 558 Processing sheet with id= X, first strand: chain 'G' and resid 820 through 822 removed outlier: 3.537A pdb=" N MET G 822 " --> pdb=" O VAL G 880 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL G 880 " --> pdb=" O MET G 822 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 956 through 958 removed outlier: 3.546A pdb=" N ILE G 958 " --> pdb=" O GLU G1009 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU G1009 " --> pdb=" O ILE G 958 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 1046 through 1048 removed outlier: 4.318A pdb=" N THR G1047 " --> pdb=" O VAL G1060 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL G1060 " --> pdb=" O THR G1047 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA G1105 " --> pdb=" O VAL G1061 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 1279 through 1281 Processing sheet with id= AB, first strand: chain 'G' and resid 145 through 148 removed outlier: 4.191A pdb=" N ILE G 147 " --> pdb=" O ASP G 177 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ASP G 177 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 981 through 985 removed outlier: 4.374A pdb=" N GLU G 993 " --> pdb=" O LEU G 984 " (cutoff:3.500A) 778 hydrogen bonds defined for protein. 2180 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 126 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 11.07 Time building geometry restraints manager: 11.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8516 1.34 - 1.46: 3571 1.46 - 1.57: 14387 1.57 - 1.69: 136 1.69 - 1.81: 187 Bond restraints: 26797 Sorted by residual: bond pdb=" O3' TTD B 14 " pdb=" P DC B 16 " ideal model delta sigma weight residual 1.600 1.793 -0.193 2.00e-02 2.50e+03 9.34e+01 bond pdb=" C2T TTD B 14 " pdb=" N1T TTD B 14 " ideal model delta sigma weight residual 1.506 1.316 0.190 2.00e-02 2.50e+03 9.05e+01 bond pdb=" C2 TTD B 14 " pdb=" N3 TTD B 14 " ideal model delta sigma weight residual 1.510 1.327 0.183 2.00e-02 2.50e+03 8.41e+01 bond pdb=" C2T TTD B 14 " pdb=" N3T TTD B 14 " ideal model delta sigma weight residual 1.494 1.320 0.174 2.00e-02 2.50e+03 7.60e+01 bond pdb=" O4' DA B 13 " pdb=" C1' DA B 13 " ideal model delta sigma weight residual 1.414 1.553 -0.139 2.00e-02 2.50e+03 4.85e+01 ... (remaining 26792 not shown) Histogram of bond angle deviations from ideal: 80.70 - 94.86: 7 94.86 - 109.01: 2280 109.01 - 123.16: 32741 123.16 - 137.32: 1466 137.32 - 151.47: 1 Bond angle restraints: 36495 Sorted by residual: angle pdb=" C5' DA B 13 " pdb=" C4' DA B 13 " pdb=" C3' DA B 13 " ideal model delta sigma weight residual 114.90 82.32 32.58 1.50e+00 4.44e-01 4.72e+02 angle pdb=" C4' DA B 13 " pdb=" C3' DA B 13 " pdb=" O3' DA B 13 " ideal model delta sigma weight residual 110.00 127.76 -17.76 1.50e+00 4.44e-01 1.40e+02 angle pdb=" C3' TTD B 14 " pdb=" O3' TTD B 14 " pdb=" P DC B 16 " ideal model delta sigma weight residual 120.00 151.47 -31.47 3.00e+00 1.11e-01 1.10e+02 angle pdb=" O3' TTD B 14 " pdb=" C3' TTD B 14 " pdb=" C2R TTD B 14 " ideal model delta sigma weight residual 110.12 84.52 25.60 3.00e+00 1.11e-01 7.28e+01 angle pdb=" N1 TTD B 14 " pdb=" C6 TTD B 14 " pdb=" C6T TTD B 14 " ideal model delta sigma weight residual 114.33 136.70 -22.37 3.00e+00 1.11e-01 5.56e+01 ... (remaining 36490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 15868 35.99 - 71.98: 456 71.98 - 107.98: 30 107.98 - 143.97: 2 143.97 - 179.96: 3 Dihedral angle restraints: 16359 sinusoidal: 7247 harmonic: 9112 Sorted by residual: dihedral pdb=" O4' U R 9 " pdb=" C1' U R 9 " pdb=" N1 U R 9 " pdb=" C2 U R 9 " ideal model delta sinusoidal sigma weight residual 232.00 52.04 179.96 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CD ARG G 901 " pdb=" NE ARG G 901 " pdb=" CZ ARG G 901 " pdb=" NH1 ARG G 901 " ideal model delta sinusoidal sigma weight residual 0.00 -47.27 47.27 1 1.00e+01 1.00e-02 3.09e+01 dihedral pdb=" C3R TTD B 14 " pdb=" O3R TTD B 14 " pdb=" PB TTD B 14 " pdb=" O5R TTD B 14 " ideal model delta sinusoidal sigma weight residual 18.60 -148.82 167.42 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 16356 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 4160 0.181 - 0.361: 7 0.361 - 0.542: 3 0.542 - 0.723: 1 0.723 - 0.903: 2 Chirality restraints: 4173 Sorted by residual: chirality pdb=" C4' DA B 13 " pdb=" C5' DA B 13 " pdb=" O4' DA B 13 " pdb=" C3' DA B 13 " both_signs ideal model delta sigma weight residual False -2.53 -3.43 0.90 2.00e-01 2.50e+01 2.04e+01 chirality pdb=" C3' TTD B 14 " pdb=" C4' TTD B 14 " pdb=" O3' TTD B 14 " pdb=" C2R TTD B 14 " both_signs ideal model delta sigma weight residual False -2.46 -3.20 0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" C3' DA B 13 " pdb=" C4' DA B 13 " pdb=" O3' DA B 13 " pdb=" C2' DA B 13 " both_signs ideal model delta sigma weight residual False -2.66 -2.05 -0.61 2.00e-01 2.50e+01 9.35e+00 ... (remaining 4170 not shown) Planarity restraints: 4537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' TTD B 14 " -0.720 2.00e-02 2.50e+03 3.34e-01 2.51e+03 pdb=" N1 TTD B 14 " 0.116 2.00e-02 2.50e+03 pdb=" C2 TTD B 14 " 0.195 2.00e-02 2.50e+03 pdb=" O2 TTD B 14 " 0.182 2.00e-02 2.50e+03 pdb=" N3 TTD B 14 " 0.088 2.00e-02 2.50e+03 pdb=" C4 TTD B 14 " -0.027 2.00e-02 2.50e+03 pdb=" O4 TTD B 14 " -0.428 2.00e-02 2.50e+03 pdb=" C5 TTD B 14 " 0.168 2.00e-02 2.50e+03 pdb=" C6 TTD B 14 " 0.426 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1R TTD B 14 " 0.102 2.00e-02 2.50e+03 6.80e-02 1.04e+02 pdb=" C2T TTD B 14 " -0.023 2.00e-02 2.50e+03 pdb=" C4T TTD B 14 " 0.057 2.00e-02 2.50e+03 pdb=" C5T TTD B 14 " -0.009 2.00e-02 2.50e+03 pdb=" C6T TTD B 14 " -0.124 2.00e-02 2.50e+03 pdb=" N1T TTD B 14 " 0.066 2.00e-02 2.50e+03 pdb=" N3T TTD B 14 " -0.019 2.00e-02 2.50e+03 pdb=" O2T TTD B 14 " -0.080 2.00e-02 2.50e+03 pdb=" O4T TTD B 14 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 901 " -0.803 9.50e-02 1.11e+02 3.60e-01 7.87e+01 pdb=" NE ARG G 901 " 0.048 2.00e-02 2.50e+03 pdb=" CZ ARG G 901 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG G 901 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG G 901 " -0.024 2.00e-02 2.50e+03 ... (remaining 4534 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 675 2.69 - 3.24: 25225 3.24 - 3.79: 42329 3.79 - 4.35: 56121 4.35 - 4.90: 89374 Nonbonded interactions: 213724 Sorted by model distance: nonbonded pdb=" O ILE G 923 " pdb=" OH TYR G1241 " model vdw 2.137 2.440 nonbonded pdb=" OE1 GLU F 562 " pdb=" OG SER F 662 " model vdw 2.147 2.440 nonbonded pdb=" O PHE G 773 " pdb=" OG1 THR G 776 " model vdw 2.153 2.440 nonbonded pdb=" O ALA G 482 " pdb=" ND2 ASN G 488 " model vdw 2.167 2.520 nonbonded pdb=" O PRO D 179 " pdb=" OG1 THR D 207 " model vdw 2.169 2.440 ... (remaining 213719 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 'D' and (resid 7 through 158 or resid 169 through 233)) selection = (chain 'E' and resid 7 through 233) } 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=0.19 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: 7.180 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: 0.030 Extract box with map and model: 26.230 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 89.160 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.150 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:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5486 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 : 0.005 0.193 26797 Z= 0.277 Angle : 0.765 32.576 36495 Z= 0.426 Chirality : 0.049 0.903 4173 Planarity : 0.008 0.360 4537 Dihedral : 15.606 179.961 10499 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.18 % Allowed : 0.15 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % 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: -0.47 (0.15), residues: 3154 helix: 0.69 (0.16), residues: 1075 sheet: -0.38 (0.26), residues: 370 loop : -0.93 (0.14), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 183 HIS 0.007 0.001 HIS G 430 PHE 0.018 0.001 PHE F 972 TYR 0.019 0.001 TYR G 269 ARG 0.006 0.000 ARG G 250 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 525 time to evaluate : 3.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 12 ARG cc_start: 0.4611 (ttm-80) cc_final: 0.4317 (mmm160) REVERT: D 60 GLU cc_start: 0.5400 (tt0) cc_final: 0.4481 (mm-30) REVERT: D 77 ASP cc_start: 0.6510 (m-30) cc_final: 0.6083 (t70) REVERT: D 79 LEU cc_start: 0.6590 (tt) cc_final: 0.6318 (tp) REVERT: D 80 GLU cc_start: 0.5879 (tp30) cc_final: 0.5618 (tp30) REVERT: D 226 GLU cc_start: 0.6153 (mt-10) cc_final: 0.5818 (tm-30) REVERT: D 229 GLU cc_start: 0.5177 (mt-10) cc_final: 0.4804 (pp20) REVERT: E 96 ASP cc_start: 0.6192 (p0) cc_final: 0.5645 (p0) REVERT: E 142 MET cc_start: 0.2538 (mmp) cc_final: 0.2324 (mmt) REVERT: E 186 ASN cc_start: 0.4792 (p0) cc_final: 0.4571 (p0) REVERT: E 200 LYS cc_start: 0.3988 (tttt) cc_final: 0.3558 (mtpp) REVERT: E 205 MET cc_start: 0.4344 (tpt) cc_final: 0.4024 (mmm) REVERT: E 223 ILE cc_start: 0.4554 (mt) cc_final: 0.4315 (mt) REVERT: E 226 GLU cc_start: 0.5445 (tt0) cc_final: 0.5190 (tt0) REVERT: F 81 ASP cc_start: 0.5470 (t70) cc_final: 0.4653 (p0) REVERT: F 186 PHE cc_start: 0.5257 (m-80) cc_final: 0.4865 (m-10) REVERT: F 392 GLU cc_start: 0.6619 (mt-10) cc_final: 0.6293 (mt-10) REVERT: F 422 LYS cc_start: 0.5830 (ptpt) cc_final: 0.4863 (mmtm) REVERT: F 430 LYS cc_start: 0.4332 (mttt) cc_final: 0.3577 (ttpt) REVERT: F 459 MET cc_start: 0.5717 (mtm) cc_final: 0.5233 (mtt) REVERT: F 488 MET cc_start: 0.1818 (mmp) cc_final: 0.0796 (pp-130) REVERT: F 527 LYS cc_start: 0.6673 (mttt) cc_final: 0.6350 (mtmt) REVERT: F 542 ARG cc_start: 0.3987 (mmt180) cc_final: 0.3680 (mmt180) REVERT: F 548 ARG cc_start: 0.7414 (mtt-85) cc_final: 0.7099 (mtt-85) REVERT: F 555 TYR cc_start: 0.5985 (t80) cc_final: 0.5727 (t80) REVERT: F 568 ASN cc_start: 0.7584 (m-40) cc_final: 0.7348 (m-40) REVERT: F 584 TYR cc_start: 0.6284 (m-80) cc_final: 0.5775 (m-80) REVERT: F 602 GLU cc_start: 0.5548 (tp30) cc_final: 0.5200 (mp0) REVERT: F 604 HIS cc_start: 0.6496 (m90) cc_final: 0.6256 (m-70) REVERT: F 639 LYS cc_start: 0.6706 (tttt) cc_final: 0.6356 (mtmm) REVERT: F 651 ASP cc_start: 0.6585 (m-30) cc_final: 0.6195 (m-30) REVERT: F 657 THR cc_start: 0.7385 (m) cc_final: 0.7002 (t) REVERT: F 677 ASN cc_start: 0.6309 (m110) cc_final: 0.5635 (t0) REVERT: F 688 GLN cc_start: 0.6116 (tt0) cc_final: 0.5745 (mt0) REVERT: F 694 ARG cc_start: 0.7313 (mtm-85) cc_final: 0.7083 (mtp85) REVERT: F 723 VAL cc_start: 0.7591 (t) cc_final: 0.7261 (p) REVERT: F 754 THR cc_start: 0.6719 (p) cc_final: 0.6199 (t) REVERT: F 785 ASP cc_start: 0.6243 (m-30) cc_final: 0.6006 (m-30) REVERT: F 790 ASP cc_start: 0.4905 (t70) cc_final: 0.4584 (t70) REVERT: F 814 ASP cc_start: 0.6062 (m-30) cc_final: 0.5782 (t0) REVERT: F 820 GLU cc_start: 0.7590 (tp30) cc_final: 0.6887 (tp30) REVERT: F 825 GLU cc_start: 0.6585 (mt-10) cc_final: 0.6240 (mt-10) REVERT: F 835 GLU cc_start: 0.6223 (tt0) cc_final: 0.5993 (tm-30) REVERT: F 873 ILE cc_start: 0.6903 (mm) cc_final: 0.6677 (tt) REVERT: F 1038 GLN cc_start: 0.5943 (tp40) cc_final: 0.5560 (tp-100) REVERT: F 1080 ASN cc_start: 0.6339 (t0) cc_final: 0.5932 (t0) REVERT: F 1188 ASP cc_start: 0.5464 (t0) cc_final: 0.5152 (t0) REVERT: F 1191 LYS cc_start: 0.5393 (mmmt) cc_final: 0.4833 (mtpp) REVERT: F 1203 ASP cc_start: 0.5185 (m-30) cc_final: 0.4831 (m-30) REVERT: F 1230 MET cc_start: 0.6389 (ttp) cc_final: 0.5999 (ttp) REVERT: F 1272 GLU cc_start: 0.4850 (tt0) cc_final: 0.4510 (tt0) REVERT: F 1338 GLU cc_start: 0.5867 (pm20) cc_final: 0.5419 (pp20) REVERT: G 134 ASP cc_start: 0.5663 (m-30) cc_final: 0.4958 (t0) REVERT: G 233 LYS cc_start: 0.6019 (mtpt) cc_final: 0.5656 (mtpp) REVERT: G 278 ARG cc_start: 0.5703 (ttp80) cc_final: 0.5318 (ttt180) REVERT: G 329 ASP cc_start: 0.6637 (m-30) cc_final: 0.6384 (m-30) REVERT: G 438 GLU cc_start: 0.5671 (mt-10) cc_final: 0.5208 (tt0) REVERT: G 460 ASP cc_start: 0.5302 (p0) cc_final: 0.4954 (p0) REVERT: G 580 TRP cc_start: 0.6807 (t-100) cc_final: 0.6299 (t-100) REVERT: G 648 GLU cc_start: 0.6902 (pm20) cc_final: 0.6662 (tp30) REVERT: G 649 LYS cc_start: 0.5449 (mmpt) cc_final: 0.5211 (pmtt) REVERT: G 678 ARG cc_start: 0.4990 (ttp80) cc_final: 0.4551 (ttt90) REVERT: G 771 GLN cc_start: 0.6525 (mt0) cc_final: 0.6182 (mt0) REVERT: G 781 LYS cc_start: 0.6493 (tttt) cc_final: 0.6067 (ttpp) REVERT: G 785 ASP cc_start: 0.6021 (t0) cc_final: 0.5794 (t70) REVERT: G 816 THR cc_start: 0.5250 (t) cc_final: 0.4822 (m) REVERT: G 913 GLU cc_start: 0.7045 (tt0) cc_final: 0.6070 (tp30) REVERT: G 983 LYS cc_start: 0.2190 (pttp) cc_final: 0.1746 (pmmt) REVERT: G 1144 LEU cc_start: 0.6752 (tt) cc_final: 0.6550 (mp) REVERT: G 1152 GLU cc_start: 0.6036 (pt0) cc_final: 0.5285 (pp20) REVERT: G 1276 GLU cc_start: 0.5234 (mm-30) cc_final: 0.3802 (pp20) REVERT: G 1280 VAL cc_start: 0.6470 (t) cc_final: 0.6196 (p) REVERT: G 1327 GLU cc_start: 0.5434 (mt-10) cc_final: 0.5201 (mp0) REVERT: G 1370 MET cc_start: 0.4583 (mmp) cc_final: 0.4146 (mmm) outliers start: 3 outliers final: 1 residues processed: 527 average time/residue: 1.6001 time to fit residues: 963.5158 Evaluate side-chains 349 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 348 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1304 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 270 optimal weight: 3.9990 chunk 242 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 163 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 250 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 186 optimal weight: 0.0570 chunk 290 optimal weight: 0.0010 overall best weight: 0.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 ASN E 132 HIS F 327 GLN F 406 ASN F 463 GLN ** F 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1129 ASN G 274 ASN ** G 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 ASN G 910 ASN G1326 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5518 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26797 Z= 0.165 Angle : 0.540 11.641 36495 Z= 0.275 Chirality : 0.042 0.234 4173 Planarity : 0.004 0.059 4537 Dihedral : 15.188 179.641 4282 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.62 % Allowed : 8.43 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % 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: -0.33 (0.15), residues: 3154 helix: 0.74 (0.16), residues: 1077 sheet: -0.23 (0.26), residues: 369 loop : -0.82 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 115 HIS 0.006 0.001 HIS G 430 PHE 0.020 0.001 PHE F1221 TYR 0.016 0.001 TYR G1282 ARG 0.007 0.000 ARG F 731 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 372 time to evaluate : 2.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 12 ARG cc_start: 0.4716 (ttm-80) cc_final: 0.4440 (mmm160) REVERT: D 77 ASP cc_start: 0.6273 (m-30) cc_final: 0.6067 (t70) REVERT: D 80 GLU cc_start: 0.5953 (tp30) cc_final: 0.5611 (tp30) REVERT: D 166 ARG cc_start: 0.5610 (mtm180) cc_final: 0.5323 (pmm-80) REVERT: D 226 GLU cc_start: 0.6083 (mt-10) cc_final: 0.5704 (tm-30) REVERT: D 229 GLU cc_start: 0.5047 (mt-10) cc_final: 0.4728 (pp20) REVERT: E 150 ARG cc_start: 0.5012 (mtm110) cc_final: 0.4008 (ptm160) REVERT: E 200 LYS cc_start: 0.3823 (tttt) cc_final: 0.3385 (mtpp) REVERT: E 223 ILE cc_start: 0.4463 (mt) cc_final: 0.4171 (mt) REVERT: E 226 GLU cc_start: 0.5533 (tt0) cc_final: 0.5266 (tt0) REVERT: F 81 ASP cc_start: 0.5526 (t70) cc_final: 0.5293 (p0) REVERT: F 83 GLN cc_start: 0.6314 (tm130) cc_final: 0.5887 (mp-120) REVERT: F 211 ARG cc_start: 0.4268 (OUTLIER) cc_final: 0.3341 (mtt90) REVERT: F 422 LYS cc_start: 0.5792 (ptpt) cc_final: 0.4836 (mmtm) REVERT: F 430 LYS cc_start: 0.4315 (mttt) cc_final: 0.3569 (ttpt) REVERT: F 459 MET cc_start: 0.5510 (mtm) cc_final: 0.5081 (mtt) REVERT: F 488 MET cc_start: 0.1789 (mmp) cc_final: 0.0688 (pp-130) REVERT: F 527 LYS cc_start: 0.6515 (mttt) cc_final: 0.6231 (mtmt) REVERT: F 542 ARG cc_start: 0.4106 (mmt180) cc_final: 0.3808 (mmt180) REVERT: F 555 TYR cc_start: 0.5892 (t80) cc_final: 0.5609 (t80) REVERT: F 584 TYR cc_start: 0.6349 (m-80) cc_final: 0.5653 (m-80) REVERT: F 602 GLU cc_start: 0.5601 (tp30) cc_final: 0.5249 (mp0) REVERT: F 604 HIS cc_start: 0.6519 (m90) cc_final: 0.6309 (m170) REVERT: F 639 LYS cc_start: 0.6664 (tttt) cc_final: 0.6349 (mmmt) REVERT: F 651 ASP cc_start: 0.6521 (m-30) cc_final: 0.6134 (m-30) REVERT: F 657 THR cc_start: 0.7372 (m) cc_final: 0.6896 (t) REVERT: F 677 ASN cc_start: 0.6314 (m110) cc_final: 0.5662 (t0) REVERT: F 688 GLN cc_start: 0.6074 (tt0) cc_final: 0.5782 (mt0) REVERT: F 694 ARG cc_start: 0.7353 (mtm-85) cc_final: 0.7077 (mtp85) REVERT: F 723 VAL cc_start: 0.7571 (t) cc_final: 0.7247 (p) REVERT: F 754 THR cc_start: 0.6626 (p) cc_final: 0.6146 (t) REVERT: F 756 TYR cc_start: 0.5312 (m-80) cc_final: 0.4997 (m-10) REVERT: F 768 MET cc_start: 0.6260 (mtp) cc_final: 0.5640 (mmm) REVERT: F 778 GLU cc_start: 0.5590 (OUTLIER) cc_final: 0.5277 (mp0) REVERT: F 785 ASP cc_start: 0.6303 (m-30) cc_final: 0.6080 (m-30) REVERT: F 790 ASP cc_start: 0.4854 (t70) cc_final: 0.4541 (t70) REVERT: F 820 GLU cc_start: 0.7562 (tp30) cc_final: 0.7073 (tp30) REVERT: F 835 GLU cc_start: 0.6224 (tt0) cc_final: 0.6021 (tm-30) REVERT: F 873 ILE cc_start: 0.6846 (mm) cc_final: 0.6583 (tt) REVERT: F 1038 GLN cc_start: 0.6098 (tp40) cc_final: 0.5716 (tp-100) REVERT: F 1053 TYR cc_start: 0.5811 (m-80) cc_final: 0.5453 (m-10) REVERT: F 1073 LYS cc_start: 0.8066 (ttmm) cc_final: 0.7707 (ttmm) REVERT: F 1085 MET cc_start: 0.6685 (mmm) cc_final: 0.6411 (mmm) REVERT: F 1160 ASP cc_start: 0.4928 (OUTLIER) cc_final: 0.4417 (t0) REVERT: F 1188 ASP cc_start: 0.5595 (t0) cc_final: 0.5254 (t0) REVERT: F 1191 LYS cc_start: 0.5225 (mmmt) cc_final: 0.4588 (mtpp) REVERT: F 1203 ASP cc_start: 0.5007 (m-30) cc_final: 0.4655 (m-30) REVERT: F 1211 ARG cc_start: 0.7321 (ttm170) cc_final: 0.7036 (ttm170) REVERT: F 1338 GLU cc_start: 0.5838 (pm20) cc_final: 0.5464 (pp20) REVERT: G 123 ARG cc_start: 0.5707 (OUTLIER) cc_final: 0.4626 (tpp-160) REVERT: G 134 ASP cc_start: 0.5678 (m-30) cc_final: 0.5072 (OUTLIER) REVERT: G 233 LYS cc_start: 0.5947 (mtpt) cc_final: 0.5646 (mtpp) REVERT: G 278 ARG cc_start: 0.5676 (ttp80) cc_final: 0.5301 (ttt180) REVERT: G 329 ASP cc_start: 0.6684 (m-30) cc_final: 0.6352 (m-30) REVERT: G 363 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6940 (tm) REVERT: G 400 MET cc_start: 0.4546 (mtp) cc_final: 0.4011 (ttt) REVERT: G 417 ARG cc_start: 0.4623 (tpp80) cc_final: 0.4328 (tpp-160) REVERT: G 438 GLU cc_start: 0.5740 (mt-10) cc_final: 0.5475 (tt0) REVERT: G 449 LEU cc_start: 0.6899 (tp) cc_final: 0.6555 (tt) REVERT: G 537 TYR cc_start: 0.6003 (t80) cc_final: 0.5744 (t80) REVERT: G 580 TRP cc_start: 0.6791 (t-100) cc_final: 0.6340 (t-100) REVERT: G 634 ARG cc_start: 0.6400 (ttm-80) cc_final: 0.6123 (ttm-80) REVERT: G 648 GLU cc_start: 0.6894 (pm20) cc_final: 0.6592 (tp30) REVERT: G 660 GLU cc_start: 0.6033 (pt0) cc_final: 0.5383 (tt0) REVERT: G 678 ARG cc_start: 0.4933 (ttp80) cc_final: 0.4469 (ttt90) REVERT: G 781 LYS cc_start: 0.6421 (tttt) cc_final: 0.6027 (ttpp) REVERT: G 822 MET cc_start: 0.4003 (OUTLIER) cc_final: 0.3787 (mpp) REVERT: G 983 LYS cc_start: 0.2403 (pttp) cc_final: 0.1915 (pmmt) REVERT: G 1144 LEU cc_start: 0.6779 (tt) cc_final: 0.6452 (mp) REVERT: G 1152 GLU cc_start: 0.5959 (pt0) cc_final: 0.5216 (pp20) REVERT: G 1247 LYS cc_start: 0.6848 (tptp) cc_final: 0.6613 (tptp) REVERT: G 1250 ASP cc_start: 0.5513 (OUTLIER) cc_final: 0.5205 (m-30) REVERT: G 1276 GLU cc_start: 0.5354 (mm-30) cc_final: 0.3873 (pp20) REVERT: G 1280 VAL cc_start: 0.6528 (t) cc_final: 0.6247 (p) REVERT: G 1370 MET cc_start: 0.4401 (mmp) cc_final: 0.3658 (mpm) outliers start: 69 outliers final: 30 residues processed: 406 average time/residue: 1.4393 time to fit residues: 677.5399 Evaluate side-chains 358 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 322 time to evaluate : 2.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain E residue 51 MET Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain F residue 211 ARG Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain F residue 394 ARG Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 539 THR Chi-restraints excluded: chain F residue 589 THR Chi-restraints excluded: chain F residue 778 GLU Chi-restraints excluded: chain F residue 811 ASN Chi-restraints excluded: chain F residue 871 VAL Chi-restraints excluded: chain F residue 1155 VAL Chi-restraints excluded: chain F residue 1160 ASP Chi-restraints excluded: chain F residue 1172 LEU Chi-restraints excluded: chain F residue 1254 VAL Chi-restraints excluded: chain G residue 123 ARG Chi-restraints excluded: chain G residue 144 TYR Chi-restraints excluded: chain G residue 363 LEU Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 602 SER Chi-restraints excluded: chain G residue 622 ASP Chi-restraints excluded: chain G residue 793 SER Chi-restraints excluded: chain G residue 803 VAL Chi-restraints excluded: chain G residue 810 THR Chi-restraints excluded: chain G residue 822 MET Chi-restraints excluded: chain G residue 932 MET Chi-restraints excluded: chain G residue 1141 VAL Chi-restraints excluded: chain G residue 1250 ASP Chi-restraints excluded: chain G residue 1310 THR Chi-restraints excluded: chain H residue 30 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 161 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 241 optimal weight: 0.5980 chunk 197 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 291 optimal weight: 9.9990 chunk 314 optimal weight: 7.9990 chunk 259 optimal weight: 10.0000 chunk 288 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 233 optimal weight: 0.7980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 128 HIS E 227 GLN ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 554 HIS F1070 HIS ** F1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 ASN ** G 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 669 GLN G 771 GLN ** G1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1326 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5622 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 26797 Z= 0.367 Angle : 0.729 13.011 36495 Z= 0.374 Chirality : 0.048 0.342 4173 Planarity : 0.006 0.067 4537 Dihedral : 15.619 179.587 4279 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.33 % Allowed : 11.83 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.14), residues: 3154 helix: -0.12 (0.15), residues: 1077 sheet: -0.25 (0.26), residues: 374 loop : -1.15 (0.14), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP G 115 HIS 0.013 0.002 HIS G 430 PHE 0.026 0.003 PHE F1221 TYR 0.025 0.003 TYR F1231 ARG 0.009 0.001 ARG G 311 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 354 time to evaluate : 2.