Starting phenix.real_space_refine on Fri Mar 22 18:01:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ltj_0974/03_2024/6ltj_0974.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ltj_0974/03_2024/6ltj_0974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ltj_0974/03_2024/6ltj_0974.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ltj_0974/03_2024/6ltj_0974.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ltj_0974/03_2024/6ltj_0974.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ltj_0974/03_2024/6ltj_0974.pdb" } resolution = 3.7 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= 0.107 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 238 5.49 5 S 150 5.16 5 C 20942 2.51 5 N 6119 2.21 5 O 6833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 47": "OE1" <-> "OE2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "F ARG 35": "NH1" <-> "NH2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "I ARG 370": "NH1" <-> "NH2" Residue "I ARG 408": "NH1" <-> "NH2" Residue "I GLU 449": "OE1" <-> "OE2" Residue "I GLU 861": "OE1" <-> "OE2" Residue "I ARG 1308": "NH1" <-> "NH2" Residue "J TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 80": "OE1" <-> "OE2" Residue "J GLU 114": "OE1" <-> "OE2" Residue "K GLU 83": "OE1" <-> "OE2" Residue "K GLU 167": "OE1" <-> "OE2" Residue "K GLU 205": "OE1" <-> "OE2" Residue "K PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 1718": "OE1" <-> "OE2" Residue "L ARG 1721": "NH1" <-> "NH2" Residue "L GLU 1956": "OE1" <-> "OE2" Residue "L GLU 2120": "OE1" <-> "OE2" Residue "L ARG 2232": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M ARG 190": "NH1" <-> "NH2" Residue "M ARG 201": "NH1" <-> "NH2" Residue "M PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 246": "OE1" <-> "OE2" Residue "M ARG 261": "NH1" <-> "NH2" Residue "M GLU 360": "OE1" <-> "OE2" Residue "N ARG 443": "NH1" <-> "NH2" Residue "N ARG 487": "NH1" <-> "NH2" Residue "N ARG 630": "NH1" <-> "NH2" Residue "N GLU 893": "OE1" <-> "OE2" Residue "N ARG 917": "NH1" <-> "NH2" Residue "N GLU 937": "OE1" <-> "OE2" Residue "O ARG 466": "NH1" <-> "NH2" Residue "O ARG 599": "NH1" <-> "NH2" Residue "O GLU 600": "OE1" <-> "OE2" Residue "O GLU 611": "OE1" <-> "OE2" Residue "O ARG 630": "NH1" <-> "NH2" Residue "O ARG 882": "NH1" <-> "NH2" Residue "P GLU 429": "OE1" <-> "OE2" Residue "P ARG 446": "NH1" <-> "NH2" Residue "P GLU 480": "OE1" <-> "OE2" Residue "P GLU 489": "OE1" <-> "OE2" Residue "P ARG 503": "NH1" <-> "NH2" Residue "Q ARG 201": "NH1" <-> "NH2" Residue "Q GLU 209": "OE1" <-> "OE2" Residue "Q ARG 223": "NH1" <-> "NH2" Residue "R GLU 58": "OE1" <-> "OE2" Residue "R ARG 62": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34283 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 739 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 726 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "D" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 682 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "E" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 739 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "F" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "G" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 727 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "H" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 700 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "I" Number of atoms: 4606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4606 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 14, 'TRANS': 536} Chain breaks: 11 Chain: "J" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2612 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 15, 'TRANS': 318} Chain breaks: 4 Chain: "K" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2482 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain breaks: 3 Chain: "L" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3670 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 25, 'TRANS': 440} Chain breaks: 4 Chain: "M" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2277 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 13, 'TRANS': 269} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "N" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2120 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 6, 'TRANS': 254} Chain breaks: 3 Chain: "O" Number of atoms: 2632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2632 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 19, 'TRANS': 305} Chain breaks: 3 Chain: "P" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 2015 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 14, 'TRANS': 224} Chain breaks: 2 Chain: "Q" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 860 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "R" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 580 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "X" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2424 Classifications: {'DNA': 119} Link IDs: {'rna3p': 118} Chain: "Y" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2455 Classifications: {'DNA': 119} Link IDs: {'rna3p': 118} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17569 SG CYS L2094 67.231 67.353 64.589 1.00 48.48 S Time building chain proxies: 18.52, per 1000 atoms: 0.54 Number of scatterers: 34283 At special positions: 0 Unit cell: (223.6, 175.76, 183.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 150 16.00 P 238 15.00 O 6833 8.00 N 6119 7.00 C 20942 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.10 Conformation dependent library (CDL) restraints added in 5.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L2301 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L2019 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L2021 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L2090 " pdb="ZN ZN L2301 " - pdb=" SG CYS L2094 " Number of angles added : 3 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6972 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 27 sheets defined 63.5% alpha, 5.3% beta 100 base pairs and 205 stacking pairs defined. Time for finding SS restraints: 12.78 Creating SS restraints... Processing helix chain 'A' and resid 42 through 54 Processing helix chain 'A' and resid 60 through 76 Processing helix chain 'A' and resid 82 through 111 Processing helix chain 'A' and resid 117 through 128 removed outlier: 3.876A pdb=" N ILE A 121 " --> pdb=" O MET A 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.808A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.985A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.640A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.690A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.885A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.569A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 119 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.875A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 50 through 76 removed outlier: 4.368A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.648A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.370A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.521A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 35 through 43 removed outlier: 3.865A pdb=" N VAL H 41 " --> pdb=" O TYR H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.520A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.633A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 387 removed outlier: 3.565A pdb=" N ASN I 387 " --> pdb=" O GLN I 383 " (cutoff:3.500A) Processing helix chain 'I' and resid 397 through 409 Processing helix chain 'I' and resid 409 through 428 removed outlier: 3.552A pdb=" N GLN I 415 " --> pdb=" O ASN I 411 " (cutoff:3.500A) Processing helix chain 'I' and resid 430 through 434 Processing helix chain 'I' and resid 446 through 517 removed outlier: 3.882A pdb=" N ALA I 450 " --> pdb=" O SER I 446 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN I 477 " --> pdb=" O GLN I 473 " (cutoff:3.500A) Processing helix chain 'I' and resid 757 through 768 Processing helix chain 'I' and resid 784 through 795 removed outlier: 4.023A pdb=" N TYR I 795 " --> pdb=" O ALA I 791 " (cutoff:3.500A) Processing helix chain 'I' and resid 812 through 826 removed outlier: 3.501A pdb=" N ASN I 817 " --> pdb=" O SER I 813 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N TRP I 818 " --> pdb=" O THR I 814 " (cutoff:3.500A) Processing helix chain 'I' and resid 839 through 844 Processing helix chain 'I' and resid 845 through 849 removed outlier: 3.794A pdb=" N LEU I 848 " --> pdb=" O VAL I 845 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG I 849 " --> pdb=" O PRO I 846 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 845 through 849' Processing helix chain 'I' and resid 893 through 898 removed outlier: 4.253A pdb=" N ASN I 898 " --> pdb=" O THR I 894 " (cutoff:3.500A) Processing helix chain 'I' and resid 899 through 901 No H-bonds generated for 'chain 'I' and resid 899 through 901' Processing helix chain 'I' and resid 917 through 925 Processing helix chain 'I' and resid 931 through 939 removed outlier: 3.712A pdb=" N SER I 935 " --> pdb=" O THR I 931 " (cutoff:3.500A) Processing helix chain 'I' and resid 972 through 976 removed outlier: 3.924A pdb=" N PHE I 975 " --> pdb=" O LEU I 972 " (cutoff:3.500A) Processing helix chain 'I' and resid 1001 through 1013 Processing helix chain 'I' and resid 1039 through 1048 Processing helix chain 'I' and resid 1055 through 1059 Processing helix chain 'I' and resid 1079 through 1089 Processing helix chain 'I' and resid 1107 through 1120 Processing helix chain 'I' and resid 1179 through 1182 removed outlier: 4.069A pdb=" N GLN I1182 " --> pdb=" O ASN I1179 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1179 through 1182' Processing helix chain 'I' and resid 1183 through 1192 removed outlier: 4.986A pdb=" N ALA I1190 " --> pdb=" O ALA I1186 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG I1192 " --> pdb=" O ASP I1188 " (cutoff:3.500A) Processing helix chain 'I' and resid 1300 through 1306 Processing helix chain 'I' and resid 1311 through 1323 removed outlier: 4.561A pdb=" N ARG I1323 " --> pdb=" O MET I1319 " (cutoff:3.500A) Processing helix chain 'I' and resid 1352 through 1362 Processing helix chain 'J' and resid 70 through 77 Processing helix chain 'J' and resid 95 through 110 Processing helix chain 'J' and resid 129 through 143 removed outlier: 3.709A pdb=" N HIS J 143 " --> pdb=" O LEU J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 154 through 162 Processing helix chain 'J' and resid 198 through 213 removed outlier: 3.555A pdb=" N MET J 213 " --> pdb=" O LEU J 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 248 through 266 Processing helix chain 'J' and resid 304 through 310 removed outlier: 3.549A pdb=" N GLY J 307 " --> pdb=" O ILE J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 324 through 335 Processing helix chain 'J' and resid 340 through 347 Processing helix chain 'J' and resid 359 through 371 removed outlier: 4.058A pdb=" N ARG J 363 " --> pdb=" O SER J 359 " (cutoff:3.500A) Processing helix chain 'J' and resid 391 through 399 Processing helix chain 'J' and resid 404 through 409 Processing helix chain 'K' and resid 80 through 91 Processing helix chain 'K' and resid 112 through 125 Processing helix chain 'K' and resid 137 through 146 Processing helix chain 'K' and resid 181 through 196 removed outlier: 4.067A pdb=" N ARG K 196 " --> pdb=" O ILE K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 204 through 216 removed outlier: 4.961A pdb=" N ARG K 210 " --> pdb=" O ARG K 206 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ASP K 211 " --> pdb=" O GLU K 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 231 Processing helix chain 'K' and resid 252 through 257 Processing helix chain 'K' and resid 258 through 261 Processing helix chain 'K' and resid 263 through 268 Processing helix chain 'K' and resid 273 through 284 Processing helix chain 'K' and resid 289 through 296 Processing helix chain 'K' and resid 301 through 305 Processing helix chain 'K' and resid 308 through 321 Processing helix chain 'K' and resid 337 through 345 removed outlier: 3.581A pdb=" N ILE K 345 " --> pdb=" O ILE K 341 " (cutoff:3.500A) Processing helix chain 'K' and resid 346 through 353 removed outlier: 5.799A pdb=" N SER K 350 " --> pdb=" O ALA K 347 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N THR K 351 " --> pdb=" O SER K 348 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN K 353 " --> pdb=" O SER K 350 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 366 Processing helix chain 'K' and resid 367 through 372 removed outlier: 3.577A pdb=" N ARG K 372 " --> pdb=" O ILE K 369 " (cutoff:3.500A) Processing helix chain 'L' and resid 1645 through 1649 Processing helix chain 'L' and resid 1668 through 1679 removed outlier: 4.055A pdb=" N GLY L1679 " --> pdb=" O SER L1675 " (cutoff:3.500A) Processing helix chain 'L' and resid 1680 through 1697 Processing helix chain 'L' and resid 1698 through 1701 removed outlier: 3.727A pdb=" N ILE L1701 " --> pdb=" O ASP L1698 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1698 through 1701' Processing helix chain 'L' and resid 1705 through 1709 Processing helix chain 'L' and resid 1711 through 1729 Processing helix chain 'L' and resid 1740 through 1745 Processing helix chain 'L' and resid 1840 through 1846 removed outlier: 3.578A pdb=" N TRP L1844 " --> pdb=" O GLY L1840 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE L1846 " --> pdb=" O LEU L1842 " (cutoff:3.500A) Processing helix chain 'L' and resid 1971 through 1992 Processing helix chain 'L' and resid 1996 through 2002 removed outlier: 4.201A pdb=" N GLU L2000 " --> pdb=" O GLY L1996 " (cutoff:3.500A) Processing helix chain 'L' and resid 2004 through 2016 removed outlier: 4.406A pdb=" N LEU L2016 " --> pdb=" O GLY L2012 " (cutoff:3.500A) Processing helix chain 'L' and resid 2049 through 2068 removed outlier: 3.644A pdb=" N MET L2055 " --> pdb=" O ASP L2051 " (cutoff:3.500A) Processing helix chain 'L' and resid 2069 through 2071 No H-bonds generated for 'chain 'L' and resid 2069 through 2071' Processing helix chain 'L' and resid 2077 through 2094 Proline residue: L2083 - end of helix Processing helix chain 'L' and resid 2113 through 2127 Processing helix chain 'L' and resid 2128 through 2137 Processing helix chain 'L' and resid 2140 through 2158 removed outlier: 3.723A pdb=" N LEU L2144 " --> pdb=" O PRO L2140 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ARG L2158 " --> pdb=" O PHE L2154 " (cutoff:3.500A) Processing helix chain 'L' and resid 2160 through 2178 Processing helix chain 'L' and resid 2178 through 2187 removed outlier: 3.654A pdb=" N ALA L2182 " --> pdb=" O ASP L2178 " (cutoff:3.500A) Processing helix chain 'L' and resid 2190 through 2209 removed outlier: 3.703A pdb=" N GLN L2209 " --> pdb=" O ALA L2205 " (cutoff:3.500A) Processing helix chain 'L' and resid 2228 through 2243 Processing helix chain 'L' and resid 2247 through 2252 removed outlier: 3.552A pdb=" N PHE L2251 " --> pdb=" O ASN L2247 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR L2252 " --> pdb=" O HIS L2248 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 2247 through 2252' Processing helix chain 'L' and resid 2254 through 2264 Processing helix chain 'L' and resid 2268 through 2284 Processing helix chain 'M' and resid 29 through 36 Processing helix chain 'M' and resid 41 through 47 Processing helix chain 'M' and resid 56 through 66 Processing helix chain 'M' and resid 80 through 84 Processing helix chain 'M' and resid 93 through 98 Processing helix chain 'M' and resid 173 through 181 Processing helix chain 'M' and resid 214 through 226 Processing helix chain 'M' and resid 229 through 248 Proline residue: M 235 - end of helix Processing helix chain 'M' and resid 289 through 302 Processing helix chain 'M' and resid 305 through 324 removed outlier: 4.135A pdb=" N THR M 309 " --> pdb=" O GLY M 305 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA M 312 " --> pdb=" O VAL M 308 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS M 324 " --> pdb=" O SER M 320 " (cutoff:3.500A) Processing helix chain 'M' and resid 342 through 348 Processing helix chain 'M' and resid 357 through 381 removed outlier: 3.741A pdb=" N THR M 381 " --> pdb=" O ARG M 377 " (cutoff:3.500A) Processing helix chain 'N' and resid 427 through 431 Processing helix chain 'N' and resid 440 through 446 Processing helix chain 'N' and resid 447 through 452 removed outlier: 4.692A pdb=" N GLY N 452 " --> pdb=" O GLU N 448 " (cutoff:3.500A) Processing helix chain 'N' and resid 458 through 475 removed outlier: 3.532A pdb=" N LEU N 475 " --> pdb=" O ASP N 471 " (cutoff:3.500A) Processing helix chain 'N' and resid 482 through 490 removed outlier: 3.677A pdb=" N ASN N 489 " --> pdb=" O ALA N 485 " (cutoff:3.500A) Processing helix chain 'N' and resid 493 through 507 Processing helix chain 'N' and resid 603 through 616 Processing helix chain 'N' and resid 620 through 628 removed outlier: 3.553A pdb=" N SER N 624 " --> pdb=" O TRP N 620 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY N 628 " --> pdb=" O SER N 624 " (cutoff:3.500A) Processing helix chain 'N' and resid 631 through 641 Processing helix chain 'N' and resid 672 through 682 Processing helix chain 'N' and resid 685 through 702 Processing helix chain 'N' and resid 859 through 949 Processing helix chain 'O' and resid 439 through 446 removed outlier: 3.599A pdb=" N ARG O 443 " --> pdb=" O HIS O 439 " (cutoff:3.500A) Processing helix chain 'O' and resid 447 through 450 Processing helix chain 'O' and resid 458 through 475 Processing helix chain 'O' and resid 482 through 490 removed outlier: 3.824A pdb=" N CYS O 486 " --> pdb=" O THR O 482 " (cutoff:3.500A) Processing helix chain 'O' and resid 493 through 507 Processing helix chain 'O' and resid 602 through 616 Processing helix chain 'O' and resid 619 through 628 Processing helix chain 'O' and resid 631 through 641 Processing helix chain 'O' and resid 645 through 650 Processing helix chain 'O' and resid 657 through 661 removed outlier: 4.133A pdb=" N TYR O 661 " --> pdb=" O PRO O 658 " (cutoff:3.500A) Processing helix chain 'O' and resid 671 through 684 removed outlier: 3.740A pdb=" N THR O 676 " --> pdb=" O PRO O 672 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE O 679 " --> pdb=" O SER O 675 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL O 684 " --> pdb=" O LEU O 680 " (cutoff:3.500A) Processing helix chain 'O' and resid 685 through 705 removed outlier: 3.535A pdb=" N GLU O 705 " --> pdb=" O SER O 701 " (cutoff:3.500A) Processing helix chain 'O' and resid 711 through 716 Processing helix chain 'O' and resid 868 through 952 removed outlier: 4.276A pdb=" N LYS O 872 " --> pdb=" O ALA O 868 " (cutoff:3.500A) Processing helix chain 'P' and resid 128 through 132 removed outlier: 3.688A pdb=" N LYS P 131 " --> pdb=" O MET P 128 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE P 132 " --> pdb=" O ALA P 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 128 through 132' Processing helix chain 'P' and resid 134 through 141 Processing helix chain 'P' and resid 143 through 173 removed outlier: 3.606A pdb=" N TYR P 147 " --> pdb=" O GLU P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 298 through 306 Processing helix chain 'P' and resid 312 through 327 Processing helix chain 'P' and resid 353 through 355 No H-bonds generated for 'chain 'P' and resid 353 through 355' Processing helix chain 'P' and resid 356 through 361 Processing helix chain 'P' and resid 400 through 411 Processing helix chain 'P' and resid 414 through 447 removed outlier: 3.830A pdb=" N ASP P 447 " --> pdb=" O SER P 443 " (cutoff:3.500A) Processing helix chain 'P' and resid 447 through 468 Processing helix chain 'P' and resid 478 through 484 removed outlier: 3.701A pdb=" N PHE P 483 " --> pdb=" O GLU P 480 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN P 484 " --> pdb=" O PHE P 481 " (cutoff:3.500A) Processing helix chain 'P' and resid 486 through 505 Processing helix chain 'Q' and resid 186 