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 215 GLU cc_start: 0.5923 (OUTLIER) cc_final: 0.5662 (tp30) REVERT: D 226 GLU cc_start: 0.5875 (mt-10) cc_final: 0.5502 (tm-30) REVERT: E 54 CYS cc_start: 0.5749 (OUTLIER) cc_final: 0.4840 (p) REVERT: E 81 ILE cc_start: 0.5624 (OUTLIER) cc_final: 0.5419 (tp) REVERT: E 132 HIS cc_start: 0.5086 (m90) cc_final: 0.4830 (m170) REVERT: E 148 ARG cc_start: 0.6018 (ttt-90) cc_final: 0.5319 (ttt90) REVERT: E 200 LYS cc_start: 0.3969 (tttt) cc_final: 0.3366 (mtpm) REVERT: E 223 ILE cc_start: 0.4486 (mt) cc_final: 0.4118 (mt) REVERT: E 226 GLU cc_start: 0.5581 (tt0) cc_final: 0.5279 (tt0) REVERT: F 81 ASP cc_start: 0.5492 (t70) cc_final: 0.5210 (p0) REVERT: F 203 LYS cc_start: 0.6483 (mtmt) cc_final: 0.6235 (mtmm) REVERT: F 334 GLU cc_start: 0.5271 (mm-30) cc_final: 0.4579 (pm20) REVERT: F 349 GLU cc_start: 0.6079 (mt-10) cc_final: 0.5267 (tp30) REVERT: F 417 SER cc_start: 0.6995 (p) cc_final: 0.6542 (t) REVERT: F 430 LYS cc_start: 0.4053 (mttt) cc_final: 0.3232 (ttpp) REVERT: F 459 MET cc_start: 0.5595 (mtm) cc_final: 0.4981 (mtt) REVERT: F 461 GLU cc_start: 0.6773 (pp20) cc_final: 0.6152 (pt0) REVERT: F 527 LYS cc_start: 0.6607 (mttt) cc_final: 0.6215 (mtmt) REVERT: F 542 ARG cc_start: 0.3952 (mmt180) cc_final: 0.3677 (mmt180) REVERT: F 602 GLU cc_start: 0.5655 (tp30) cc_final: 0.5179 (mm-30) REVERT: F 639 LYS cc_start: 0.6871 (tttt) cc_final: 0.6489 (mmmt) REVERT: F 657 THR cc_start: 0.7328 (OUTLIER) cc_final: 0.6657 (t) REVERT: F 659 GLN cc_start: 0.7571 (tt0) cc_final: 0.7319 (tt0) REVERT: F 688 GLN cc_start: 0.6136 (tt0) cc_final: 0.5849 (mt0) REVERT: F 694 ARG cc_start: 0.7377 (mtm-85) cc_final: 0.7158 (mtp85) REVERT: F 754 THR cc_start: 0.6591 (p) cc_final: 0.6028 (t) REVERT: F 756 TYR cc_start: 0.5366 (m-80) cc_final: 0.5030 (m-10) REVERT: F 768 MET cc_start: 0.6442 (mtp) cc_final: 0.6119 (mtp) REVERT: F 778 GLU cc_start: 0.5865 (OUTLIER) cc_final: 0.5601 (mp0) REVERT: F 820 GLU cc_start: 0.7546 (tp30) cc_final: 0.6853 (tp30) REVERT: F 873 ILE cc_start: 0.6846 (mm) cc_final: 0.6587 (tt) REVERT: F 968 GLU cc_start: 0.3945 (OUTLIER) cc_final: 0.3733 (pm20) REVERT: F 1030 GLU cc_start: 0.6688 (mm-30) cc_final: 0.6419 (mm-30) REVERT: F 1038 GLN cc_start: 0.6538 (tp40) cc_final: 0.6217 (tp-100) REVERT: F 1053 TYR cc_start: 0.5934 (m-80) cc_final: 0.5462 (m-10) REVERT: F 1066 MET cc_start: 0.7588 (ttp) cc_final: 0.7221 (mmm) REVERT: F 1073 LYS cc_start: 0.8016 (ttmm) cc_final: 0.7620 (tttm) REVERT: F 1160 ASP cc_start: 0.4974 (OUTLIER) cc_final: 0.4394 (t0) REVERT: F 1188 ASP cc_start: 0.6004 (t0) cc_final: 0.5672 (t0) REVERT: F 1191 LYS cc_start: 0.5452 (mmmt) cc_final: 0.4743 (mtmm) REVERT: F 1203 ASP cc_start: 0.5176 (m-30) cc_final: 0.4840 (m-30) REVERT: F 1211 ARG cc_start: 0.7429 (ttm170) cc_final: 0.7154 (ttm170) REVERT: F 1279 GLU cc_start: 0.6321 (mt-10) cc_final: 0.6052 (mm-30) REVERT: F 1306 LYS cc_start: 0.5475 (mttt) cc_final: 0.4850 (ttpp) REVERT: G 211 GLU cc_start: 0.5652 (OUTLIER) cc_final: 0.5117 (pm20) REVERT: G 233 LYS cc_start: 0.5975 (mtpt) cc_final: 0.5714 (mtpp) REVERT: G 278 ARG cc_start: 0.5686 (ttp80) cc_final: 0.5462 (ttp80) REVERT: G 329 ASP cc_start: 0.6823 (m-30) cc_final: 0.6507 (m-30) REVERT: G 335 GLN cc_start: 0.5930 (mm110) cc_final: 0.5657 (mm-40) REVERT: G 400 MET cc_start: 0.4784 (mtp) cc_final: 0.4208 (ttt) REVERT: G 484 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.5983 (mmm) REVERT: G 552 ILE cc_start: 0.5879 (pt) cc_final: 0.5616 (mp) REVERT: G 580 TRP cc_start: 0.6912 (t-100) cc_final: 0.6521 (t-100) REVERT: G 648 GLU cc_start: 0.6943 (pm20) cc_final: 0.6553 (tp30) REVERT: G 660 GLU cc_start: 0.6074 (pt0) cc_final: 0.5535 (tt0) REVERT: G 678 ARG cc_start: 0.5106 (ttp80) cc_final: 0.4499 (ttt90) REVERT: G 691 ASP cc_start: 0.5118 (m-30) cc_final: 0.4905 (m-30) REVERT: G 725 MET cc_start: 0.5813 (mtt) cc_final: 0.5567 (mtp) REVERT: G 781 LYS cc_start: 0.6507 (tttt) cc_final: 0.6091 (ttpp) REVERT: G 822 MET cc_start: 0.4266 (OUTLIER) cc_final: 0.3929 (mpp) REVERT: G 833 GLU cc_start: 0.6869 (mt-10) cc_final: 0.6451 (mm-30) REVERT: G 837 ASP cc_start: 0.5660 (m-30) cc_final: 0.5337 (m-30) REVERT: G 1152 GLU cc_start: 0.5962 (pt0) cc_final: 0.5286 (pp20) REVERT: G 1250 ASP cc_start: 0.5670 (OUTLIER) cc_final: 0.5325 (m-30) REVERT: G 1327 GLU cc_start: 0.6281 (OUTLIER) cc_final: 0.5773 (mm-30) REVERT: G 1365 TYR cc_start: 0.5189 (t80) cc_final: 0.4279 (t80) REVERT: G 1370 MET cc_start: 0.4204 (mmp) cc_final: 0.3705 (mmm) outliers start: 88 outliers final: 38 residues processed: 406 average time/residue: 1.4760 time to fit residues: 692.8004 Evaluate side-chains 369 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 319 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain E residue 51 MET Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 227 GLN Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 36 GLN Chi-restraints excluded: chain F residue 394 ARG Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 539 THR Chi-restraints excluded: chain F residue 589 THR Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 657 THR Chi-restraints excluded: chain F residue 704 MET Chi-restraints excluded: chain F residue 778 GLU Chi-restraints excluded: chain F residue 811 ASN Chi-restraints excluded: chain F residue 871 VAL Chi-restraints excluded: chain F residue 968 GLU Chi-restraints excluded: chain F residue 1155 VAL Chi-restraints excluded: chain F residue 1160 ASP Chi-restraints excluded: chain F residue 1172 LEU Chi-restraints excluded: chain F residue 1254 VAL Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain G residue 151 MET Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 225 GLU Chi-restraints excluded: chain G residue 363 LEU Chi-restraints excluded: chain G residue 466 MET Chi-restraints excluded: chain G residue 484 MET Chi-restraints excluded: chain G residue 602 SER Chi-restraints excluded: chain G residue 614 LEU Chi-restraints excluded: chain G residue 721 SER Chi-restraints excluded: chain G residue 793 SER Chi-restraints excluded: chain G residue 803 VAL Chi-restraints excluded: chain G residue 810 THR Chi-restraints excluded: chain G residue 822 MET Chi-restraints excluded: chain G residue 982 LEU Chi-restraints excluded: chain G residue 1141 VAL Chi-restraints excluded: chain G residue 1250 ASP Chi-restraints excluded: chain G residue 1310 THR Chi-restraints excluded: chain G residue 1321 SER Chi-restraints excluded: chain G residue 1327 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 287 optimal weight: 9.9990 chunk 218 optimal weight: 0.9990 chunk 151 optimal weight: 0.6980 chunk 32 optimal weight: 0.0770 chunk 138 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 chunk 292 optimal weight: 4.9990 chunk 309 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 276 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 339 ASN ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 HIS F 573 ASN F 622 ASN F1256 GLN ** F1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 ASN G 364 HIS G 489 ASN ** G1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1326 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5577 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26797 Z= 0.186 Angle : 0.570 11.158 36495 Z= 0.291 Chirality : 0.043 0.252 4173 Planarity : 0.004 0.061 4537 Dihedral : 15.326 179.807 4279 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.14 % Allowed : 13.72 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % 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: -0.72 (0.14), residues: 3154 helix: 0.29 (0.15), residues: 1078 sheet: -0.15 (0.26), residues: 358 loop : -1.04 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 183 HIS 0.010 0.001 HIS G 430 PHE 0.017 0.001 PHE F1221 TYR 0.016 0.001 TYR G 382 ARG 0.008 0.000 ARG F 478 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 344 time to evaluate : 2.