through 207 Processing helix chain 'Q' and resid 220 through 276 Processing helix chain 'R' and resid 14 through 38 Processing helix chain 'R' and resid 58 through 62 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.224A pdb=" N ARG A 80 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 116 removed outlier: 3.589A pdb=" N ILE A 116 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.194A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.768A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.133A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.470A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'I' and resid 991 through 992 Processing sheet with id=AB3, first strand: chain 'I' and resid 991 through 992 removed outlier: 5.702A pdb=" N LEU I1100 " --> pdb=" O ILE I1172 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 35 through 38 removed outlier: 6.529A pdb=" N LEU J 14 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N SER J 123 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N PHE J 16 " --> pdb=" O SER J 123 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 41 through 43 Processing sheet with id=AB6, first strand: chain 'J' and resid 88 through 89 Processing sheet with id=AB7, first strand: chain 'J' and resid 186 through 187 Processing sheet with id=AB8, first strand: chain 'J' and resid 186 through 187 removed outlier: 6.166A pdb=" N LEU J 168 " --> pdb=" O ILE J 349 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ALA J 351 " --> pdb=" O LEU J 168 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU J 170 " --> pdb=" O ALA J 351 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 18 through 21 removed outlier: 6.498A pdb=" N LEU K 8 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N THR K 106 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL K 10 " --> pdb=" O THR K 106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 176 through 178 Processing sheet with id=AC2, first strand: chain 'L' and resid 1814 through 1816 removed outlier: 6.197A pdb=" N LYS L1815 " --> pdb=" O ILE O 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'M' and resid 26 through 28 Processing sheet with id=AC4, first strand: chain 'M' and resid 186 through 195 Processing sheet with id=AC5, first strand: chain 'M' and resid 261 through 270 Processing sheet with id=AC6, first strand: chain 'N' and resid 424 through 426 removed outlier: 7.442A pdb=" N ILE N 424 " --> pdb=" O LEU O 534 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'N' and resid 437 through 439 removed outlier: 6.782A pdb=" N VAL N 438 " --> pdb=" O LEU R 71 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 523 through 524 Processing sheet with id=AC9, first strand: chain 'P' and resid 309 through 311 removed outlier: 3.549A pdb=" N MET P 366 " --> pdb=" O LYS P 296 " (cutoff:3.500A) 1703 hydrogen bonds defined for protein. 4950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 256 hydrogen bonds 508 hydrogen bond angles 0 basepair planarities 100 basepair parallelities 205 stacking parallelities Total time for adding SS restraints: 21.73 Time building geometry restraints manager: 16.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8601 1.33 - 1.46: 9240 1.46 - 1.58: 16840 1.58 - 1.71: 469 1.71 - 1.83: 252 Bond restraints: 35402 Sorted by residual: bond pdb=" C HIS H 46 " pdb=" N PRO H 47 " ideal model delta sigma weight residual 1.334 1.297 0.037 8.40e-03 1.42e+04 1.93e+01 bond pdb=" N VAL I 832 " pdb=" CA VAL I 832 " ideal model delta sigma weight residual 1.456 1.502 -0.046 1.11e-02 8.12e+03 1.74e+01 bond pdb=" CA SER I 478 " pdb=" CB SER I 478 " ideal model delta sigma weight residual 1.528 1.472 0.057 1.56e-02 4.11e+03 1.33e+01 bond pdb=" C THR I 494 " pdb=" O THR I 494 " ideal model delta sigma weight residual 1.237 1.278 -0.041 1.17e-02 7.31e+03 1.23e+01 bond pdb=" N LEU I 928 " pdb=" CA LEU I 928 " ideal model delta sigma weight residual 1.453 1.493 -0.040 1.18e-02 7.18e+03 1.15e+01 ... (remaining 35397 not shown) Histogram of bond angle deviations from ideal: 96.51 - 104.46: 1380 104.46 - 112.42: 18610 112.42 - 120.38: 16352 120.38 - 128.34: 11964 128.34 - 136.29: 505 Bond angle restraints: 48811 Sorted by residual: angle pdb=" N GLN I 515 " pdb=" CA GLN I 515 " pdb=" C GLN I 515 " ideal model delta sigma weight residual 111.36 97.71 13.65 1.09e+00 8.42e-01 1.57e+02 angle pdb=" N GLU I 514 " pdb=" CA GLU I 514 " pdb=" C GLU I 514 " ideal model delta sigma weight residual 113.23 102.27 10.96 1.24e+00 6.50e-01 7.81e+01 angle pdb=" O3' DC X 122 " pdb=" C3' DC X 122 " pdb=" C2' DC X 122 " ideal model delta sigma weight residual 111.50 98.46 13.04 1.50e+00 4.44e-01 7.56e+01 angle pdb=" N PRO I 913 " pdb=" CA PRO I 913 " pdb=" C PRO I 913 " ideal model delta sigma weight residual 111.41 99.48 11.93 1.50e+00 4.44e-01 6.33e+01 angle pdb=" O3' DC X 56 " pdb=" C3' DC X 56 " pdb=" C2' DC X 56 " ideal model delta sigma weight residual 111.50 99.95 11.55 1.50e+00 4.44e-01 5.93e+01 ... (remaining 48806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.23: 19063 34.23 - 68.46: 1745 68.46 - 102.69: 91 102.69 - 136.92: 4 136.92 - 171.16: 8 Dihedral angle restraints: 20911 sinusoidal: 10213 harmonic: 10698 Sorted by residual: dihedral pdb=" C ASP J 339 " pdb=" N ASP J 339 " pdb=" CA ASP J 339 " pdb=" CB ASP J 339 " ideal model delta harmonic sigma weight residual -122.60 -141.57 18.97 0 2.50e+00 1.60e-01 5.76e+01 dihedral pdb=" C ASP J 71 " pdb=" N ASP J 71 " pdb=" CA ASP J 71 " pdb=" CB ASP J 71 " ideal model delta harmonic sigma weight residual -122.60 -140.47 17.87 0 2.50e+00 1.60e-01 5.11e+01 dihedral pdb=" C ASP K 288 " pdb=" N ASP K 288 " pdb=" CA ASP K 288 " pdb=" CB ASP K 288 " ideal model delta harmonic sigma weight residual -122.60 -140.43 17.83 0 2.50e+00 1.60e-01 5.09e+01 ... (remaining 20908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 5243 0.138 - 0.276: 211 0.276 - 0.414: 31 0.414 - 0.552: 3 0.552 - 0.689: 3 Chirality restraints: 5491 Sorted by residual: chirality pdb=" CA ASP J 339 " pdb=" N ASP J 339 " pdb=" C ASP J 339 " pdb=" CB ASP J 339 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" CA ASP J 71 " pdb=" N ASP J 71 " pdb=" C ASP J 71 " pdb=" CB ASP J 71 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CA ASP K 288 " pdb=" N ASP K 288 " pdb=" C ASP K 288 " pdb=" CB ASP K 288 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.89e+00 ... (remaining 5488 not shown) Planarity restraints: 5406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR M 355 " 0.027 2.00e-02 2.50e+03 5.35e-02 2.86e+01 pdb=" C THR M 355 " -0.093 2.00e-02 2.50e+03 pdb=" O THR M 355 " 0.035 2.00e-02 2.50e+03 pdb=" N LEU M 356 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS I 487 " -0.023 2.00e-02 2.50e+03 4.72e-02 2.23e+01 pdb=" C LYS I 487 " 0.082 2.00e-02 2.50e+03 pdb=" O LYS I 487 " -0.031 2.00e-02 2.50e+03 pdb=" N GLU I 488 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU I 768 " 0.023 2.00e-02 2.50e+03 4.64e-02 2.16e+01 pdb=" C LEU I 768 " -0.080 2.00e-02 2.50e+03 pdb=" O LEU I 768 " 0.030 2.00e-02 2.50e+03 pdb=" N TYR I 769 " 0.027 2.00e-02 2.50e+03 ... (remaining 5403 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 2847 2.72 - 3.26: 34746 3.26 - 3.81: 61067 3.81 - 4.35: 75387 4.35 - 4.90: 116660 Nonbonded interactions: 290707 Sorted by model distance: nonbonded pdb=" OD1 ASP L2157 " pdb=" N ARG L2158 " model vdw 2.173 2.520 nonbonded pdb=" OG SER L1645 " pdb=" OG SER O 669 " model vdw 2.202 2.440 nonbonded pdb=" O SER P 410 " pdb=" OG SER P 413 " model vdw 2.212 2.440 nonbonded pdb=" OG SER L2096 " pdb=" OE1 GLU L2098 " model vdw 2.214 2.440 nonbonded pdb=" O LEU L2017 " pdb=" NH2 ARG L2057 " model vdw 2.214 2.520 ... (remaining 290702 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 25 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 16 through 109) selection = (chain 'G' and resid 16 through 109) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 33 through 120) } 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=0.21 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 8.480 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: 30.230 Check model and map are aligned: 0.540 Set scattering table: 0.290 Process input model: 115.040 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.160 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0836 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 : 0.010 0.102 35402 Z= 0.628 Angle : 1.078 13.650 48811 Z= 0.657 Chirality : 0.069 0.689 5491 Planarity : 0.007 0.073 5406 Dihedral : 22.177 171.156 13939 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.45 % Favored : 93.27 % Rotamer: Outliers : 2.63 % Allowed : 9.75 % Favored : 87.61 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.12), residues: 3552 helix: -2.03 (0.09), residues: 2151 sheet: -2.61 (0.37), residues: 152 loop : -2.90 (0.15), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 250 HIS 0.011 0.002 HIS J 105 PHE 0.053 0.003 PHE K 200 TYR 0.040 0.003 TYR I 862 ARG 0.010 0.001 ARG I1009 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 489 time to evaluate : 3.866 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.1759 (mmm) cc_final: 0.0494 (ptp) REVERT: I 482 HIS cc_start: 0.6824 (OUTLIER) cc_final: 0.6550 (t-90) REVERT: I 880 VAL cc_start: 0.0536 (OUTLIER) cc_final: 0.0160 (p) REVERT: I 893 LEU cc_start: -0.0528 (OUTLIER) cc_final: -0.0892 (tp) REVERT: I 915 GLN cc_start: -0.1225 (OUTLIER) cc_final: -0.2344 (pm20) REVERT: I 1040 MET cc_start: -0.3201 (ttp) cc_final: -0.3706 (mtm) REVERT: I 1112 MET cc_start: -0.0488 (mmp) cc_final: -0.3704 (mtm) REVERT: I 1182 GLN cc_start: -0.0680 (OUTLIER) cc_final: -0.2080 (tm-30) REVERT: I 1189 ARG cc_start: 0.2501 (OUTLIER) cc_final: 0.1323 (mtt-85) REVERT: I 1305 MET cc_start: 0.2911 (ppp) cc_final: 0.1891 (mpp) REVERT: I 1317 MET cc_start: 0.3048 (tpt) cc_final: 0.2579 (ttp) REVERT: J 79 ARG cc_start: 0.0826 (OUTLIER) cc_final: -0.0929 (mmt180) REVERT: J 294 ASN cc_start: 0.0579 (OUTLIER) cc_final: -0.0771 (m110) REVERT: K 84 LYS cc_start: 0.7902 (mttt) cc_final: 0.6469 (ptmm) REVERT: K 190 MET cc_start: 0.3940 (mmm) cc_final: 0.3343 (mmm) REVERT: K 250 ILE cc_start: -0.3068 (OUTLIER) cc_final: -0.3417 (pt) REVERT: K 283 MET cc_start: 0.0812 (mmp) cc_final: 0.0474 (tpp) REVERT: K 367 PRO cc_start: 0.0527 (Cg_endo) cc_final: -0.0887 (Cg_exo) REVERT: L 2166 MET cc_start: -0.0361 (mtt) cc_final: -0.2535 (tpp) REVERT: M 44 TYR cc_start: 0.1178 (m-80) cc_final: 0.0632 (t80) REVERT: N 906 PHE cc_start: 0.4703 (t80) cc_final: 0.4454 (t80) REVERT: P 333 GLU cc_start: 0.2022 (tt0) cc_final: 0.1347 (tp30) REVERT: Q 188 MET cc_start: 0.1784 (ppp) cc_final: 0.1419 (mpp) outliers start: 84 outliers final: 6 residues processed: 569 average time/residue: 0.5773 time to fit residues: 501.5431 Evaluate side-chains 275 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 260 time to evaluate : 3.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain I residue 482 HIS Chi-restraints excluded: chain I residue 857 LEU Chi-restraints excluded: chain I residue 880 VAL Chi-restraints excluded: chain I residue 893 LEU Chi-restraints excluded: chain I residue 909 LEU Chi-restraints excluded: chain I residue 915 GLN Chi-restraints excluded: chain I residue 1048 HIS Chi-restraints excluded: chain I residue 1182 GLN Chi-restraints excluded: chain I residue 1189 ARG Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 335 ARG Chi-restraints excluded: chain O residue 521 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 320 optimal weight: 8.9990 chunk 288 optimal weight: 0.9990 chunk 159 optimal weight: 30.0000 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 297 optimal weight: 0.0980 chunk 115 optimal weight: 8.9990 chunk 181 optimal weight: 6.9990 chunk 221 optimal weight: 1.9990 chunk 345 optimal weight: 7.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 90 GLN B 25 ASN C 38 ASN D 44 GLN D 81 ASN D 92 GLN D 106 HIS E 93 GLN F 25 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS ** I 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 473 GLN I 477 ASN I 854 ASN ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1048 HIS I1054 HIS I1182 GLN I1191 HIS I1195 GLN J 183 HIS J 205 GLN J 251 HIS ** J 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1835 GLN ** L1858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1997 ASN L2248 HIS L2268 ASN ** N 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 638 HIS O 439 HIS ** O 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 935 HIS ** P 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 321 GLN P 425 HIS P 432 ASN P 457 GLN Q 232 GLN ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 267 ASN ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 HIS R 70 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1346 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 35402 Z= 0.253 Angle : 0.758 10.866 48811 Z= 0.404 Chirality : 0.045 0.336 5491 Planarity : 0.005 0.059 5406 Dihedral : 24.491 173.734 6601 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.87 % Favored : 95.10 % Rotamer: Outliers : 3.17 % Allowed : 15.30 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.13), residues: 3552 helix: -0.35 (0.10), residues: 2207 sheet: -1.78 (0.40), residues: 154 loop : -2.30 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP N 620 HIS 0.015 0.002 HIS J 183 PHE 0.036 0.002 PHE L2103 TYR 0.022 0.002 TYR I1008 ARG 0.013 0.001 ARG P 334 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 292 time to evaluate : 3.549 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.2595 (mmm) cc_final: 0.0724 (ptp) REVERT: E 131 ARG cc_start: 0.0533 (tpm170) cc_final: -0.0562 (tpp-160) REVERT: I 482 HIS cc_start: 0.6667 (OUTLIER) cc_final: 0.6265 (t-90) REVERT: I 915 GLN cc_start: -0.1335 (OUTLIER) cc_final: -0.2399 (pm20) REVERT: I 1010 HIS cc_start: 0.2368 (OUTLIER) cc_final: 0.0965 (m-70) REVERT: I 1112 MET cc_start: -0.0188 (mmp) cc_final: -0.3061 (mtm) REVERT: I 1164 ASN cc_start: 0.4491 (OUTLIER) cc_final: 0.4280 (t0) REVERT: I 1174 PHE cc_start: 0.2670 (OUTLIER) cc_final: 0.1508 (t80) REVERT: I 1182 GLN cc_start: -0.1517 (OUTLIER) cc_final: -0.2027 (tm-30) REVERT: I 1305 MET cc_start: 0.2758 (ppp) cc_final: 0.1934 (mmt) REVERT: I 1317 MET cc_start: 0.3380 (tpt) cc_final: 0.2165 (ttp) REVERT: J 79 ARG cc_start: 0.0890 (OUTLIER) cc_final: -0.0907 (mmt-90) REVERT: J 92 MET cc_start: -0.4789 (mtt) cc_final: -0.5085 (ttm) REVERT: J 254 MET cc_start: -0.7165 (tpp) cc_final: -0.7437 (tmm) REVERT: J 294 ASN cc_start: 0.0175 (OUTLIER) cc_final: -0.1156 (m110) REVERT: J 365 ASN cc_start: -0.1380 (OUTLIER) cc_final: -0.1890 (m-40) REVERT: K 84 LYS cc_start: 0.7368 (mttt) cc_final: 0.6438 (ptmm) REVERT: K 190 MET cc_start: 0.4332 (mmm) cc_final: 0.3759 (mmm) REVERT: K 250 ILE cc_start: -0.3664 (OUTLIER) cc_final: -0.4214 (pt) REVERT: K 287 VAL cc_start: -0.0505 (p) cc_final: -0.0912 (m) REVERT: L 2058 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.6010 (mm-30) REVERT: L 2166 MET cc_start: 0.0817 (mtt) cc_final: -0.2501 (tpp) REVERT: M 44 TYR cc_start: 0.1867 (m-80) cc_final: 0.1150 (t80) REVERT: M 213 MET cc_start: -0.0595 (mtt) cc_final: -0.0957 (mtt) REVERT: M 375 MET cc_start: 0.2540 (mtm) cc_final: 0.2330 (ttt) REVERT: N 674 MET cc_start: 0.0624 (mmm) cc_final: 0.0404 (mpp) REVERT: N 936 MET cc_start: 0.7380 (mmm) cc_final: 0.6710 (ppp) REVERT: P 333 GLU cc_start: 0.3023 (tt0) cc_final: 0.1391 (tp30) REVERT: P 352 MET cc_start: 0.0762 (tpt) cc_final: 0.0436 (tpt) REVERT: Q 188 MET cc_start: 0.1992 (ppp) cc_final: 0.1517 (mpp) REVERT: Q 257 ARG cc_start: 0.7539 (ttp80) cc_final: 0.7196 (ttp80) outliers start: 101 outliers final: 31 residues processed: 379 average time/residue: 0.5039 time to fit residues: 306.4339 Evaluate side-chains 274 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 232 time to evaluate : 3.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 482 HIS Chi-restraints excluded: chain I residue 857 LEU Chi-restraints excluded: chain I residue 909 LEU Chi-restraints excluded: chain I residue 915 GLN Chi-restraints excluded: chain I residue 924 LEU Chi-restraints excluded: chain I residue 1010 HIS Chi-restraints excluded: chain I residue 1038 THR Chi-restraints excluded: chain I residue 1050 TYR Chi-restraints excluded: chain I residue 1164 ASN Chi-restraints excluded: chain I residue 1174 PHE Chi-restraints excluded: chain I residue 1182 GLN Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 365 ASN Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 252 ASN Chi-restraints excluded: chain L residue 1645 SER Chi-restraints excluded: chain L residue 1812 LEU Chi-restraints excluded: chain L residue 1837 PHE Chi-restraints excluded: chain L residue 2058 GLU Chi-restraints excluded: chain L residue 2206 THR Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain M residue 60 ARG Chi-restraints excluded: chain M residue 263 ILE Chi-restraints excluded: chain M residue 365 ILE Chi-restraints excluded: chain O residue 423 HIS Chi-restraints excluded: chain O residue 437 SER Chi-restraints excluded: chain O residue 458 THR Chi-restraints excluded: chain O residue 521 THR Chi-restraints excluded: chain Q residue 184 ASP Chi-restraints excluded: chain Q residue 190 HIS Chi-restraints excluded: chain Q residue 269 GLU Chi-restraints excluded: chain R residue 42 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 191 optimal weight: 0.8980 chunk 107 optimal weight: 20.0000 chunk 287 optimal weight: 6.9990 chunk 234 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 345 optimal weight: 8.9990 chunk 373 optimal weight: 8.9990 chunk 307 optimal weight: 8.9990 chunk 342 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 chunk 277 optimal weight: 20.0000 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS D 92 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 ASN K 354 GLN ** L1854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1858 HIS ** L1986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 278 GLN ** N 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 513 GLN N 925 GLN ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 513 GLN O 638 HIS O 925 GLN ** O 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 344 GLN P 500 GLN ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1631 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 35402 Z= 0.267 Angle : 0.736 13.910 48811 Z= 0.391 Chirality : 0.044 0.230 5491 Planarity : 0.005 0.059 5406 Dihedral : 24.173 171.112 6588 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.45 % Allowed : 17.40 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.13), residues: 3552 helix: 0.08 (0.10), residues: 2205 sheet: -1.53 (0.39), residues: 166 loop : -2.07 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP N 620 HIS 0.020 0.002 HIS Q 237 PHE 0.031 0.002 PHE L2103 TYR 0.031 0.002 TYR G 50 ARG 0.016 0.001 ARG P 334 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 263 time to evaluate : 3.534 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.4873 (mm) cc_final: 0.4622 (mm) REVERT: B 84 MET cc_start: 0.2883 (mmm) cc_final: 0.1850 (mtm) REVERT: C 91 GLU cc_start: 0.2627 (mp0) cc_final: 0.2172 (pm20) REVERT: I 482 HIS cc_start: 0.6849 (OUTLIER) cc_final: 0.6638 (t-90) REVERT: I 815 LEU cc_start: 0.0339 (OUTLIER) cc_final: -0.0563 (tt) REVERT: I 915 GLN cc_start: -0.1032 (OUTLIER) cc_final: -0.2137 (pm20) REVERT: I 1010 HIS cc_start: 0.2664 (OUTLIER) cc_final: 0.0805 (m-70) REVERT: I 1040 MET cc_start: -0.1709 (mtm) cc_final: -0.1959 (mtm) REVERT: I 1174 PHE cc_start: 0.3270 (OUTLIER) cc_final: 0.1632 (t80) REVERT: I 1182 GLN cc_start: -0.1830 (OUTLIER) cc_final: -0.2323 (tm-30) REVERT: I 1305 MET cc_start: 0.2814 (ppp) cc_final: 0.2177 (mmt) REVERT: I 1317 MET cc_start: 0.3327 (tpt) cc_final: 0.2267 (ttp) REVERT: J 43 MET cc_start: -0.3369 (OUTLIER) cc_final: -0.4809 (mmt) REVERT: J 79 ARG cc_start: 0.1042 (OUTLIER) cc_final: -0.0880 (mmp-170) REVERT: J 254 MET cc_start: -0.7028 (tpp) cc_final: -0.7344 (tmm) REVERT: J 294 ASN cc_start: 0.0328 (OUTLIER) cc_final: -0.1196 (m110) REVERT: J 365 ASN cc_start: -0.1219 (OUTLIER) cc_final: -0.1728 (m110) REVERT: J 376 MET cc_start: -0.0851 (ttp) cc_final: -0.1239 (ptm) REVERT: K 84 LYS cc_start: 0.7397 (mttt) cc_final: 0.6405 (ptmm) REVERT: K 190 MET cc_start: 0.4057 (mmm) cc_final: 0.3513 (mmm) REVERT: K 250 ILE cc_start: -0.4070 (OUTLIER) cc_final: -0.4747 (pt) REVERT: K 287 VAL cc_start: -0.0213 (p) cc_final: -0.0454 (m) REVERT: L 1702 MET cc_start: 0.0784 (mmt) cc_final: -0.0510 (ptt) REVERT: L 2057 ARG cc_start: 0.8255 (mmp80) cc_final: 0.6368 (ttp-110) REVERT: M 44 TYR cc_start: 0.2574 (m-80) cc_final: 0.1417 (t80) REVERT: N 439 HIS cc_start: 0.2601 (t-90) cc_final: 0.2233 (t-90) REVERT: N 444 ARG cc_start: 0.4056 (mtp-110) cc_final: 0.3066 (mtp-110) REVERT: N 498 MET cc_start: 0.0197 (mtp) cc_final: -0.1381 (tpt) REVERT: N 896 MET cc_start: 0.4962 (ptm) cc_final: 0.4679 (ppp) REVERT: N 936 MET cc_start: 0.7048 (mmm) cc_final: 0.6842 (ppp) REVERT: P 333 GLU cc_start: 0.3175 (tt0) cc_final: 0.0804 (tp30) REVERT: Q 188 MET cc_start: 0.2109 (ppp) cc_final: 0.1611 (mpp) REVERT: Q 201 ARG cc_start: 0.6348 (mmt90) cc_final: 0.6130 (mtt180) REVERT: Q 205 GLU cc_start: 0.3400 (pt0) cc_final: 0.2049 (tp30) REVERT: Q 257 ARG cc_start: 0.7689 (ttp80) cc_final: 0.7416 (ttp80) outliers start: 110 outliers final: 48 residues processed: 356 average time/residue: 0.4958 time to fit residues: 282.4620 Evaluate side-chains 301 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 242 time to evaluate : 3.