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 60 GLU cc_start: 0.4716 (OUTLIER) cc_final: 0.4257 (mp0) REVERT: D 80 GLU cc_start: 0.6198 (tp30) cc_final: 0.5968 (tp30) REVERT: D 215 GLU cc_start: 0.5871 (OUTLIER) cc_final: 0.5652 (tm-30) REVERT: D 229 GLU cc_start: 0.4498 (OUTLIER) cc_final: 0.4221 (pt0) REVERT: E 54 CYS cc_start: 0.5886 (m) cc_final: 0.4924 (p) REVERT: E 81 ILE cc_start: 0.5604 (OUTLIER) cc_final: 0.5398 (tp) REVERT: E 132 HIS cc_start: 0.5092 (m90) cc_final: 0.4853 (m-70) REVERT: E 148 ARG cc_start: 0.6006 (ttt-90) cc_final: 0.5393 (ttt90) REVERT: E 150 ARG cc_start: 0.5135 (mtm110) cc_final: 0.4202 (ptm160) REVERT: E 188 GLU cc_start: 0.5516 (pm20) cc_final: 0.5295 (pm20) REVERT: E 200 LYS cc_start: 0.3852 (tttt) cc_final: 0.3417 (mtpp) REVERT: E 223 ILE cc_start: 0.4440 (mt) cc_final: 0.4046 (mp) REVERT: E 226 GLU cc_start: 0.5551 (tt0) cc_final: 0.5282 (tt0) REVERT: F 20 GLN cc_start: 0.5872 (tt0) cc_final: 0.5462 (tp-100) REVERT: F 81 ASP cc_start: 0.5480 (t70) cc_final: 0.5246 (p0) REVERT: F 195 PHE cc_start: 0.5882 (m-10) cc_final: 0.5544 (m-10) REVERT: F 203 LYS cc_start: 0.6458 (mtmt) cc_final: 0.5904 (mptm) REVERT: F 417 SER cc_start: 0.7068 (p) cc_final: 0.6582 (t) REVERT: F 430 LYS cc_start: 0.4322 (mttt) cc_final: 0.3524 (ttpt) REVERT: F 461 GLU cc_start: 0.6796 (pp20) cc_final: 0.6177 (pt0) REVERT: F 527 LYS cc_start: 0.6520 (mttt) cc_final: 0.6159 (mtmt) REVERT: F 542 ARG cc_start: 0.3969 (mmt180) cc_final: 0.3750 (mmt180) REVERT: F 602 GLU cc_start: 0.5600 (tp30) cc_final: 0.5155 (mm-30) REVERT: F 639 LYS cc_start: 0.6850 (tttt) cc_final: 0.6466 (mmmt) REVERT: F 657 THR cc_start: 0.7354 (OUTLIER) cc_final: 0.6739 (t) REVERT: F 659 GLN cc_start: 0.7515 (tt0) cc_final: 0.7274 (tt0) REVERT: F 688 GLN cc_start: 0.6259 (tt0) cc_final: 0.5914 (mt0) REVERT: F 754 THR cc_start: 0.6591 (p) cc_final: 0.6059 (t) REVERT: F 756 TYR cc_start: 0.5210 (m-80) cc_final: 0.5002 (m-10) REVERT: F 778 GLU cc_start: 0.5741 (OUTLIER) cc_final: 0.5468 (mp0) REVERT: F 820 GLU cc_start: 0.7515 (tp30) cc_final: 0.6815 (tp30) REVERT: F 873 ILE cc_start: 0.6845 (mm) cc_final: 0.6578 (tt) REVERT: F 1030 GLU cc_start: 0.6752 (mm-30) cc_final: 0.6448 (mp0) REVERT: F 1038 GLN cc_start: 0.6459 (tp40) cc_final: 0.6163 (tp-100) REVERT: F 1053 TYR cc_start: 0.5913 (m-80) cc_final: 0.5475 (m-10) REVERT: F 1160 ASP cc_start: 0.5049 (OUTLIER) cc_final: 0.4488 (t0) REVERT: F 1188 ASP cc_start: 0.5712 (t0) cc_final: 0.5376 (t0) REVERT: F 1191 LYS cc_start: 0.5410 (mmmt) cc_final: 0.4749 (mtmm) REVERT: F 1203 ASP cc_start: 0.5088 (m-30) cc_final: 0.4767 (m-30) REVERT: F 1211 ARG cc_start: 0.7321 (ttm170) cc_final: 0.7081 (ttm170) REVERT: F 1279 GLU cc_start: 0.6308 (mt-10) cc_final: 0.5996 (mm-30) REVERT: F 1328 LYS cc_start: 0.6142 (mmmt) cc_final: 0.5878 (tppt) REVERT: G 233 LYS cc_start: 0.5998 (mtpt) cc_final: 0.5726 (mtpp) REVERT: G 270 ARG cc_start: 0.4309 (ttp80) cc_final: 0.3837 (ttp80) REVERT: G 278 ARG cc_start: 0.5682 (ttp80) cc_final: 0.5135 (ttp-170) REVERT: G 329 ASP cc_start: 0.6815 (m-30) cc_final: 0.6442 (m-30) REVERT: G 335 GLN cc_start: 0.5994 (mm110) cc_final: 0.5710 (mm-40) REVERT: G 551 ARG cc_start: 0.6392 (OUTLIER) cc_final: 0.5979 (mtp180) REVERT: G 580 TRP cc_start: 0.6791 (t-100) cc_final: 0.6458 (t-100) REVERT: G 603 LYS cc_start: 0.7428 (tmmm) cc_final: 0.7088 (tmmt) REVERT: G 634 ARG cc_start: 0.6789 (ttm-80) cc_final: 0.6522 (ttm-80) REVERT: G 648 GLU cc_start: 0.6912 (pm20) cc_final: 0.6556 (tp30) REVERT: G 678 ARG cc_start: 0.4982 (ttp80) cc_final: 0.4255 (ttt180) REVERT: G 691 ASP cc_start: 0.5130 (m-30) cc_final: 0.4886 (m-30) REVERT: G 781 LYS cc_start: 0.6490 (tttt) cc_final: 0.6054 (ttpp) REVERT: G 833 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6481 (mm-30) REVERT: G 925 GLU cc_start: 0.6939 (tm-30) cc_final: 0.6591 (tm-30) REVERT: G 1152 GLU cc_start: 0.5916 (pt0) cc_final: 0.5300 (pp20) REVERT: G 1250 ASP cc_start: 0.5541 (OUTLIER) cc_final: 0.5258 (m-30) REVERT: G 1327 GLU cc_start: 0.6324 (OUTLIER) cc_final: 0.5861 (mm-30) REVERT: G 1370 MET cc_start: 0.4088 (mmp) cc_final: 0.3634 (mmm) outliers start: 83 outliers final: 42 residues processed: 390 average time/residue: 1.4910 time to fit residues: 671.8998 Evaluate side-chains 360 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 308 time to evaluate : 2.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 51 MET Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain F residue 394 ARG Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 539 THR Chi-restraints excluded: chain F residue 589 THR Chi-restraints excluded: chain F residue 657 THR Chi-restraints excluded: chain F residue 704 MET Chi-restraints excluded: chain F residue 778 GLU Chi-restraints excluded: chain F residue 811 ASN Chi-restraints excluded: chain F residue 871 VAL Chi-restraints excluded: chain F residue 1155 VAL Chi-restraints excluded: chain F residue 1160 ASP Chi-restraints excluded: chain F residue 1172 LEU Chi-restraints excluded: chain F residue 1235 LEU Chi-restraints excluded: chain F residue 1254 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 151 MET Chi-restraints excluded: chain G residue 225 GLU Chi-restraints excluded: chain G residue 330 MET Chi-restraints excluded: chain G residue 363 LEU Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 434 ILE Chi-restraints excluded: chain G residue 551 ARG Chi-restraints excluded: chain G residue 602 SER Chi-restraints excluded: chain G residue 614 LEU Chi-restraints excluded: chain G residue 622 ASP Chi-restraints excluded: chain G residue 697 MET Chi-restraints excluded: chain G residue 721 SER Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain G residue 803 VAL Chi-restraints excluded: chain G residue 810 THR Chi-restraints excluded: chain G residue 982 LEU Chi-restraints excluded: chain G residue 1248 ILE Chi-restraints excluded: chain G residue 1250 ASP Chi-restraints excluded: chain G residue 1321 SER Chi-restraints excluded: chain G residue 1327 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 257 optimal weight: 0.9980 chunk 175 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 230 optimal weight: 0.0870 chunk 127 optimal weight: 3.9990 chunk 263 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 157 optimal weight: 0.6980 chunk 277 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 147 GLN F 462 ASN F 551 HIS F 622 ASN F1072 ASN ** F1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 157 GLN G 274 ASN G 364 HIS G 489 ASN G 907 HIS ** G1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1326 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5585 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26797 Z= 0.201 Angle : 0.573 11.472 36495 Z= 0.292 Chirality : 0.043 0.263 4173 Planarity : 0.004 0.060 4537 Dihedral : 15.271 179.420 4279 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.51 % Allowed : 14.94 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % 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: -0.69 (0.14), residues: 3154 helix: 0.37 (0.16), residues: 1071 sheet: -0.25 (0.26), residues: 357 loop : -1.03 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 183 HIS 0.009 0.001 HIS G 430 PHE 0.017 0.002 PHE F 514 TYR 0.018 0.002 TYR G 382 ARG 0.006 0.000 ARG F1058 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 331 time to evaluate : 3.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 60 GLU cc_start: 0.4713 (OUTLIER) cc_final: 0.4203 (mp0) REVERT: D 215 GLU cc_start: 0.5846 (OUTLIER) cc_final: 0.5615 (tm-30) REVERT: E 54 CYS cc_start: 0.5821 (m) cc_final: 0.4901 (p) REVERT: E 123 ILE cc_start: 0.5508 (mm) cc_final: 0.4950 (tp) REVERT: E 132 HIS cc_start: 0.5071 (m90) cc_final: 0.4725 (m170) REVERT: E 148 ARG cc_start: 0.6086 (ttt-90) cc_final: 0.5474 (ttt90) REVERT: E 150 ARG cc_start: 0.5203 (mtm110) cc_final: 0.4274 (ptm160) REVERT: E 200 LYS cc_start: 0.3852 (tttt) cc_final: 0.3392 (mtpp) REVERT: E 223 ILE cc_start: 0.4418 (mt) cc_final: 0.4034 (mp) REVERT: E 226 GLU cc_start: 0.5556 (tt0) cc_final: 0.5251 (tt0) REVERT: F 20 GLN cc_start: 0.5857 (tt0) cc_final: 0.5508 (tp-100) REVERT: F 81 ASP cc_start: 0.5401 (t70) cc_final: 0.5183 (p0) REVERT: F 196 VAL cc_start: 0.6164 (t) cc_final: 0.5468 (m) REVERT: F 430 LYS cc_start: 0.4268 (mttt) cc_final: 0.3465 (ttpt) REVERT: F 459 MET cc_start: 0.5475 (mtp) cc_final: 0.4913 (mtt) REVERT: F 461 GLU cc_start: 0.6822 (pp20) cc_final: 0.6207 (pt0) REVERT: F 478 ARG cc_start: 0.4349 (tpt-90) cc_final: 0.4140 (tpt90) REVERT: F 527 LYS cc_start: 0.6579 (mttt) cc_final: 0.6177 (mtmt) REVERT: F 542 ARG cc_start: 0.3962 (mmt180) cc_final: 0.3695 (mmt180) REVERT: F 602 GLU cc_start: 0.5640 (tp30) cc_final: 0.5241 (mm-30) REVERT: F 639 LYS cc_start: 0.6795 (tttt) cc_final: 0.6442 (mmmt) REVERT: F 657 THR cc_start: 0.7350 (OUTLIER) cc_final: 0.6720 (t) REVERT: F 685 MET cc_start: 0.6255 (tpp) cc_final: 0.5999 (ttp) REVERT: F 688 GLN cc_start: 0.6254 (tt0) cc_final: 0.6008 (mt0) REVERT: F 754 THR cc_start: 0.6605 (p) cc_final: 0.6068 (t) REVERT: F 756 TYR cc_start: 0.5215 (m-80) cc_final: 0.4993 (m-10) REVERT: F 768 MET cc_start: 0.6140 (mtp) cc_final: 0.5885 (mmm) REVERT: F 778 GLU cc_start: 0.5740 (OUTLIER) cc_final: 0.5465 (mp0) REVERT: F 820 GLU cc_start: 0.7528 (tp30) cc_final: 0.6806 (tp30) REVERT: F 873 ILE cc_start: 0.6843 (mm) cc_final: 0.6561 (tt) REVERT: F 1030 GLU cc_start: 0.6878 (mm-30) cc_final: 0.6546 (mp0) REVERT: F 1038 GLN cc_start: 0.6570 (tp40) cc_final: 0.6355 (tp-100) REVERT: F 1053 TYR cc_start: 0.5911 (m-10) cc_final: 0.5449 (m-10) REVERT: F 1066 MET cc_start: 0.7206 (ttp) cc_final: 0.6886 (mmm) REVERT: F 1160 ASP cc_start: 0.5014 (OUTLIER) cc_final: 0.4418 (t0) REVERT: F 1188 ASP cc_start: 0.5724 (t0) cc_final: 0.5369 (t0) REVERT: F 1191 LYS cc_start: 0.5379 (mmmt) cc_final: 0.4737 (mtmm) REVERT: F 1203 ASP cc_start: 0.5079 (m-30) cc_final: 0.4757 (m-30) REVERT: F 1211 ARG cc_start: 0.7306 (ttm170) cc_final: 0.7072 (ttm170) REVERT: F 1264 GLN cc_start: 0.6021 (mt0) cc_final: 0.5709 (mt0) REVERT: F 1279 GLU cc_start: 0.6260 (mt-10) cc_final: 0.5967 (mm-30) REVERT: G 40 LYS cc_start: 0.6035 (OUTLIER) cc_final: 0.5627 (mptp) REVERT: G 211 GLU cc_start: 0.5452 (OUTLIER) cc_final: 0.4880 (pm20) REVERT: G 222 LYS cc_start: 0.7476 (mtpm) cc_final: 0.7178 (ttmm) REVERT: G 233 LYS cc_start: 0.5963 (mtpt) cc_final: 0.5687 (mtpp) REVERT: G 278 ARG cc_start: 0.5701 (ttp80) cc_final: 0.5409 (ttp80) REVERT: G 329 ASP cc_start: 0.6798 (m-30) cc_final: 0.6435 (m-30) REVERT: G 335 GLN cc_start: 0.6029 (mm110) cc_final: 0.5713 (mm-40) REVERT: G 417 ARG cc_start: 0.4704 (tpp80) cc_final: 0.4132 (tpp-160) REVERT: G 442 ILE cc_start: 0.5588 (OUTLIER) cc_final: 0.5321 (tt) REVERT: G 551 ARG cc_start: 0.6370 (OUTLIER) cc_final: 0.6017 (mtp180) REVERT: G 580 TRP cc_start: 0.6756 (t-100) cc_final: 0.6404 (t-100) REVERT: G 603 LYS cc_start: 0.7455 (tmmm) cc_final: 0.7144 (tmmt) REVERT: G 648 GLU cc_start: 0.6840 (pm20) cc_final: 0.6545 (tp30) REVERT: G 678 ARG cc_start: 0.4951 (ttp80) cc_final: 0.4344 (ttt180) REVERT: G 691 ASP cc_start: 0.5151 (m-30) cc_final: 0.4835 (m-30) REVERT: G 725 MET cc_start: 0.5780 (mtt) cc_final: 0.5557 (mtt) REVERT: G 738 ARG cc_start: 0.6105 (mtp180) cc_final: 0.5196 (ptp-170) REVERT: G 822 MET cc_start: 0.3599 (mpp) cc_final: 0.3391 (mpp) REVERT: G 925 GLU cc_start: 0.6887 (tm-30) cc_final: 0.6545 (tm-30) REVERT: G 1152 GLU cc_start: 0.5841 (pt0) cc_final: 0.5297 (pp20) REVERT: G 1327 GLU cc_start: 0.6326 (mt-10) cc_final: 0.5874 (mm-30) REVERT: G 1355 ARG cc_start: 0.4669 (tpp80) cc_final: 0.3708 (ptp-170) REVERT: G 1370 MET cc_start: 0.4027 (mmp) cc_final: 0.3605 (mmm) outliers start: 93 outliers final: 43 residues processed: 384 average time/residue: 1.4381 time to fit residues: 640.9893 Evaluate side-chains 363 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 311 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 51 MET Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 539 THR Chi-restraints excluded: chain F residue 589 THR Chi-restraints excluded: chain F residue 657 THR Chi-restraints excluded: chain F residue 704 MET Chi-restraints excluded: chain F residue 778 GLU Chi-restraints excluded: chain F residue 811 ASN Chi-restraints excluded: chain F residue 816 ILE Chi-restraints excluded: chain F residue 871 VAL Chi-restraints excluded: chain F residue 1060 ILE Chi-restraints excluded: chain F residue 1155 VAL Chi-restraints excluded: chain F residue 1160 ASP Chi-restraints excluded: chain F residue 1172 LEU Chi-restraints excluded: chain F residue 1254 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 40 LYS Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 151 MET Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 225 GLU Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 434 ILE Chi-restraints excluded: chain G residue 442 ILE Chi-restraints excluded: chain G residue 551 ARG Chi-restraints excluded: chain G residue 602 SER Chi-restraints excluded: chain G residue 614 LEU Chi-restraints excluded: chain G residue 622 ASP Chi-restraints excluded: chain G residue 644 MET Chi-restraints excluded: chain G residue 697 MET Chi-restraints excluded: chain G residue 721 SER Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain G residue 793 SER Chi-restraints excluded: chain G residue 803 VAL Chi-restraints excluded: chain G residue 810 THR Chi-restraints excluded: chain G residue 923 ILE Chi-restraints excluded: chain G residue 982 LEU Chi-restraints excluded: chain G residue 1163 VAL Chi-restraints excluded: chain G residue 1229 VAL Chi-restraints excluded: chain G residue 1321 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 104 optimal weight: 0.7980 chunk 278 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 181 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 309 optimal weight: 0.8980 chunk 257 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 162 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 173 ASN F 462 ASN F 551 HIS F 618 GLN F 622 ASN ** F1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 ASN G 907 HIS ** G1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1326 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5568 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26797 Z= 0.175 Angle : 0.552 10.994 36495 Z= 0.280 Chirality : 0.042 0.244 4173 Planarity : 0.004 0.060 4537 Dihedral : 15.182 179.228 4279 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.88 % Allowed : 16.34 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % 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: -0.57 (0.14), residues: 3154 helix: 0.49 (0.16), residues: 1071 sheet: -0.25 (0.26), residues: 356 loop : -0.95 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 183 HIS 0.007 0.001 HIS G 430 PHE 0.017 0.001 PHE G1145 TYR 0.022 0.001 TYR G 679 ARG 0.006 0.000 ARG F1058 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 329 time to evaluate : 2.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 60 GLU cc_start: 0.4712 (OUTLIER) cc_final: 0.4254 (mp0) REVERT: D 215 GLU cc_start: 0.5815 (OUTLIER) cc_final: 0.5585 (tm-30) REVERT: D 229 GLU cc_start: 0.4458 (pt0) cc_final: 0.4241 (pp20) REVERT: E 54 CYS cc_start: 0.5862 (m) cc_final: 0.4915 (p) REVERT: E 132 HIS cc_start: 0.5102 (m90) cc_final: 0.4740 (m170) REVERT: E 148 ARG cc_start: 0.6037 (ttt-90) cc_final: 0.5409 (ttt90) REVERT: E 150 ARG cc_start: 0.5188 (mtm110) cc_final: 0.4236 (ptm160) REVERT: E 200 LYS cc_start: 0.3879 (tttt) cc_final: 0.3433 (mtpp) REVERT: E 223 ILE cc_start: 0.4444 (mt) cc_final: 0.4046 (mp) REVERT: E 226 GLU cc_start: 0.5533 (tt0) cc_final: 0.5223 (tt0) REVERT: F 20 GLN cc_start: 0.5804 (tt0) cc_final: 0.5521 (tp-100) REVERT: F 81 ASP cc_start: 0.5399 (t70) cc_final: 0.5169 (p0) REVERT: F 86 GLN cc_start: 0.6350 (OUTLIER) cc_final: 0.5798 (mt0) REVERT: F 196 VAL cc_start: 0.6079 (t) cc_final: 0.5397 (m) REVERT: F 197 ARG cc_start: 0.5440 (ttt180) cc_final: 0.4119 (tmm160) REVERT: F 203 LYS cc_start: 0.5870 (mtmm) cc_final: 0.5405 (mptm) REVERT: F 394 ARG cc_start: 0.4471 (tpt90) cc_final: 0.4109 (tpp80) REVERT: F 430 LYS cc_start: 0.4277 (mttt) cc_final: 0.3470 (ttpt) REVERT: F 459 MET cc_start: 0.5479 (mtp) cc_final: 0.4901 (mtt) REVERT: F 461 GLU cc_start: 0.6819 (pp20) cc_final: 0.6193 (pt0) REVERT: F 478 ARG cc_start: 0.4364 (tpt-90) cc_final: 0.4158 (tpt90) REVERT: F 527 LYS cc_start: 0.6560 (mttt) cc_final: 0.6169 (mtmt) REVERT: F 542 ARG cc_start: 0.4013 (mmt180) cc_final: 0.3737 (mmt180) REVERT: F 602 GLU cc_start: 0.5659 (tp30) cc_final: 0.5289 (mm-30) REVERT: F 639 LYS cc_start: 0.6803 (tttt) cc_final: 0.6454 (mmmt) REVERT: F 657 THR cc_start: 0.7323 (OUTLIER) cc_final: 0.6710 (t) REVERT: F 685 MET cc_start: 0.6201 (tpp) cc_final: 0.5596 (ttp) REVERT: F 688 GLN cc_start: 0.6343 (tt0) cc_final: 0.6045 (mt0) REVERT: F 754 THR cc_start: 0.6605 (p) cc_final: 0.6082 (t) REVERT: F 756 TYR cc_start: 0.5220 (m-80) cc_final: 0.4999 (m-10) REVERT: F 778 GLU cc_start: 0.5738 (OUTLIER) cc_final: 0.5458 (mp0) REVERT: F 785 ASP cc_start: 0.6370 (m-30) cc_final: 0.6067 (m-30) REVERT: F 820 GLU cc_start: 0.7499 (tp30) cc_final: 0.6779 (tp30) REVERT: F 835 GLU cc_start: 0.6594 (tt0) cc_final: 0.6376 (pt0) REVERT: F 873 ILE cc_start: 0.6933 (mm) cc_final: 0.6606 (tt) REVERT: F 1030 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6564 (mp0) REVERT: F 1038 GLN cc_start: 0.6578 (tp40) cc_final: 0.6363 (tp-100) REVERT: F 1053 TYR cc_start: 0.5937 (m-10) cc_final: 0.5411 (m-10) REVERT: F 1066 MET cc_start: 0.7067 (ttp) cc_final: 0.6837 (tpp) REVERT: F 1073 LYS cc_start: 0.8010 (ttmm) cc_final: 0.7667 (tttp) REVERT: F 1160 ASP cc_start: 0.5001 (OUTLIER) cc_final: 0.4412 (t0) REVERT: F 1188 ASP cc_start: 0.5548 (t0) cc_final: 0.5224 (t0) REVERT: F 1191 LYS cc_start: 0.5289 (mmmt) cc_final: 0.4655 (mtmm) REVERT: F 1203 ASP cc_start: 0.5110 (m-30) cc_final: 0.4814 (m-30) REVERT: F 1211 ARG cc_start: 0.7269 (ttm170) cc_final: 0.7041 (ttm170) REVERT: F 1264 GLN cc_start: 0.5997 (mt0) cc_final: 0.5659 (mt0) REVERT: F 1279 GLU cc_start: 0.6257 (mt-10) cc_final: 0.5963 (mm-30) REVERT: F 1321 GLU cc_start: 0.4644 (mt-10) cc_final: 0.4440 (pp20) REVERT: G 40 LYS cc_start: 0.6010 (OUTLIER) cc_final: 0.5454 (mptp) REVERT: G 211 GLU cc_start: 0.5404 (OUTLIER) cc_final: 0.4813 (pm20) REVERT: G 222 LYS cc_start: 0.7476 (mtpm) cc_final: 0.7179 (ttmm) REVERT: G 233 LYS cc_start: 0.5917 (mtpt) cc_final: 0.5650 (mtpp) REVERT: G 270 ARG cc_start: 0.4348 (ttp80) cc_final: 0.3880 (ttp80) REVERT: G 278 ARG cc_start: 0.5709 (ttp80) cc_final: 0.5427 (ttp80) REVERT: G 329 ASP cc_start: 0.6829 (m-30) cc_final: 0.6466 (m-30) REVERT: G 335 GLN cc_start: 0.6031 (mm110) cc_final: 0.5690 (mm-40) REVERT: G 417 ARG cc_start: 0.4744 (tpp80) cc_final: 0.4173 (tpp-160) REVERT: G 551 ARG cc_start: 0.6379 (OUTLIER) cc_final: 0.5961 (mtp180) REVERT: G 580 TRP cc_start: 0.6687 (t-100) cc_final: 0.6302 (t-100) REVERT: G 603 LYS cc_start: 0.7483 (tmmm) cc_final: 0.7112 (tmmt) REVERT: G 644 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.6527 (mmm) REVERT: G 648 GLU cc_start: 0.6820 (pm20) cc_final: 0.6443 (tp30) REVERT: G 677 GLU cc_start: 0.5715 (tp30) cc_final: 0.5207 (tm-30) REVERT: G 678 ARG cc_start: 0.5014 (ttp80) cc_final: 0.4366 (ttt180) REVERT: G 691 ASP cc_start: 0.5157 (m-30) cc_final: 0.4832 (m-30) REVERT: G 738 ARG cc_start: 0.6091 (mtp180) cc_final: 0.5205 (ptp-170) REVERT: G 822 MET cc_start: 0.3563 (mpp) cc_final: 0.3314 (mpp) REVERT: G 907 HIS cc_start: 0.5361 (p-80) cc_final: 0.5081 (p90) REVERT: G 925 GLU cc_start: 0.6845 (tm-30) cc_final: 0.6561 (tm-30) REVERT: G 1152 GLU cc_start: 0.5815 (pt0) cc_final: 0.5294 (pp20) REVERT: G 1258 ARG cc_start: 0.6330 (tmt90) cc_final: 0.5843 (tpt-90) REVERT: G 1327 GLU cc_start: 0.6312 (mt-10) cc_final: 0.5827 (mm-30) REVERT: G 1355 ARG cc_start: 0.4670 (tpp80) cc_final: 0.3754 (ptp-170) REVERT: G 1370 MET cc_start: 0.4001 (mmp) cc_final: 0.3587 (mmm) outliers start: 76 outliers final: 38 residues processed: 372 average time/residue: 1.4619 time to fit residues: 630.2984 Evaluate side-chains 358 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 310 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain F residue 86 GLN Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 539 THR Chi-restraints excluded: chain F residue 589 THR Chi-restraints excluded: chain F residue 657 THR Chi-restraints excluded: chain F residue 704 MET Chi-restraints excluded: chain F residue 778 GLU Chi-restraints excluded: chain F residue 811 ASN Chi-restraints excluded: chain F residue 816 ILE Chi-restraints excluded: chain F residue 871 VAL Chi-restraints excluded: chain F residue 951 MET Chi-restraints excluded: chain F residue 1060 ILE Chi-restraints excluded: chain F residue 1155 VAL Chi-restraints excluded: chain F residue 1160 ASP Chi-restraints excluded: chain F residue 1172 LEU Chi-restraints excluded: chain F residue 1254 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 40 LYS Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 151 MET Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 225 GLU Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 434 ILE Chi-restraints excluded: chain G residue 551 ARG Chi-restraints excluded: chain G residue 602 SER Chi-restraints excluded: chain G residue 614 LEU Chi-restraints excluded: chain G residue 622 ASP Chi-restraints excluded: chain G residue 644 MET Chi-restraints excluded: chain G residue 721 SER Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain G residue 803 VAL Chi-restraints excluded: chain G residue 810 THR Chi-restraints excluded: chain G residue 982 LEU Chi-restraints excluded: chain G residue 1040 MET Chi-restraints excluded: chain G residue 1141 VAL Chi-restraints excluded: chain G residue 1163 VAL Chi-restraints excluded: chain G residue 1321 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 298 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 chunk 176 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 chunk 260 optimal weight: 0.2980 chunk 172 optimal weight: 8.9990 chunk 308 optimal weight: 6.9990 chunk 193 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 227 GLN F 462 ASN F 551 HIS F 622 ASN ** F1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 ASN ** G1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1326 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5595 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26797 Z= 0.224 Angle : 0.602 11.411 36495 Z= 0.306 Chirality : 0.044 0.274 4173 Planarity : 0.004 0.061 4537 Dihedral : 15.183 179.458 4279 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.18 % Allowed : 16.82 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % 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: -0.71 (0.14), residues: 3154 helix: 0.32 (0.16), residues: 1066 sheet: -0.24 (0.26), residues: 360 loop : -1.02 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 183 HIS 0.008 0.001 HIS G 430 PHE 0.016 0.002 PHE F 514 TYR 0.027 0.002 TYR G 382 ARG 0.006 0.000 ARG F1058 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 319 time to evaluate : 4.