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 475 TYR Chi-restraints excluded: chain I residue 482 HIS Chi-restraints excluded: chain I residue 815 LEU Chi-restraints excluded: chain I residue 857 LEU Chi-restraints excluded: chain I residue 902 VAL Chi-restraints excluded: chain I residue 909 LEU Chi-restraints excluded: chain I residue 915 GLN Chi-restraints excluded: chain I residue 924 LEU Chi-restraints excluded: chain I residue 971 VAL Chi-restraints excluded: chain I residue 1010 HIS Chi-restraints excluded: chain I residue 1050 TYR Chi-restraints excluded: chain I residue 1174 PHE Chi-restraints excluded: chain I residue 1182 GLN Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 365 ASN Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain J residue 403 LEU Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 252 ASN Chi-restraints excluded: chain K residue 305 MET Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain L residue 1645 SER Chi-restraints excluded: chain L residue 1812 LEU Chi-restraints excluded: chain L residue 1837 PHE Chi-restraints excluded: chain L residue 1846 ILE Chi-restraints excluded: chain L residue 2007 LEU Chi-restraints excluded: chain L residue 2010 ILE Chi-restraints excluded: chain L residue 2052 CYS Chi-restraints excluded: chain L residue 2058 GLU Chi-restraints excluded: chain L residue 2152 VAL Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain O residue 458 THR Chi-restraints excluded: chain O residue 521 THR Chi-restraints excluded: chain O residue 646 ASP Chi-restraints excluded: chain O residue 688 VAL Chi-restraints excluded: chain P residue 297 LEU Chi-restraints excluded: chain P residue 337 VAL Chi-restraints excluded: chain Q residue 184 ASP Chi-restraints excluded: chain Q residue 190 HIS Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain Q residue 251 ARG Chi-restraints excluded: chain Q residue 269 GLU Chi-restraints excluded: chain R residue 42 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 341 optimal weight: 6.9990 chunk 259 optimal weight: 1.9990 chunk 179 optimal weight: 50.0000 chunk 38 optimal weight: 4.9990 chunk 164 optimal weight: 8.9990 chunk 232 optimal weight: 9.9990 chunk 346 optimal weight: 3.9990 chunk 367 optimal weight: 7.9990 chunk 181 optimal weight: 0.9980 chunk 328 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN F 25 ASN ** I 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 190 GLN J 365 ASN ** K 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1705 ASN ** L1854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L2173 ASN ** L2194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 260 GLN ** N 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1720 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 35402 Z= 0.226 Angle : 0.677 10.126 48811 Z= 0.362 Chirality : 0.042 0.259 5491 Planarity : 0.005 0.078 5406 Dihedral : 23.986 172.451 6588 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.57 % Allowed : 18.50 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.14), residues: 3552 helix: 0.36 (0.11), residues: 2203 sheet: -1.24 (0.40), residues: 171 loop : -1.94 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP N 620 HIS 0.015 0.001 HIS A 110 PHE 0.028 0.002 PHE L2103 TYR 0.017 0.002 TYR O 922 ARG 0.016 0.001 ARG P 461 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 257 time to evaluate : 3.687 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.4632 (mm) cc_final: 0.4428 (mm) REVERT: B 84 MET cc_start: 0.2882 (mmm) cc_final: 0.1742 (mtm) REVERT: C 91 GLU cc_start: 0.3109 (mp0) cc_final: 0.2423 (pm20) REVERT: E 131 ARG cc_start: 0.0197 (tpm170) cc_final: -0.0559 (tpp-160) REVERT: I 482 HIS cc_start: 0.6983 (OUTLIER) cc_final: 0.6780 (t-170) REVERT: I 886 MET cc_start: 0.1065 (mtt) cc_final: -0.0064 (ptt) REVERT: I 915 GLN cc_start: -0.0879 (OUTLIER) cc_final: -0.2017 (pm20) REVERT: I 971 VAL cc_start: 0.3124 (OUTLIER) cc_final: 0.2880 (p) REVERT: I 1010 HIS cc_start: 0.3038 (OUTLIER) cc_final: 0.0912 (m-70) REVERT: I 1112 MET cc_start: 0.1169 (mmm) cc_final: -0.2729 (ttt) REVERT: I 1174 PHE cc_start: 0.3096 (OUTLIER) cc_final: 0.1485 (t80) REVERT: I 1182 GLN cc_start: -0.1964 (OUTLIER) cc_final: -0.2626 (tm-30) REVERT: I 1189 ARG cc_start: 0.2553 (mpt180) cc_final: 0.1940 (ttm170) REVERT: I 1305 MET cc_start: 0.2990 (ppp) cc_final: 0.2363 (mmt) REVERT: I 1317 MET cc_start: 0.3004 (tpt) cc_final: 0.1994 (ttp) REVERT: J 43 MET cc_start: -0.3513 (OUTLIER) cc_final: -0.4733 (mmt) REVERT: J 79 ARG cc_start: 0.0884 (OUTLIER) cc_final: -0.0788 (mmt-90) REVERT: J 141 PHE cc_start: -0.1438 (OUTLIER) cc_final: -0.2172 (m-80) REVERT: J 177 THR cc_start: -0.4517 (OUTLIER) cc_final: -0.5244 (t) REVERT: J 294 ASN cc_start: 0.0011 (OUTLIER) cc_final: -0.1386 (m110) REVERT: J 365 ASN cc_start: -0.1477 (OUTLIER) cc_final: -0.2032 (m-40) REVERT: K 84 LYS cc_start: 0.7420 (mttt) cc_final: 0.6463 (pttp) REVERT: K 123 MET cc_start: 0.0151 (tpp) cc_final: -0.0682 (tpt) REVERT: K 190 MET cc_start: 0.3976 (mmm) cc_final: 0.3473 (mmm) REVERT: K 250 ILE cc_start: -0.4310 (OUTLIER) cc_final: -0.5070 (pt) REVERT: K 316 GLU cc_start: -0.2823 (OUTLIER) cc_final: -0.3248 (mt-10) REVERT: L 1702 MET cc_start: 0.0410 (mmt) cc_final: -0.0161 (tpt) REVERT: L 2057 ARG cc_start: 0.8109 (mmp80) cc_final: 0.6650 (ttp-110) REVERT: M 44 TYR cc_start: 0.2627 (m-80) cc_final: 0.1634 (t80) REVERT: N 700 PHE cc_start: -0.1905 (m-80) cc_final: -0.2191 (m-80) REVERT: N 896 MET cc_start: 0.4993 (ptm) cc_final: 0.4773 (ppp) REVERT: O 674 MET cc_start: -0.4113 (tpt) cc_final: -0.4455 (tpt) REVERT: P 364 LEU cc_start: 0.2007 (mt) cc_final: 0.0261 (mp) REVERT: P 431 ILE cc_start: 0.2702 (OUTLIER) cc_final: 0.2397 (tt) REVERT: Q 188 MET cc_start: 0.2090 (ppp) cc_final: 0.1614 (mpp) REVERT: Q 201 ARG cc_start: 0.6453 (mmt90) cc_final: 0.6069 (mmt90) REVERT: Q 205 GLU cc_start: 0.3137 (pt0) cc_final: 0.2198 (tp30) REVERT: Q 257 ARG cc_start: 0.7579 (ttp80) cc_final: 0.7192 (ttp80) outliers start: 114 outliers final: 55 residues processed: 352 average time/residue: 0.4830 time to fit residues: 273.3757 Evaluate side-chains 302 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 232 time to evaluate : 3.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 475 TYR Chi-restraints excluded: chain I residue 482 HIS Chi-restraints excluded: chain I residue 762 LEU Chi-restraints excluded: chain I residue 857 LEU Chi-restraints excluded: chain I residue 902 VAL Chi-restraints excluded: chain I residue 915 GLN Chi-restraints excluded: chain I residue 924 LEU Chi-restraints excluded: chain I residue 971 VAL Chi-restraints excluded: chain I residue 1010 HIS Chi-restraints excluded: chain I residue 1050 TYR Chi-restraints excluded: chain I residue 1174 PHE Chi-restraints excluded: chain I residue 1182 GLN Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 365 ASN Chi-restraints excluded: chain J residue 403 LEU Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 252 ASN Chi-restraints excluded: chain K residue 305 MET Chi-restraints excluded: chain K residue 316 GLU Chi-restraints excluded: chain L residue 1812 LEU Chi-restraints excluded: chain L residue 1837 PHE Chi-restraints excluded: chain L residue 1846 ILE Chi-restraints excluded: chain L residue 2052 CYS Chi-restraints excluded: chain L residue 2053 LEU Chi-restraints excluded: chain L residue 2093 VAL Chi-restraints excluded: chain L residue 2152 VAL Chi-restraints excluded: chain L residue 2267 MET Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain M residue 365 ILE Chi-restraints excluded: chain N residue 446 LEU Chi-restraints excluded: chain N residue 625 GLU Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 915 ARG Chi-restraints excluded: chain N residue 920 LEU Chi-restraints excluded: chain N residue 927 LEU Chi-restraints excluded: chain O residue 458 THR Chi-restraints excluded: chain O residue 521 THR Chi-restraints excluded: chain O residue 673 VAL Chi-restraints excluded: chain O residue 677 VAL Chi-restraints excluded: chain O residue 925 GLN Chi-restraints excluded: chain P residue 337 VAL Chi-restraints excluded: chain P residue 431 ILE Chi-restraints excluded: chain P residue 443 SER Chi-restraints excluded: chain Q residue 184 ASP Chi-restraints excluded: chain Q residue 190 HIS Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain Q residue 269 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 305 optimal weight: 8.9990 chunk 208 optimal weight: 0.5980 chunk 5 optimal weight: 8.9990 chunk 273 optimal weight: 6.9990 chunk 151 optimal weight: 30.0000 chunk 313 optimal weight: 4.9990 chunk 253 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 187 optimal weight: 10.0000 chunk 329 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 445 GLN ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 327 HIS ** J 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 370 GLN J 384 ASN ** K 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1705 ASN ** L1854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1986 ASN ** L2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L2176 GLN ** L2194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L2268 ASN ** M 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 278 GLN ** N 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 359 GLN P 432 ASN Q 190 HIS ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2203 moved from start: 0.6694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.181 35402 Z= 0.360 Angle : 0.864 20.447 48811 Z= 0.455 Chirality : 0.047 0.280 5491 Planarity : 0.007 0.136 5406 Dihedral : 24.038 174.445 6586 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 28.