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 13 LEU cc_start: 0.6045 (mt) cc_final: 0.5808 (tp) REVERT: D 60 GLU cc_start: 0.4693 (OUTLIER) cc_final: 0.4233 (mp0) REVERT: D 80 GLU cc_start: 0.6065 (tp30) cc_final: 0.5863 (tp30) REVERT: D 215 GLU cc_start: 0.5869 (OUTLIER) cc_final: 0.5643 (tm-30) REVERT: E 54 CYS cc_start: 0.5772 (m) cc_final: 0.5011 (p) REVERT: E 132 HIS cc_start: 0.5057 (m90) cc_final: 0.4772 (m170) REVERT: E 148 ARG cc_start: 0.6103 (ttt-90) cc_final: 0.5483 (ttt90) REVERT: E 150 ARG cc_start: 0.5229 (mtm110) cc_final: 0.4287 (ptm160) REVERT: E 200 LYS cc_start: 0.3885 (tttt) cc_final: 0.3363 (mtpp) REVERT: E 223 ILE cc_start: 0.4495 (mt) cc_final: 0.4147 (mt) REVERT: E 226 GLU cc_start: 0.5543 (tt0) cc_final: 0.5212 (tt0) REVERT: F 20 GLN cc_start: 0.5849 (tt0) cc_final: 0.5605 (tp-100) REVERT: F 86 GLN cc_start: 0.6367 (OUTLIER) cc_final: 0.5782 (mt0) REVERT: F 196 VAL cc_start: 0.6266 (t) cc_final: 0.5596 (m) REVERT: F 349 GLU cc_start: 0.6117 (mt-10) cc_final: 0.5367 (tp30) REVERT: F 430 LYS cc_start: 0.4202 (mttt) cc_final: 0.3420 (ttpt) REVERT: F 459 MET cc_start: 0.5413 (mtp) cc_final: 0.4854 (mtt) REVERT: F 461 GLU cc_start: 0.6823 (pp20) cc_final: 0.6194 (pt0) REVERT: F 478 ARG cc_start: 0.4391 (tpt-90) cc_final: 0.4164 (tpt90) REVERT: F 527 LYS cc_start: 0.6544 (mttt) cc_final: 0.6160 (mtmt) REVERT: F 542 ARG cc_start: 0.4115 (mmt180) cc_final: 0.3798 (mmt180) REVERT: F 546 GLU cc_start: 0.5928 (tm-30) cc_final: 0.5694 (tm-30) REVERT: F 602 GLU cc_start: 0.5650 (tp30) cc_final: 0.5023 (mp0) REVERT: F 639 LYS cc_start: 0.6790 (tttt) cc_final: 0.6431 (mmmt) REVERT: F 657 THR cc_start: 0.7316 (OUTLIER) cc_final: 0.6648 (t) REVERT: F 685 MET cc_start: 0.6317 (tpp) cc_final: 0.5803 (ttp) REVERT: F 688 GLN cc_start: 0.6319 (tt0) cc_final: 0.5992 (mt0) REVERT: F 754 THR cc_start: 0.6606 (p) cc_final: 0.6083 (t) REVERT: F 756 TYR cc_start: 0.5179 (m-80) cc_final: 0.4957 (m-10) REVERT: F 778 GLU cc_start: 0.5750 (OUTLIER) cc_final: 0.5500 (mp0) REVERT: F 820 GLU cc_start: 0.7548 (tp30) cc_final: 0.6844 (tp30) REVERT: F 873 ILE cc_start: 0.6935 (mm) cc_final: 0.6637 (tt) REVERT: F 972 PHE cc_start: 0.3803 (p90) cc_final: 0.3320 (p90) REVERT: F 1030 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6530 (mp0) REVERT: F 1053 TYR cc_start: 0.5934 (m-10) cc_final: 0.5497 (m-10) REVERT: F 1073 LYS cc_start: 0.8091 (ttmm) cc_final: 0.7649 (tttp) REVERT: F 1160 ASP cc_start: 0.4989 (OUTLIER) cc_final: 0.4405 (t0) REVERT: F 1188 ASP cc_start: 0.5799 (t0) cc_final: 0.5453 (t0) REVERT: F 1191 LYS cc_start: 0.5237 (mmmt) cc_final: 0.4590 (mtmm) REVERT: F 1203 ASP cc_start: 0.5085 (m-30) cc_final: 0.4788 (m-30) REVERT: F 1211 ARG cc_start: 0.7289 (ttm170) cc_final: 0.7057 (ttm170) REVERT: F 1264 GLN cc_start: 0.6014 (mt0) cc_final: 0.5716 (mt0) REVERT: F 1279 GLU cc_start: 0.6303 (mt-10) cc_final: 0.6016 (mm-30) REVERT: F 1339 LEU cc_start: 0.5145 (mt) cc_final: 0.4923 (pt) REVERT: G 211 GLU cc_start: 0.5419 (OUTLIER) cc_final: 0.4858 (pm20) REVERT: G 222 LYS cc_start: 0.7459 (mtpm) cc_final: 0.7167 (ttmm) REVERT: G 233 LYS cc_start: 0.5956 (mtpt) cc_final: 0.5696 (mtpp) REVERT: G 278 ARG cc_start: 0.5682 (ttp80) cc_final: 0.5390 (ttp80) REVERT: G 298 MET cc_start: 0.4906 (mmt) cc_final: 0.4587 (mmp) REVERT: G 329 ASP cc_start: 0.6841 (m-30) cc_final: 0.6486 (m-30) REVERT: G 335 GLN cc_start: 0.6014 (mm110) cc_final: 0.5697 (mm-40) REVERT: G 484 MET cc_start: 0.6163 (mmm) cc_final: 0.5849 (mmm) REVERT: G 551 ARG cc_start: 0.6400 (OUTLIER) cc_final: 0.6024 (mtp180) REVERT: G 552 ILE cc_start: 0.5860 (pt) cc_final: 0.5587 (mp) REVERT: G 580 TRP cc_start: 0.6686 (t-100) cc_final: 0.6274 (t-100) REVERT: G 603 LYS cc_start: 0.7425 (tmmm) cc_final: 0.7061 (tmmt) REVERT: G 648 GLU cc_start: 0.6804 (pm20) cc_final: 0.6509 (tp30) REVERT: G 677 GLU cc_start: 0.5757 (tp30) cc_final: 0.5359 (pp20) REVERT: G 691 ASP cc_start: 0.5168 (m-30) cc_final: 0.4841 (m-30) REVERT: G 738 ARG cc_start: 0.6146 (mtp180) cc_final: 0.5217 (ptp-170) REVERT: G 822 MET cc_start: 0.3717 (mpp) cc_final: 0.3508 (mpp) REVERT: G 833 GLU cc_start: 0.6286 (tm-30) cc_final: 0.5592 (tp30) REVERT: G 871 LEU cc_start: 0.5898 (mt) cc_final: 0.5537 (tm) REVERT: G 907 HIS cc_start: 0.5394 (p-80) cc_final: 0.5101 (p90) REVERT: G 925 GLU cc_start: 0.6885 (tm-30) cc_final: 0.6617 (tm-30) REVERT: G 1152 GLU cc_start: 0.5681 (pt0) cc_final: 0.5244 (pp20) REVERT: G 1258 ARG cc_start: 0.6387 (tmt90) cc_final: 0.5920 (tpt-90) REVERT: G 1327 GLU cc_start: 0.6282 (mt-10) cc_final: 0.5835 (mm-30) REVERT: G 1355 ARG cc_start: 0.4634 (tpp80) cc_final: 0.3728 (ptp-170) REVERT: G 1370 MET cc_start: 0.4049 (mmp) cc_final: 0.3642 (mmm) outliers start: 84 outliers final: 49 residues processed: 372 average time/residue: 1.4428 time to fit residues: 630.4978 Evaluate side-chains 369 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 312 time to evaluate : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 51 MET Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain F residue 36 GLN Chi-restraints excluded: chain F residue 86 GLN Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 539 THR Chi-restraints excluded: chain F residue 589 THR Chi-restraints excluded: chain F residue 657 THR Chi-restraints excluded: chain F residue 677 ASN Chi-restraints excluded: chain F residue 704 MET Chi-restraints excluded: chain F residue 778 GLU Chi-restraints excluded: chain F residue 811 ASN Chi-restraints excluded: chain F residue 816 ILE Chi-restraints excluded: chain F residue 871 VAL Chi-restraints excluded: chain F residue 1060 ILE Chi-restraints excluded: chain F residue 1155 VAL Chi-restraints excluded: chain F residue 1160 ASP Chi-restraints excluded: chain F residue 1172 LEU Chi-restraints excluded: chain F residue 1254 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 40 LYS Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 151 MET Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 225 GLU Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 434 ILE Chi-restraints excluded: chain G residue 551 ARG Chi-restraints excluded: chain G residue 602 SER Chi-restraints excluded: chain G residue 614 LEU Chi-restraints excluded: chain G residue 617 THR Chi-restraints excluded: chain G residue 622 ASP Chi-restraints excluded: chain G residue 644 MET Chi-restraints excluded: chain G residue 705 THR Chi-restraints excluded: chain G residue 721 SER Chi-restraints excluded: chain G residue 747 MET Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain G residue 793 SER Chi-restraints excluded: chain G residue 803 VAL Chi-restraints excluded: chain G residue 810 THR Chi-restraints excluded: chain G residue 982 LEU Chi-restraints excluded: chain G residue 1163 VAL Chi-restraints excluded: chain G residue 1248 ILE Chi-restraints excluded: chain G residue 1280 VAL Chi-restraints excluded: chain G residue 1321 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 190 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 184 optimal weight: 0.0470 chunk 92 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 196 optimal weight: 0.7980 chunk 210 optimal weight: 2.9990 chunk 152 optimal weight: 0.0370 chunk 28 optimal weight: 4.9990 chunk 242 optimal weight: 0.4980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 HIS F 622 ASN ** F1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 ASN G 489 ASN ** G1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1326 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5545 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 26797 Z= 0.159 Angle : 0.546 11.272 36495 Z= 0.276 Chirality : 0.042 0.280 4173 Planarity : 0.004 0.060 4537 Dihedral : 14.981 178.962 4279 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.33 % Allowed : 17.82 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % 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: -0.42 (0.15), residues: 3154 helix: 0.60 (0.16), residues: 1075 sheet: -0.16 (0.26), residues: 348 loop : -0.84 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 183 HIS 0.007 0.001 HIS G 430 PHE 0.016 0.001 PHE F 828 TYR 0.031 0.001 TYR G 382 ARG 0.008 0.000 ARG F1058 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 328 time to evaluate : 2.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 13 LEU cc_start: 0.5879 (mt) cc_final: 0.5656 (tp) REVERT: D 60 GLU cc_start: 0.4685 (OUTLIER) cc_final: 0.4311 (mp0) REVERT: D 215 GLU cc_start: 0.5822 (OUTLIER) cc_final: 0.5581 (tm-30) REVERT: E 54 CYS cc_start: 0.5835 (m) cc_final: 0.4943 (p) REVERT: E 132 HIS cc_start: 0.5057 (m90) cc_final: 0.4789 (m170) REVERT: E 148 ARG cc_start: 0.6007 (ttt-90) cc_final: 0.5392 (ttt90) REVERT: E 150 ARG cc_start: 0.5217 (mtm110) cc_final: 0.4225 (ptm160) REVERT: E 200 LYS cc_start: 0.3866 (tttt) cc_final: 0.3389 (mtpp) REVERT: E 223 ILE cc_start: 0.4425 (mt) cc_final: 0.3973 (mp) REVERT: E 226 GLU cc_start: 0.5650 (tt0) cc_final: 0.5272 (tt0) REVERT: F 20 GLN cc_start: 0.5817 (tt0) cc_final: 0.5616 (tp-100) REVERT: F 86 GLN cc_start: 0.6348 (OUTLIER) cc_final: 0.5787 (mt0) REVERT: F 196 VAL cc_start: 0.6184 (t) cc_final: 0.5591 (m) REVERT: F 203 LYS cc_start: 0.5779 (mtmm) cc_final: 0.5333 (mptm) REVERT: F 430 LYS cc_start: 0.4337 (mttt) cc_final: 0.3553 (ttpt) REVERT: F 459 MET cc_start: 0.5491 (mtp) cc_final: 0.4904 (mtt) REVERT: F 461 GLU cc_start: 0.6811 (pp20) cc_final: 0.6178 (pt0) REVERT: F 527 LYS cc_start: 0.6556 (mttt) cc_final: 0.6164 (mtmt) REVERT: F 542 ARG cc_start: 0.4124 (mmt180) cc_final: 0.3838 (mmt180) REVERT: F 602 GLU cc_start: 0.5509 (tp30) cc_final: 0.4990 (mp0) REVERT: F 639 LYS cc_start: 0.6763 (tttt) cc_final: 0.6420 (mmmt) REVERT: F 657 THR cc_start: 0.7305 (OUTLIER) cc_final: 0.6699 (t) REVERT: F 685 MET cc_start: 0.6191 (tpp) cc_final: 0.5682 (ttp) REVERT: F 688 GLN cc_start: 0.6339 (tt0) cc_final: 0.6084 (mt0) REVERT: F 754 THR cc_start: 0.6618 (p) cc_final: 0.6107 (t) REVERT: F 756 TYR cc_start: 0.5207 (m-80) cc_final: 0.4925 (m-10) REVERT: F 785 ASP cc_start: 0.6363 (m-30) cc_final: 0.6106 (m-30) REVERT: F 820 GLU cc_start: 0.7517 (tp30) cc_final: 0.6800 (tp30) REVERT: F 873 ILE cc_start: 0.6932 (mm) cc_final: 0.6602 (tt) REVERT: F 1030 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6573 (mp0) REVERT: F 1053 TYR cc_start: 0.5940 (m-10) cc_final: 0.5427 (m-10) REVERT: F 1066 MET cc_start: 0.6996 (ttp) cc_final: 0.6740 (tpp) REVERT: F 1073 LYS cc_start: 0.7960 (ttmm) cc_final: 0.7596 (tttp) REVERT: F 1160 ASP cc_start: 0.5062 (OUTLIER) cc_final: 0.4466 (t0) REVERT: F 1188 ASP cc_start: 0.5458 (t0) cc_final: 0.5141 (t0) REVERT: F 1191 LYS cc_start: 0.5226 (mmmt) cc_final: 0.4624 (mtmm) REVERT: F 1203 ASP cc_start: 0.5043 (m-30) cc_final: 0.4752 (m-30) REVERT: F 1211 ARG cc_start: 0.7214 (ttm170) cc_final: 0.6916 (ttm110) REVERT: F 1264 GLN cc_start: 0.5895 (mt0) cc_final: 0.5560 (mt0) REVERT: F 1279 GLU cc_start: 0.6256 (mt-10) cc_final: 0.5958 (mm-30) REVERT: F 1339 LEU cc_start: 0.5123 (mt) cc_final: 0.4905 (pt) REVERT: G 40 LYS cc_start: 0.6011 (OUTLIER) cc_final: 0.5454 (mptp) REVERT: G 211 GLU cc_start: 0.5391 (OUTLIER) cc_final: 0.4635 (pp20) REVERT: G 222 LYS cc_start: 0.7485 (mtpm) cc_final: 0.7190 (ttmm) REVERT: G 233 LYS cc_start: 0.5901 (mtpt) cc_final: 0.5609 (mtpp) REVERT: G 278 ARG cc_start: 0.5736 (ttp80) cc_final: 0.5209 (ttp-170) REVERT: G 298 MET cc_start: 0.4865 (mmt) cc_final: 0.4608 (mmp) REVERT: G 329 ASP cc_start: 0.6834 (m-30) cc_final: 0.6459 (m-30) REVERT: G 335 GLN cc_start: 0.6086 (mm110) cc_final: 0.5738 (mm-40) REVERT: G 417 ARG cc_start: 0.4816 (tpp80) cc_final: 0.4205 (tpp-160) REVERT: G 449 LEU cc_start: 0.6872 (tp) cc_final: 0.6545 (tt) REVERT: G 489 ASN cc_start: 0.7355 (m-40) cc_final: 0.6885 (m-40) REVERT: G 551 ARG cc_start: 0.6308 (mtp180) cc_final: 0.5884 (mtp180) REVERT: G 552 ILE cc_start: 0.5910 (pt) cc_final: 0.5601 (mp) REVERT: G 580 TRP cc_start: 0.6588 (t-100) cc_final: 0.6222 (t-100) REVERT: G 603 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.7128 (tmmt) REVERT: G 644 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.6511 (mmm) REVERT: G 648 GLU cc_start: 0.6754 (pm20) cc_final: 0.6467 (tp30) REVERT: G 677 GLU cc_start: 0.5756 (tp30) cc_final: 0.5381 (pp20) REVERT: G 678 ARG cc_start: 0.5029 (ttp80) cc_final: 0.4372 (ttt180) REVERT: G 691 ASP cc_start: 0.5207 (m-30) cc_final: 0.4918 (m-30) REVERT: G 833 GLU cc_start: 0.6228 (OUTLIER) cc_final: 0.5422 (tp30) REVERT: G 871 LEU cc_start: 0.5860 (mt) cc_final: 0.5511 (tm) REVERT: G 907 HIS cc_start: 0.5313 (p-80) cc_final: 0.5027 (p90) REVERT: G 987 GLU cc_start: 0.3697 (pm20) cc_final: 0.3480 (mp0) REVERT: G 1152 GLU cc_start: 0.5712 (pt0) cc_final: 0.5224 (pp20) REVERT: G 1258 ARG cc_start: 0.6341 (tmt90) cc_final: 0.5844 (tpt-90) REVERT: G 1327 GLU cc_start: 0.6244 (mt-10) cc_final: 0.5794 (mm-30) REVERT: G 1355 ARG cc_start: 0.4649 (tpp80) cc_final: 0.3763 (ptp-170) REVERT: G 1370 MET cc_start: 0.4046 (mmp) cc_final: 0.3626 (mmm) outliers start: 61 outliers final: 35 residues processed: 370 average time/residue: 1.4062 time to fit residues: 607.0864 Evaluate side-chains 346 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 301 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain F residue 86 GLN Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 539 THR Chi-restraints excluded: chain F residue 589 THR Chi-restraints excluded: chain F residue 657 THR Chi-restraints excluded: chain F residue 704 MET Chi-restraints excluded: chain F residue 811 ASN Chi-restraints excluded: chain F residue 816 ILE Chi-restraints excluded: chain F residue 871 VAL Chi-restraints excluded: chain F residue 1060 ILE Chi-restraints excluded: chain F residue 1155 VAL Chi-restraints excluded: chain F residue 1160 ASP Chi-restraints excluded: chain F residue 1172 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 40 LYS Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 151 MET Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 225 GLU Chi-restraints excluded: chain G residue 227 PHE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 602 SER Chi-restraints excluded: chain G residue 603 LYS Chi-restraints excluded: chain G residue 617 THR Chi-restraints excluded: chain G residue 622 ASP Chi-restraints excluded: chain G residue 644 MET Chi-restraints excluded: chain G residue 697 MET Chi-restraints excluded: chain G residue 705 THR Chi-restraints excluded: chain G residue 721 SER Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain G residue 803 VAL Chi-restraints excluded: chain G residue 833 GLU Chi-restraints excluded: chain G residue 982 LEU Chi-restraints excluded: chain G residue 1141 VAL Chi-restraints excluded: chain G residue 1280 VAL Chi-restraints excluded: chain G residue 1321 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 280 optimal weight: 0.8980 chunk 295 optimal weight: 0.1980 chunk 269 optimal weight: 0.5980 chunk 287 optimal weight: 8.9990 chunk 172 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 225 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 259 optimal weight: 3.9990 chunk 271 optimal weight: 1.9990 chunk 286 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 HIS F 622 ASN F1038 GLN ** F1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 ASN ** G1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1326 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5562 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26797 Z= 0.183 Angle : 0.571 11.097 36495 Z= 0.287 Chirality : 0.043 0.301 4173 Planarity : 0.004 0.061 4537 Dihedral : 14.918 179.208 4279 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.44 % Allowed : 18.08 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % 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: -0.42 (0.14), residues: 3154 helix: 0.58 (0.16), residues: 1077 sheet: -0.14 (0.26), residues: 356 loop : -0.84 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 183 HIS 0.006 0.001 HIS G 430 PHE 0.023 0.001 PHE G1145 TYR 0.027 0.001 TYR G 382 ARG 0.010 0.000 ARG F 478 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 311 time to evaluate : 3.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 13 LEU cc_start: 0.5860 (mt) cc_final: 0.5637 (tp) REVERT: D 60 GLU cc_start: 0.4683 (OUTLIER) cc_final: 0.4264 (mp0) REVERT: D 215 GLU cc_start: 0.5828 (OUTLIER) cc_final: 0.5590 (tm-30) REVERT: E 54 CYS cc_start: 0.5821 (m) cc_final: 0.4932 (p) REVERT: E 132 HIS cc_start: 0.5023 (m90) cc_final: 0.4769 (m170) REVERT: E 148 ARG cc_start: 0.6037 (ttt-90) cc_final: 0.5424 (ttt90) REVERT: E 150 ARG cc_start: 0.5226 (mtm110) cc_final: 0.4235 (ptm160) REVERT: E 200 LYS cc_start: 0.3857 (tttt) cc_final: 0.3367 (mtpp) REVERT: E 223 ILE cc_start: 0.4457 (mt) cc_final: 0.3994 (mp) REVERT: E 226 GLU cc_start: 0.5619 (tt0) cc_final: 0.5292 (tt0) REVERT: F 20 GLN cc_start: 0.5873 (tt0) cc_final: 0.5641 (tp-100) REVERT: F 81 ASP cc_start: 0.5378 (p0) cc_final: 0.4856 (t0) REVERT: F 86 GLN cc_start: 0.6340 (OUTLIER) cc_final: 0.5805 (mt0) REVERT: F 196 VAL cc_start: 0.6288 (t) cc_final: 0.5657 (m) REVERT: F 349 GLU cc_start: 0.6095 (mt-10) cc_final: 0.5423 (tp30) REVERT: F 392 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7121 (mp0) REVERT: F 430 LYS cc_start: 0.4288 (mttt) cc_final: 0.3509 (ttpt) REVERT: F 459 MET cc_start: 0.5550 (mtp) cc_final: 0.4979 (mtt) REVERT: F 461 GLU cc_start: 0.6831 (pp20) cc_final: 0.6215 (pt0) REVERT: F 527 LYS cc_start: 0.6516 (mttt) cc_final: 0.6155 (mtmt) REVERT: F 542 ARG cc_start: 0.4128 (mmt180) cc_final: 0.3820 (mmt180) REVERT: F 602 GLU cc_start: 0.5529 (tp30) cc_final: 0.5012 (mp0) REVERT: F 639 LYS cc_start: 0.6736 (tttt) cc_final: 0.6379 (mmmt) REVERT: F 657 THR cc_start: 0.7315 (OUTLIER) cc_final: 0.6690 (t) REVERT: F 685 MET cc_start: 0.6201 (tpp) cc_final: 0.5661 (ttp) REVERT: F 688 GLN cc_start: 0.6315 (tt0) cc_final: 0.6008 (mt0) REVERT: F 754 THR cc_start: 0.6608 (p) cc_final: 0.6098 (t) REVERT: F 756 TYR cc_start: 0.5234 (m-80) cc_final: 0.5007 (m-10) REVERT: F 785 ASP cc_start: 0.6356 (m-30) cc_final: 0.6081 (m-30) REVERT: F 820 GLU cc_start: 0.7517 (tp30) cc_final: 0.6924 (tp30) REVERT: F 873 ILE cc_start: 0.6959 (mm) cc_final: 0.6635 (tt) REVERT: F 1030 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6578 (mp0) REVERT: F 1053 TYR cc_start: 0.5938 (m-10) cc_final: 0.5505 (m-10) REVERT: F 1066 MET cc_start: 0.7132 (ttp) cc_final: 0.6687 (tpp) REVERT: F 1073 LYS cc_start: 0.7796 (ttmm) cc_final: 0.7059 (ttpp) REVERT: F 1160 ASP cc_start: 0.5025 (OUTLIER) cc_final: 0.4431 (t0) REVERT: F 1188 ASP cc_start: 0.5549 (t0) cc_final: 0.5203 (t0) REVERT: F 1191 LYS cc_start: 0.5176 (mmmt) cc_final: 0.4582 (mtmm) REVERT: F 1203 ASP cc_start: 0.5063 (m-30) cc_final: 0.4772 (m-30) REVERT: F 1211 ARG cc_start: 0.7220 (ttm170) cc_final: 0.6920 (ttm110) REVERT: F 1264 GLN cc_start: 0.5942 (mt0) cc_final: 0.5590 (mt0) REVERT: F 1279 GLU cc_start: 0.6282 (mt-10) cc_final: 0.5982 (mm-30) REVERT: F 1315 MET cc_start: 0.3150 (mmm) cc_final: 0.2230 (mmt) REVERT: F 1339 LEU cc_start: 0.5166 (mt) cc_final: 0.4917 (pt) REVERT: G 222 LYS cc_start: 0.7493 (mtpm) cc_final: 0.7194 (ttmm) REVERT: G 233 LYS cc_start: 0.5925 (mtpt) cc_final: 0.5628 (mtpp) REVERT: G 278 ARG cc_start: 0.5720 (ttp80) cc_final: 0.5448 (ttp80) REVERT: G 298 MET cc_start: 0.4873 (mmt) cc_final: 0.4560 (mmp) REVERT: G 329 ASP cc_start: 0.6721 (m-30) cc_final: 0.6345 (m-30) REVERT: G 335 GLN cc_start: 0.6060 (mm110) cc_final: 0.5719 (mm-40) REVERT: G 449 LEU cc_start: 0.6868 (tp) cc_final: 0.6546 (tt) REVERT: G 551 ARG cc_start: 0.6381 (OUTLIER) cc_final: 0.5968 (mtp180) REVERT: G 552 ILE cc_start: 0.5921 (pt) cc_final: 0.5625 (mp) REVERT: G 603 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.7117 (tmmt) REVERT: G 644 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.6482 (mmm) REVERT: G 648 GLU cc_start: 0.6752 (pm20) cc_final: 0.6546 (tp30) REVERT: G 677 GLU cc_start: 0.5742 (tp30) cc_final: 0.5209 (tm-30) REVERT: G 691 ASP cc_start: 0.5287 (m-30) cc_final: 0.4947 (m-30) REVERT: G 738 ARG cc_start: 0.6140 (mtp180) cc_final: 0.5243 (ptp-170) REVERT: G 822 MET cc_start: 0.3857 (mpp) cc_final: 0.3542 (mpp) REVERT: G 833 GLU cc_start: 0.6231 (OUTLIER) cc_final: 0.5415 (tp30) REVERT: G 871 LEU cc_start: 0.5877 (mt) cc_final: 0.5519 (tm) REVERT: G 907 HIS cc_start: 0.5349 (p-80) cc_final: 0.5070 (p90) REVERT: G 987 GLU cc_start: 0.3564 (pm20) cc_final: 0.3314 (mp0) REVERT: G 1152 GLU cc_start: 0.5663 (pt0) cc_final: 0.5249 (pp20) REVERT: G 1258 ARG cc_start: 0.6371 (tmt90) cc_final: 0.5852 (tpt-90) REVERT: G 1327 GLU cc_start: 0.6260 (mt-10) cc_final: 0.5806 (mm-30) REVERT: G 1355 ARG cc_start: 0.4659 (tpp80) cc_final: 0.3752 (ptp-170) REVERT: G 1370 MET cc_start: 0.4015 (mmp) cc_final: 0.3601 (mmm) outliers start: 64 outliers final: 38 residues processed: 354 average time/residue: 1.4526 time to fit residues: 599.9838 Evaluate side-chains 355 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 308 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain F residue 86 GLN Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 539 THR Chi-restraints excluded: chain F residue 589 THR Chi-restraints excluded: chain F residue 641 GLU Chi-restraints excluded: chain F residue 657 THR Chi-restraints excluded: chain F residue 704 MET Chi-restraints excluded: chain F