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.43 % Favored : 94.54 % Rotamer: Outliers : 4.74 % Allowed : 19.03 % Favored : 76.23 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.45 (0.13), residues: 3552 helix: -0.28 (0.10), residues: 2206 sheet: -1.08 (0.42), residues: 166 loop : -2.13 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP N 620 HIS 0.022 0.002 HIS L2004 PHE 0.050 0.003 PHE L2103 TYR 0.035 0.002 TYR N 465 ARG 0.027 0.001 ARG P 334 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 259 time to evaluate : 3.812 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.4371 (mm) cc_final: 0.4154 (mm) REVERT: A 117 MET cc_start: 0.0518 (mmt) cc_final: -0.0002 (mpp) REVERT: B 84 MET cc_start: 0.4028 (mmm) cc_final: 0.2110 (ptp) REVERT: D 97 LEU cc_start: 0.2247 (OUTLIER) cc_final: 0.1865 (pp) REVERT: H 115 VAL cc_start: 0.1480 (p) cc_final: 0.1224 (p) REVERT: I 915 GLN cc_start: 0.0038 (OUTLIER) cc_final: -0.1609 (pm20) REVERT: I 971 VAL cc_start: 0.3556 (OUTLIER) cc_final: 0.3236 (p) REVERT: I 1010 HIS cc_start: 0.3295 (OUTLIER) cc_final: 0.0889 (m-70) REVERT: I 1112 MET cc_start: 0.1078 (mmm) cc_final: -0.2799 (ttt) REVERT: I 1150 PHE cc_start: 0.0466 (t80) cc_final: -0.0661 (m-80) REVERT: I 1174 PHE cc_start: 0.3431 (OUTLIER) cc_final: 0.1703 (t80) REVERT: I 1182 GLN cc_start: -0.1152 (OUTLIER) cc_final: -0.2295 (tm-30) REVERT: I 1305 MET cc_start: 0.3252 (ppp) cc_final: 0.2505 (mmt) REVERT: I 1317 MET cc_start: 0.3075 (tpt) cc_final: 0.2145 (ttp) REVERT: J 43 MET cc_start: -0.3671 (OUTLIER) cc_final: -0.4796 (mmt) REVERT: J 79 ARG cc_start: 0.0813 (OUTLIER) cc_final: -0.0949 (mmp-170) REVERT: J 140 MET cc_start: 0.2401 (mmp) cc_final: 0.1945 (tpt) REVERT: J 141 PHE cc_start: -0.1267 (OUTLIER) cc_final: -0.1935 (m-80) REVERT: J 335 MET cc_start: 0.2339 (ptp) cc_final: 0.2116 (ptp) REVERT: J 413 LYS cc_start: 0.6679 (OUTLIER) cc_final: 0.6311 (pttt) REVERT: K 84 LYS cc_start: 0.7355 (mttt) cc_final: 0.6428 (pttp) REVERT: K 123 MET cc_start: 0.0215 (tpp) cc_final: -0.0675 (tpt) REVERT: K 190 MET cc_start: 0.4794 (mmm) cc_final: 0.4292 (mmm) REVERT: K 250 ILE cc_start: -0.4671 (OUTLIER) cc_final: -0.5362 (pt) REVERT: L 1702 MET cc_start: -0.0106 (mmt) cc_final: -0.1840 (ptt) REVERT: L 1958 GLU cc_start: 0.0882 (OUTLIER) cc_final: -0.1036 (mt-10) REVERT: M 44 TYR cc_start: 0.2649 (m-80) cc_final: 0.1665 (t80) REVERT: M 208 MET cc_start: -0.1958 (tpt) cc_final: -0.2776 (tpt) REVERT: M 324 LYS cc_start: 0.0233 (OUTLIER) cc_final: -0.0628 (tmtt) REVERT: M 361 MET cc_start: -0.1591 (tpp) cc_final: -0.1968 (tpt) REVERT: N 444 ARG cc_start: 0.5319 (mtp-110) cc_final: 0.4038 (mtp-110) REVERT: N 498 MET cc_start: 0.0711 (mtp) cc_final: -0.0933 (tpt) REVERT: O 636 ILE cc_start: 0.3067 (tp) cc_final: 0.2663 (pt) REVERT: Q 188 MET cc_start: 0.2299 (ppp) cc_final: 0.1771 (mpp) REVERT: Q 257 ARG cc_start: 0.7682 (ttp80) cc_final: 0.7324 (ttp80) outliers start: 151 outliers final: 74 residues processed: 385 average time/residue: 0.4993 time to fit residues: 308.3970 Evaluate side-chains 320 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 233 time to evaluate : 3.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 475 TYR Chi-restraints excluded: chain I residue 762 LEU Chi-restraints excluded: chain I residue 902 VAL Chi-restraints excluded: chain I residue 910 THR Chi-restraints excluded: chain I residue 915 GLN Chi-restraints excluded: chain I residue 924 LEU Chi-restraints excluded: chain I residue 971 VAL Chi-restraints excluded: chain I residue 1010 HIS Chi-restraints excluded: chain I residue 1050 TYR Chi-restraints excluded: chain I residue 1174 PHE Chi-restraints excluded: chain I residue 1182 GLN Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 403 LEU Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain J residue 413 LYS Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 252 ASN Chi-restraints excluded: chain K residue 305 MET Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain L residue 1677 LYS Chi-restraints excluded: chain L residue 1713 LEU Chi-restraints excluded: chain L residue 1720 PHE Chi-restraints excluded: chain L residue 1812 LEU Chi-restraints excluded: chain L residue 1837 PHE Chi-restraints excluded: chain L residue 1846 ILE Chi-restraints excluded: chain L residue 1850 ASP Chi-restraints excluded: chain L residue 1958 GLU Chi-restraints excluded: chain L residue 1998 ASP Chi-restraints excluded: chain L residue 2010 ILE Chi-restraints excluded: chain L residue 2015 ILE Chi-restraints excluded: chain L residue 2052 CYS Chi-restraints excluded: chain L residue 2053 LEU Chi-restraints excluded: chain L residue 2152 VAL Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain M residue 259 ASP Chi-restraints excluded: chain M residue 277 ASP Chi-restraints excluded: chain M residue 324 LYS Chi-restraints excluded: chain M residue 362 GLU Chi-restraints excluded: chain N residue 446 LEU Chi-restraints excluded: chain N residue 635 CYS Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 920 LEU Chi-restraints excluded: chain N residue 927 LEU Chi-restraints excluded: chain O residue 470 ILE Chi-restraints excluded: chain O residue 521 THR Chi-restraints excluded: chain O residue 523 MET Chi-restraints excluded: chain O residue 631 THR Chi-restraints excluded: chain O residue 641 ARG Chi-restraints excluded: chain O residue 646 ASP Chi-restraints excluded: chain O residue 661 TYR Chi-restraints excluded: chain O residue 673 VAL Chi-restraints excluded: chain O residue 677 VAL Chi-restraints excluded: chain O residue 707 VAL Chi-restraints excluded: chain P residue 161 ILE Chi-restraints excluded: chain P residue 337 VAL Chi-restraints excluded: chain P residue 354 PHE Chi-restraints excluded: chain P residue 431 ILE Chi-restraints excluded: chain P residue 452 ILE Chi-restraints excluded: chain Q residue 183 ASP Chi-restraints excluded: chain Q residue 184 ASP Chi-restraints excluded: chain Q residue 190 HIS Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain Q residue 251 ARG Chi-restraints excluded: chain Q residue 269 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 123 optimal weight: 0.9990 chunk 330 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 90 optimal weight: 0.0170 chunk 367 optimal weight: 7.9990 chunk 305 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 193 optimal weight: 0.9980 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN I 356 GLN I 481 GLN ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 277 GLN ** J 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 407 GLN K 354 GLN ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1705 ASN ** L1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 HIS ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 229 ASN ** M 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 489 ASN ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 530 HIS ** O 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1967 moved from start: 0.6781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35402 Z= 0.190 Angle : 0.670 15.053 48811 Z= 0.354 Chirality : 0.042 0.239 5491 Planarity : 0.005 0.097 5406 Dihedral : 23.907 174.068 6581 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.01 % Allowed : 20.95 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.14), residues: 3552 helix: 0.36 (0.11), residues: 2204 sheet: -0.94 (0.42), residues: 167 loop : -1.89 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP P 320 HIS 0.013 0.001 HIS R 61 PHE 0.022 0.002 PHE A 81 TYR 0.023 0.002 TYR M 35 ARG 0.012 0.001 ARG P 334 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 257 time to evaluate : 3.579 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.4265 (mm) cc_final: 0.4046 (mm) REVERT: B 84 MET cc_start: 0.3561 (mmm) cc_final: 0.1351 (ptp) REVERT: E 131 ARG cc_start: 0.0506 (tpm170) cc_final: 0.0199 (tpp-160) REVERT: G 83 LEU cc_start: 0.1235 (mm) cc_final: 0.0832 (mt) REVERT: I 797 MET cc_start: -0.1927 (mtm) cc_final: -0.3341 (mtt) REVERT: I 886 MET cc_start: 0.0908 (mtt) cc_final: 0.0139 (ptt) REVERT: I 1010 HIS cc_start: 0.3084 (OUTLIER) cc_final: 0.0806 (m-70) REVERT: I 1112 MET cc_start: 0.1140 (mmm) cc_final: -0.2501 (mtm) REVERT: I 1150 PHE cc_start: 0.0509 (t80) cc_final: -0.0627 (m-80) REVERT: I 1174 PHE cc_start: 0.3368 (OUTLIER) cc_final: 0.1651 (t80) REVERT: I 1182 GLN cc_start: -0.1055 (OUTLIER) cc_final: -0.2293 (tm-30) REVERT: I 1305 MET cc_start: 0.3086 (ppp) cc_final: 0.2412 (mmt) REVERT: I 1317 MET cc_start: 0.3089 (tpt) cc_final: 0.2146 (ttp) REVERT: J 43 MET cc_start: -0.3513 (OUTLIER) cc_final: -0.4581 (mmt) REVERT: J 79 ARG cc_start: 0.0950 (OUTLIER) cc_final: -0.0579 (tpp-160) REVERT: J 141 PHE cc_start: -0.1415 (OUTLIER) cc_final: -0.2137 (m-80) REVERT: K 84 LYS cc_start: 0.7387 (mttt) cc_final: 0.6401 (pttp) REVERT: K 190 MET cc_start: 0.4618 (mmm) cc_final: 0.4148 (mmm) REVERT: K 316 GLU cc_start: -0.3010 (OUTLIER) cc_final: -0.3451 (mt-10) REVERT: L 1702 MET cc_start: 0.0558 (mmt) cc_final: -0.0490 (tpt) REVERT: L 1958 GLU cc_start: 0.0804 (OUTLIER) cc_final: -0.0990 (mt-10) REVERT: L 2230 MET cc_start: 0.0416 (tpt) cc_final: 0.0204 (tpp) REVERT: L 2257 ARG cc_start: 0.3325 (mmp-170) cc_final: 0.3049 (tpp-160) REVERT: M 44 TYR cc_start: 0.2196 (m-80) cc_final: 0.1612 (t80) REVERT: M 208 MET cc_start: -0.2260 (tpt) cc_final: -0.3324 (tpt) REVERT: N 444 ARG cc_start: 0.4823 (mtp-110) cc_final: 0.3741 (mtm110) REVERT: N 498 MET cc_start: 0.0124 (mtp) cc_final: -0.1049 (tpt) REVERT: N 896 MET cc_start: 0.4870 (ppp) cc_final: 0.4664 (ppp) REVERT: N 940 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.7094 (ptmt) REVERT: P 431 ILE cc_start: 0.3251 (OUTLIER) cc_final: 0.3039 (tt) REVERT: Q 188 MET cc_start: 0.1713 (ppp) cc_final: 0.0830 (mpp) REVERT: Q 201 ARG cc_start: 0.6243 (mtt180) cc_final: 0.5642 (mmt90) REVERT: Q 205 GLU cc_start: 0.2835 (pt0) cc_final: 0.2553 (tp30) REVERT: Q 257 ARG cc_start: 0.7572 (ttp80) cc_final: 0.7196 (ttp80) outliers start: 96 outliers final: 41 residues processed: 341 average time/residue: 0.4949 time to fit residues: 270.2531 Evaluate side-chains 282 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 231 time to evaluate : 3.