residue 811 ASN Chi-restraints excluded: chain F residue 871 VAL Chi-restraints excluded: chain F residue 1060 ILE Chi-restraints excluded: chain F residue 1155 VAL Chi-restraints excluded: chain F residue 1160 ASP Chi-restraints excluded: chain F residue 1172 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 40 LYS Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 151 MET Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 225 GLU Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 434 ILE Chi-restraints excluded: chain G residue 551 ARG Chi-restraints excluded: chain G residue 602 SER Chi-restraints excluded: chain G residue 603 LYS Chi-restraints excluded: chain G residue 614 LEU Chi-restraints excluded: chain G residue 617 THR Chi-restraints excluded: chain G residue 622 ASP Chi-restraints excluded: chain G residue 644 MET Chi-restraints excluded: chain G residue 697 MET Chi-restraints excluded: chain G residue 705 THR Chi-restraints excluded: chain G residue 721 SER Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain G residue 833 GLU Chi-restraints excluded: chain G residue 982 LEU Chi-restraints excluded: chain G residue 1163 VAL Chi-restraints excluded: chain G residue 1280 VAL Chi-restraints excluded: chain G residue 1321 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 188 optimal weight: 1.9990 chunk 303 optimal weight: 0.9980 chunk 185 optimal weight: 6.9990 chunk 144 optimal weight: 0.0020 chunk 211 optimal weight: 1.9990 chunk 318 optimal weight: 1.9990 chunk 293 optimal weight: 1.9990 chunk 253 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 155 optimal weight: 0.4980 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 227 GLN ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 HIS F 622 ASN ** F1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 ASN G 489 ASN G 504 GLN G 875 ASN ** G1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5574 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26797 Z= 0.204 Angle : 0.592 11.161 36495 Z= 0.298 Chirality : 0.043 0.302 4173 Planarity : 0.004 0.060 4537 Dihedral : 14.917 179.684 4279 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.14 % Allowed : 18.52 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % 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: -0.48 (0.14), residues: 3154 helix: 0.54 (0.16), residues: 1063 sheet: -0.14 (0.26), residues: 352 loop : -0.88 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 183 HIS 0.006 0.001 HIS F 551 PHE 0.017 0.001 PHE G1145 TYR 0.024 0.001 TYR G 382 ARG 0.006 0.000 ARG F1058 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 312 time to evaluate : 2.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 13 LEU cc_start: 0.5883 (mt) cc_final: 0.5668 (tp) REVERT: D 60 GLU cc_start: 0.4672 (OUTLIER) cc_final: 0.4232 (mp0) REVERT: D 215 GLU cc_start: 0.5828 (OUTLIER) cc_final: 0.5588 (tm-30) REVERT: E 54 CYS cc_start: 0.5803 (m) cc_final: 0.4997 (p) REVERT: E 132 HIS cc_start: 0.5058 (m90) cc_final: 0.4842 (m170) REVERT: E 148 ARG cc_start: 0.6055 (ttt-90) cc_final: 0.5439 (ttt90) REVERT: E 150 ARG cc_start: 0.5234 (mtm110) cc_final: 0.4253 (ptm160) REVERT: E 200 LYS cc_start: 0.3872 (tttt) cc_final: 0.3376 (mtpp) REVERT: E 223 ILE cc_start: 0.4480 (mt) cc_final: 0.4111 (mp) REVERT: E 226 GLU cc_start: 0.5620 (tt0) cc_final: 0.5299 (tt0) REVERT: F 20 GLN cc_start: 0.5878 (tt0) cc_final: 0.5663 (tp-100) REVERT: F 81 ASP cc_start: 0.5293 (p0) cc_final: 0.4756 (t0) REVERT: F 86 GLN cc_start: 0.6355 (OUTLIER) cc_final: 0.5790 (mt0) REVERT: F 119 GLU cc_start: 0.6213 (mm-30) cc_final: 0.4157 (tp30) REVERT: F 196 VAL cc_start: 0.6332 (t) cc_final: 0.5722 (m) REVERT: F 203 LYS cc_start: 0.5840 (mtmm) cc_final: 0.5295 (mmtp) REVERT: F 349 GLU cc_start: 0.6081 (mt-10) cc_final: 0.5421 (pt0) REVERT: F 430 LYS cc_start: 0.4305 (mttt) cc_final: 0.3522 (ttpt) REVERT: F 459 MET cc_start: 0.5517 (mtp) cc_final: 0.4958 (mtt) REVERT: F 461 GLU cc_start: 0.6841 (pp20) cc_final: 0.6212 (pt0) REVERT: F 478 ARG cc_start: 0.4454 (tpt-90) cc_final: 0.4247 (tpt90) REVERT: F 527 LYS cc_start: 0.6557 (mttt) cc_final: 0.6298 (mtmt) REVERT: F 542 ARG cc_start: 0.4047 (mmt180) cc_final: 0.3747 (mmt180) REVERT: F 602 GLU cc_start: 0.5493 (tp30) cc_final: 0.4972 (mp0) REVERT: F 639 LYS cc_start: 0.6805 (tttt) cc_final: 0.6439 (mmmt) REVERT: F 657 THR cc_start: 0.7315 (OUTLIER) cc_final: 0.6666 (t) REVERT: F 685 MET cc_start: 0.6075 (tpp) cc_final: 0.5550 (OUTLIER) REVERT: F 688 GLN cc_start: 0.6339 (tt0) cc_final: 0.5999 (mt0) REVERT: F 754 THR cc_start: 0.6581 (p) cc_final: 0.6065 (t) REVERT: F 756 TYR cc_start: 0.5221 (m-80) cc_final: 0.4998 (m-10) REVERT: F 785 ASP cc_start: 0.6406 (m-30) cc_final: 0.6090 (m-30) REVERT: F 820 GLU cc_start: 0.7582 (tp30) cc_final: 0.6875 (tp30) REVERT: F 873 ILE cc_start: 0.6943 (mm) cc_final: 0.6633 (tt) REVERT: F 1030 GLU cc_start: 0.6822 (mm-30) cc_final: 0.6570 (mp0) REVERT: F 1053 TYR cc_start: 0.5951 (m-10) cc_final: 0.5523 (m-10) REVERT: F 1066 MET cc_start: 0.7220 (ttp) cc_final: 0.6785 (tpp) REVERT: F 1160 ASP cc_start: 0.5018 (OUTLIER) cc_final: 0.4416 (t0) REVERT: F 1188 ASP cc_start: 0.5575 (t0) cc_final: 0.5249 (t0) REVERT: F 1191 LYS cc_start: 0.5238 (mmmt) cc_final: 0.4580 (mtmm) REVERT: F 1203 ASP cc_start: 0.5049 (m-30) cc_final: 0.4758 (m-30) REVERT: F 1211 ARG cc_start: 0.7223 (ttm170) cc_final: 0.7010 (ttm170) REVERT: F 1264 GLN cc_start: 0.5995 (mt0) cc_final: 0.5684 (mt0) REVERT: F 1279 GLU cc_start: 0.6318 (mt-10) cc_final: 0.6018 (mm-30) REVERT: F 1315 MET cc_start: 0.3185 (mmm) cc_final: 0.2275 (mmt) REVERT: F 1328 LYS cc_start: 0.5922 (OUTLIER) cc_final: 0.5689 (mptm) REVERT: F 1339 LEU cc_start: 0.5180 (mt) cc_final: 0.4930 (pt) REVERT: G 222 LYS cc_start: 0.7493 (mtpm) cc_final: 0.7199 (ttmm) REVERT: G 227 PHE cc_start: 0.6138 (OUTLIER) cc_final: 0.4814 (t80) REVERT: G 233 LYS cc_start: 0.5891 (mtpt) cc_final: 0.5353 (mtpp) REVERT: G 278 ARG cc_start: 0.5697 (ttp80) cc_final: 0.5430 (ttp80) REVERT: G 329 ASP cc_start: 0.6777 (m-30) cc_final: 0.6421 (m-30) REVERT: G 335 GLN cc_start: 0.6015 (mm110) cc_final: 0.5686 (mm-40) REVERT: G 449 LEU cc_start: 0.6859 (tp) cc_final: 0.6525 (tt) REVERT: G 551 ARG cc_start: 0.6385 (OUTLIER) cc_final: 0.6167 (mtp180) REVERT: G 552 ILE cc_start: 0.5992 (pt) cc_final: 0.5679 (mp) REVERT: G 603 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.7094 (tmmt) REVERT: G 648 GLU cc_start: 0.6778 (pm20) cc_final: 0.6520 (tp30) REVERT: G 677 GLU cc_start: 0.5745 (tp30) cc_final: 0.5195 (tm-30) REVERT: G 691 ASP cc_start: 0.5247 (m-30) cc_final: 0.4903 (m-30) REVERT: G 738 ARG cc_start: 0.6148 (mtp180) cc_final: 0.5255 (ptp-170) REVERT: G 907 HIS cc_start: 0.5329 (p-80) cc_final: 0.5035 (p90) REVERT: G 1152 GLU cc_start: 0.5639 (pt0) cc_final: 0.5236 (pp20) REVERT: G 1258 ARG cc_start: 0.6472 (tmt90) cc_final: 0.5953 (tpt-90) REVERT: G 1355 ARG cc_start: 0.4695 (tpp80) cc_final: 0.3740 (ptp-170) REVERT: G 1370 MET cc_start: 0.3948 (mmp) cc_final: 0.3549 (mmm) outliers start: 56 outliers final: 41 residues processed: 350 average time/residue: 1.4746 time to fit residues: 604.9465 Evaluate side-chains 348 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 299 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 227 GLN Chi-restraints excluded: chain F residue 86 GLN Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 539 THR Chi-restraints excluded: chain F residue 589 THR Chi-restraints excluded: chain F residue 641 GLU Chi-restraints excluded: chain F residue 657 THR Chi-restraints excluded: chain F residue 704 MET Chi-restraints excluded: chain F residue 811 ASN Chi-restraints excluded: chain F residue 871 VAL Chi-restraints excluded: chain F residue 968 GLU Chi-restraints excluded: chain F residue 1060 ILE Chi-restraints excluded: chain F residue 1155 VAL Chi-restraints excluded: chain F residue 1160 ASP Chi-restraints excluded: chain F residue 1172 LEU Chi-restraints excluded: chain F residue 1328 LYS Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 40 LYS Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 225 GLU Chi-restraints excluded: chain G residue 227 PHE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 434 ILE Chi-restraints excluded: chain G residue 551 ARG Chi-restraints excluded: chain G residue 602 SER Chi-restraints excluded: chain G residue 603 LYS Chi-restraints excluded: chain G residue 614 LEU Chi-restraints excluded: chain G residue 617 THR Chi-restraints excluded: chain G residue 622 ASP Chi-restraints excluded: chain G residue 644 MET Chi-restraints excluded: chain G residue 697 MET Chi-restraints excluded: chain G residue 705 THR Chi-restraints excluded: chain G residue 721 SER Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain G residue 803 VAL Chi-restraints excluded: chain G residue 982 LEU Chi-restraints excluded: chain G residue 1163 VAL Chi-restraints excluded: chain G residue 1280 VAL Chi-restraints excluded: chain G residue 1321 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 201 optimal weight: 0.0060 chunk 270 optimal weight: 0.0270 chunk 77 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 70 optimal weight: 0.3980 chunk 254 optimal weight: 4.9990 chunk 106 optimal weight: 0.0070 chunk 261 optimal weight: 0.4980 chunk 32 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 overall best weight: 0.1872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 HIS F 622 ASN G 274 ASN G 424 ASN G 489 ASN ** G1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.239058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.204179 restraints weight = 42504.326| |-----------------------------------------------------------------------------| r_work (start): 0.4461 rms_B_bonded: 2.98 r_work: 0.4214 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4214 r_free = 0.4214 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4214 r_free = 0.4214 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6029 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 26797 Z= 0.151 Angle : 0.566 11.471 36495 Z= 0.283 Chirality : 0.042 0.289 4173 Planarity : 0.004 0.060 4537 Dihedral : 14.810 179.456 4279 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.48 % Allowed : 19.41 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % 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: 3154 helix: 0.76 (0.16), residues: 1071 sheet: -0.04 (0.27), residues: 352 loop : -0.77 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 183 HIS 0.006 0.001 HIS G 907 PHE 0.021 0.001 PHE G1145 TYR 0.049 0.001 TYR G 723 ARG 0.006 0.000 ARG F1058 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10780.65 seconds wall clock time: 194 minutes 37.41 seconds (11677.41 seconds total)