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 475 TYR Chi-restraints excluded: chain I residue 762 LEU Chi-restraints excluded: chain I residue 902 VAL Chi-restraints excluded: chain I residue 910 THR Chi-restraints excluded: chain I residue 1010 HIS Chi-restraints excluded: chain I residue 1050 TYR Chi-restraints excluded: chain I residue 1174 PHE Chi-restraints excluded: chain I residue 1182 GLN Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain J residue 399 ILE Chi-restraints excluded: chain J residue 403 LEU Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 252 ASN Chi-restraints excluded: chain K residue 305 MET Chi-restraints excluded: chain K residue 316 GLU Chi-restraints excluded: chain K residue 371 HIS Chi-restraints excluded: chain L residue 1720 PHE Chi-restraints excluded: chain L residue 1812 LEU Chi-restraints excluded: chain L residue 1954 ILE Chi-restraints excluded: chain L residue 1958 GLU Chi-restraints excluded: chain L residue 2010 ILE Chi-restraints excluded: chain L residue 2052 CYS Chi-restraints excluded: chain L residue 2152 VAL Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain M residue 353 LEU Chi-restraints excluded: chain M residue 362 GLU Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 920 LEU Chi-restraints excluded: chain N residue 940 LYS Chi-restraints excluded: chain O residue 470 ILE Chi-restraints excluded: chain O residue 521 THR Chi-restraints excluded: chain O residue 618 ASP Chi-restraints excluded: chain O residue 661 TYR Chi-restraints excluded: chain O residue 673 VAL Chi-restraints excluded: chain O residue 677 VAL Chi-restraints excluded: chain O residue 707 VAL Chi-restraints excluded: chain P residue 431 ILE Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain Q residue 269 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 354 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 209 optimal weight: 0.9980 chunk 268 optimal weight: 3.9990 chunk 208 optimal weight: 0.8980 chunk 309 optimal weight: 1.9990 chunk 205 optimal weight: 7.9990 chunk 366 optimal weight: 9.9990 chunk 229 optimal weight: 1.9990 chunk 223 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 472 HIS ** I 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1304 GLN ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 432 ASN ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2012 moved from start: 0.7084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 35402 Z= 0.200 Angle : 0.664 12.820 48811 Z= 0.348 Chirality : 0.041 0.254 5491 Planarity : 0.005 0.083 5406 Dihedral : 23.698 174.757 6574 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.92 % Allowed : 21.20 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.14), residues: 3552 helix: 0.67 (0.11), residues: 2193 sheet: -0.84 (0.44), residues: 157 loop : -1.73 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 320 HIS 0.018 0.001 HIS M 322 PHE 0.038 0.002 PHE A 81 TYR 0.026 0.001 TYR H 37 ARG 0.010 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 249 time to evaluate : 3.435 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.4368 (mm) cc_final: 0.4158 (mm) REVERT: A 117 MET cc_start: 0.0412 (mmt) cc_final: -0.0046 (mpp) REVERT: B 84 MET cc_start: 0.3418 (mmm) cc_final: 0.1473 (ptp) REVERT: E 131 ARG cc_start: 0.0674 (tpm170) cc_final: 0.0310 (tpp-160) REVERT: G 83 LEU cc_start: 0.1727 (mm) cc_final: 0.1250 (mt) REVERT: I 797 MET cc_start: -0.1852 (mtm) cc_final: -0.2733 (mtt) REVERT: I 886 MET cc_start: 0.1042 (mtt) cc_final: -0.0284 (ttt) REVERT: I 1010 HIS cc_start: 0.3123 (OUTLIER) cc_final: 0.0780 (m-70) REVERT: I 1112 MET cc_start: 0.0789 (mmm) cc_final: -0.2844 (ttt) REVERT: I 1150 PHE cc_start: 0.0456 (t80) cc_final: -0.0602 (m-80) REVERT: I 1174 PHE cc_start: 0.3431 (OUTLIER) cc_final: 0.1687 (t80) REVERT: I 1182 GLN cc_start: -0.0951 (OUTLIER) cc_final: -0.2300 (tm-30) REVERT: I 1305 MET cc_start: 0.2974 (ppp) cc_final: 0.2430 (mmt) REVERT: I 1317 MET cc_start: 0.3103 (tpt) cc_final: 0.2164 (ttp) REVERT: J 43 MET cc_start: -0.3107 (OUTLIER) cc_final: -0.4219 (mmt) REVERT: J 79 ARG cc_start: 0.1130 (OUTLIER) cc_final: -0.0521 (mmp-170) REVERT: J 141 PHE cc_start: -0.1446 (OUTLIER) cc_final: -0.2139 (m-80) REVERT: J 338 ILE cc_start: 0.1200 (OUTLIER) cc_final: 0.0842 (tp) REVERT: J 409 MET cc_start: -0.3702 (mmt) cc_final: -0.4333 (mtt) REVERT: J 413 LYS cc_start: 0.6419 (OUTLIER) cc_final: 0.6167 (pttt) REVERT: K 84 LYS cc_start: 0.7413 (mttt) cc_final: 0.6429 (pttp) REVERT: K 123 MET cc_start: 0.0225 (tpp) cc_final: -0.0969 (tpt) REVERT: K 190 MET cc_start: 0.4543 (mmm) cc_final: 0.4083 (mmm) REVERT: K 316 GLU cc_start: -0.3076 (OUTLIER) cc_final: -0.3495 (mt-10) REVERT: L 2025 LYS cc_start: 0.5272 (tptt) cc_final: 0.4911 (mmmt) REVERT: L 2257 ARG cc_start: 0.3185 (mmp-170) cc_final: 0.2919 (tpp-160) REVERT: M 44 TYR cc_start: 0.2284 (m-80) cc_final: 0.1760 (t80) REVERT: M 89 THR cc_start: 0.0286 (OUTLIER) cc_final: -0.0049 (t) REVERT: M 208 MET cc_start: -0.2193 (OUTLIER) cc_final: -0.3217 (tpt) REVERT: N 444 ARG cc_start: 0.5025 (mtp-110) cc_final: 0.4316 (mtp-110) REVERT: N 498 MET cc_start: 0.0209 (mtp) cc_final: -0.0994 (tpt) REVERT: N 896 MET cc_start: 0.5113 (ppp) cc_final: 0.4900 (ppp) REVERT: N 940 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.7224 (ptmt) REVERT: Q 188 MET cc_start: 0.1653 (ppp) cc_final: 0.0947 (mpp) REVERT: Q 202 LEU cc_start: 0.6193 (tp) cc_final: 0.5593 (pp) outliers start: 93 outliers final: 53 residues processed: 328 average time/residue: 0.4668 time to fit residues: 247.5544 Evaluate side-chains 294 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 229 time to evaluate : 3.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 472 HIS Chi-restraints excluded: chain I residue 475 TYR Chi-restraints excluded: chain I residue 762 LEU Chi-restraints excluded: chain I residue 902 VAL Chi-restraints excluded: chain I residue 909 LEU Chi-restraints excluded: chain I residue 910 THR Chi-restraints excluded: chain I residue 924 LEU Chi-restraints excluded: chain I residue 971 VAL Chi-restraints excluded: chain I residue 1010 HIS Chi-restraints excluded: chain I residue 1050 TYR Chi-restraints excluded: chain I residue 1174 PHE Chi-restraints excluded: chain I residue 1182 GLN Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain J residue 399 ILE Chi-restraints excluded: chain J residue 403 LEU Chi-restraints excluded: chain J residue 413 LYS Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 252 ASN Chi-restraints excluded: chain K residue 305 MET Chi-restraints excluded: chain K residue 316 GLU Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain K residue 371 HIS Chi-restraints excluded: chain L residue 1713 LEU Chi-restraints excluded: chain L residue 1714 GLU Chi-restraints excluded: chain L residue 1720 PHE Chi-restraints excluded: chain L residue 1850 ASP Chi-restraints excluded: chain L residue 1954 ILE Chi-restraints excluded: chain L residue 2010 ILE Chi-restraints excluded: chain L residue 2052 CYS Chi-restraints excluded: chain L residue 2152 VAL Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain M residue 208 MET Chi-restraints excluded: chain M residue 353 LEU Chi-restraints excluded: chain M residue 362 GLU Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 920 LEU Chi-restraints excluded: chain N residue 927 LEU Chi-restraints excluded: chain N residue 935 HIS Chi-restraints excluded: chain N residue 940 LYS Chi-restraints excluded: chain O residue 469 MET Chi-restraints excluded: chain O residue 470 ILE Chi-restraints excluded: chain O residue 521 THR Chi-restraints excluded: chain O residue 530 HIS Chi-restraints excluded: chain O residue 661 TYR Chi-restraints excluded: chain O residue 673 VAL Chi-restraints excluded: chain O residue 677 VAL Chi-restraints excluded: chain O residue 707 VAL Chi-restraints excluded: chain P residue 441 MET Chi-restraints excluded: chain P residue 443 SER Chi-restraints excluded: chain Q residue 215 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 226 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 218 optimal weight: 1.9990 chunk 110 optimal weight: 30.0000 chunk 71 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 232 optimal weight: 0.8980 chunk 249 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 287 optimal weight: 8.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 470 GLN ** I 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 GLN ** J 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L2070 GLN ** L2194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L2273 GLN ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 199 ASN Q 238 GLN ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2528 moved from start: 0.8650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.212 35402 Z= 0.391 Angle : 0.946 17.385 48811 Z= 0.489 Chirality : 0.050 0.339 5491 Planarity : 0.007 0.098 5406 Dihedral : 23.869 177.617 6574 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 33.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.33 % Favored : 93.61 % Rotamer: Outliers : 3.14 % Allowed : 21.95 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.45 (0.13), residues: 3552 helix: -0.25 (0.10), residues: 2193 sheet: -0.78 (0.44), residues: 148 loop : -2.20 (0.17), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP R 56 HIS 0.042 0.003 HIS I 472 PHE 0.062 0.004 PHE N 906 TYR 0.037 0.003 TYR N 465 ARG 0.017 0.001 ARG P 334 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 247 time to evaluate : 3.940 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: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.4267 (mm) cc_final: 0.4049 (mm) REVERT: A 117 MET cc_start: 0.0135 (mmt) cc_final: -0.0168 (mpp) REVERT: B 84 MET cc_start: 0.4363 (mmm) cc_final: 0.2649 (ptp) REVERT: G 83 LEU cc_start: 0.1807 (mm) cc_final: 0.1451 (mt) REVERT: H 56 MET cc_start: -0.1088 (ppp) cc_final: -0.1372 (ppp) REVERT: I 797 MET cc_start: -0.1973 (mtm) cc_final: -0.2791 (mtt) REVERT: I 886 MET cc_start: 0.0772 (mtt) cc_final: -0.0352 (ttt) REVERT: I 915 GLN cc_start: 0.0611 (mp10) cc_final: -0.1257 (pm20) REVERT: I 1112 MET cc_start: 0.0599 (mmm) cc_final: -0.2896 (ttt) REVERT: I 1150 PHE cc_start: 0.0243 (t80) cc_final: -0.0464 (m-80) REVERT: I 1174 PHE cc_start: 0.3617 (OUTLIER) cc_final: 0.1818 (t80) REVERT: I 1182 GLN cc_start: -0.0920 (OUTLIER) cc_final: -0.2519 (tm-30) REVERT: I 1305 MET cc_start: 0.3269 (ppp) cc_final: 0.2594 (mmt) REVERT: I 1317 MET cc_start: 0.3078 (tpt) cc_final: 0.2060 (ttp) REVERT: J 43 MET cc_start: -0.3170 (OUTLIER) cc_final: -0.4299 (mmt) REVERT: J 79 ARG cc_start: 0.1209 (OUTLIER) cc_final: -0.0849 (mmp-170) REVERT: J 141 PHE cc_start: -0.0676 (OUTLIER) cc_final: -0.1138 (m-10) REVERT: J 409 MET cc_start: -0.3255 (mmt) cc_final: -0.3671 (mtt) REVERT: J 413 LYS cc_start: 0.6706 (OUTLIER) cc_final: 0.6291 (pttt) REVERT: K 84 LYS cc_start: 0.7352 (mttt) cc_final: 0.6348 (pttp) REVERT: K 190 MET cc_start: 0.4811 (mmm) cc_final: 0.4109 (mmm) REVERT: K 316 GLU cc_start: -0.2784 (OUTLIER) cc_final: -0.3209 (mt-10) REVERT: L 1958 GLU cc_start: 0.0424 (OUTLIER) cc_final: -0.1407 (mt-10) REVERT: L 2135 ILE cc_start: 0.0791 (OUTLIER) cc_final: 0.0561 (tt) REVERT: L 2231 MET cc_start: 0.2601 (tpp) cc_final: 0.2255 (tpp) REVERT: M 44 TYR cc_start: 0.2879 (m-80) cc_final: 0.2053 (t80) REVERT: M 53 ARG cc_start: 0.3431 (ttp-170) cc_final: 0.2405 (tpt170) REVERT: M 89 THR cc_start: 0.1114 (OUTLIER) cc_final: 0.0824 (t) REVERT: M 208 MET cc_start: -0.2301 (tpt) cc_final: -0.3120 (tpt) REVERT: N 498 MET cc_start: 0.1591 (mtp) cc_final: -0.0098 (tpt) REVERT: N 674 MET cc_start: -0.0356 (mpp) cc_final: -0.0651 (mpp) REVERT: N 940 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.6992 (tptp) REVERT: O 913 MET cc_start: 0.7362 (ppp) cc_final: 0.6735 (ppp) REVERT: P 352 MET cc_start: 0.4382 (tpt) cc_final: 0.1306 (ttm) REVERT: P 366 MET cc_start: -0.1264 (ptp) cc_final: -0.2549 (ttm) REVERT: P 472 ASN cc_start: 0.3833 (p0) cc_final: 0.3547 (p0) REVERT: Q 188 MET cc_start: 0.2714 (ppp) cc_final: 0.1857 (mpp) REVERT: Q 257 ARG cc_start: 0.7671 (ttp80) cc_final: 0.7399 (tmm160) REVERT: Q 261 GLU cc_start: 0.7045 (pp20) cc_final: 0.6716 (tp30) outliers start: 100 outliers final: 65 residues processed: 333 average time/residue: 0.5307 time to fit residues: 288.8146 Evaluate side-chains 300 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 224 time to evaluate : 3.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 475 TYR Chi-restraints excluded: chain I residue 762 LEU Chi-restraints excluded: chain I residue 902 VAL Chi-restraints excluded: chain I residue 909 LEU Chi-restraints excluded: chain I residue 910 THR Chi-restraints excluded: chain I residue 971 VAL Chi-restraints excluded: chain I residue 1050 TYR Chi-restraints excluded: chain I residue 1174 PHE Chi-restraints excluded: chain I residue 1182 GLN Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 274 TYR Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain J residue 403 LEU Chi-restraints excluded: chain J residue 413 LYS Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 252 ASN Chi-restraints excluded: chain K residue 305 MET Chi-restraints excluded: chain K residue 316 GLU Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain L residue 1645 SER Chi-restraints excluded: chain L residue 1677 LYS Chi-restraints excluded: chain L residue 1713 LEU Chi-restraints excluded: chain L residue 1720 PHE Chi-restraints excluded: chain L residue 1837 PHE Chi-restraints excluded: chain L residue 1846 ILE Chi-restraints excluded: chain L residue 1851 THR Chi-restraints excluded: chain L residue 1954 ILE Chi-restraints excluded: chain L residue 1958 GLU Chi-restraints excluded: chain L residue 1998 ASP Chi-restraints excluded: chain L residue 2010 ILE Chi-restraints excluded: chain L residue 2015 ILE Chi-restraints excluded: chain L residue 2052 CYS Chi-restraints excluded: chain L residue 2053 LEU Chi-restraints excluded: chain L residue 2135 ILE Chi-restraints excluded: chain L residue 2152 VAL Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 324 LYS Chi-restraints excluded: chain M residue 353 LEU Chi-restraints excluded: chain M residue 362 GLU Chi-restraints excluded: chain N residue 446 LEU Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 920 LEU Chi-restraints excluded: chain N residue 927 LEU Chi-restraints excluded: chain N residue 935 HIS Chi-restraints excluded: chain N residue 940 LYS Chi-restraints excluded: chain N residue 945 ARG Chi-restraints excluded: chain O residue 470 ILE Chi-restraints excluded: chain O residue 509 LEU Chi-restraints excluded: chain O residue 530 HIS Chi-restraints excluded: chain O residue 631 THR Chi-restraints excluded: chain O residue 633 ASP Chi-restraints excluded: chain O residue 661 TYR Chi-restraints excluded: chain O residue 677 VAL Chi-restraints excluded: chain O residue 707 VAL Chi-restraints excluded: chain P residue 161 ILE Chi-restraints excluded: chain P residue 337 VAL Chi-restraints excluded: chain P residue 441 MET Chi-restraints excluded: chain Q residue 184 ASP Chi-restraints excluded: chain Q residue 204 SER Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain Q residue 269 GLU Chi-restraints excluded: chain R residue 46 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 333 optimal weight: 5.9990 chunk 350 optimal weight: 6.9990 chunk 320 optimal weight: 10.0000 chunk 341 optimal weight: 0.8980 chunk 205 optimal weight: 0.7980 chunk 148 optimal weight: 30.0000 chunk 268 optimal weight: 0.8980 chunk 104 optimal weight: 10.0000 chunk 308 optimal weight: 20.0000 chunk 322 optimal weight: 0.6980 chunk 340 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 464 GLN I 470 GLN I 472 HIS I 888 ASN ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 323 GLN ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 199 ASN ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2271 moved from start: 0.8596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 35402 Z= 0.211 Angle : 0.719 16.709 48811 Z= 0.374 Chirality : 0.043 0.244 5491 Planarity : 0.005 0.076 5406 Dihedral : 23.697 179.217 6573 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.20 % Allowed : 23.93 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3552 helix: 0.29 (0.11), residues: 2200 sheet: -0.91 (0.44), residues: 143 loop : -1.98 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP P 320 HIS 0.011 0.001 HIS M 322 PHE 0.040 0.002 PHE N 906 TYR 0.051 0.002 TYR O 941 ARG 0.010 0.001 ARG P 334 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 242 time to evaluate : 3.413 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: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.4259 (mmm) cc_final: 0.2584 (ptp) REVERT: H 59 MET cc_start: -0.2872 (ttm) cc_final: -0.3210 (ttm) REVERT: I 797 MET cc_start: -0.2219 (mtm) cc_final: -0.2908 (mtt) REVERT: I 878 MET cc_start: 0.0775 (tpt) cc_final: 0.0277 (tpt) REVERT: I 886 MET cc_start: 0.0552 (mtt) cc_final: -0.0339 (ttt) REVERT: I 915 GLN cc_start: -0.0095 (mp10) cc_final: -0.1502 (pm20) REVERT: I 1112 MET cc_start: 0.0818 (mmm) cc_final: -0.2482 (ttt) REVERT: I 1150 PHE cc_start: 0.0306 (t80) cc_final: -0.0410 (m-80) REVERT: I 1174 PHE cc_start: 0.3533 (OUTLIER) cc_final: 0.1717 (t80) REVERT: I 1182 GLN cc_start: -0.0768 (OUTLIER) cc_final: -0.2430 (tm-30) REVERT: I 1305 MET cc_start: 0.3114 (ppp) cc_final: 0.2491 (mmt) REVERT: I 1312 GLU cc_start: 0.2560 (tm-30) cc_final: 0.2192 (mt-10) REVERT: I 1317 MET cc_start: 0.3205 (tpt) cc_final: 0.2239 (ttp) REVERT: J 43 MET cc_start: -0.2682 (OUTLIER) cc_final: -0.3743 (mmt) REVERT: J 79 ARG cc_start: 0.0907 (OUTLIER) cc_final: -0.1033 (mmp-170) REVERT: J 141 PHE cc_start: -0.1228 (OUTLIER) cc_final: -0.1693 (m-80) REVERT: J 338 ILE cc_start: 0.0432 (OUTLIER) cc_final: 0.0163 (tp) REVERT: K 84 LYS cc_start: 0.7355 (mttt) cc_final: 0.6313 (pttp) REVERT: K 123 MET cc_start: 0.0114 (tpp) cc_final: -0.0990 (tpt) REVERT: K 190 MET cc_start: 0.4704 (mmm) cc_final: 0.4236 (mmm) REVERT: K 316 GLU cc_start: -0.2828 (OUTLIER) cc_final: -0.3237 (mt-10) REVERT: L 1958 GLU cc_start: 0.0359 (OUTLIER) cc_final: -0.0954 (mt-10) REVERT: L 2057 ARG cc_start: 0.7937 (mmp80) cc_final: 0.7487 (mmp80) REVERT: L 2230 MET cc_start: 0.1770 (tpp) cc_final: 0.1078 (tpp) REVERT: L 2231 MET cc_start: 0.2519 (tpp) cc_final: 0.2122 (tpp) REVERT: L 2257 ARG cc_start: 0.4242 (OUTLIER) cc_final: 0.3707 (tpm170) REVERT: M 44 TYR cc_start: 0.2501 (m-80) cc_final: 0.2049 (t80) REVERT: M 53 ARG cc_start: 0.3457 (ttp-170) cc_final: 0.2626 (ptp90) REVERT: M 208 MET cc_start: -0.2695 (OUTLIER) cc_final: -0.3346 (tpt) REVERT: M 324 LYS cc_start: -0.0433 (OUTLIER) cc_final: -0.1320 (tmtt) REVERT: N 444 ARG cc_start: 0.5049 (mtp-110) cc_final: 0.4562 (mtm110) REVERT: N 498 MET cc_start: 0.1137 (mtp) cc_final: -0.0258 (tpt) REVERT: O 469 MET cc_start: 0.5491 (OUTLIER) cc_final: 0.3768 (mmm) REVERT: P 352 MET cc_start: 0.4141 (tpt) cc_final: 0.1573 (ttm) REVERT: P 472 ASN cc_start: 0.3408 (p0) cc_final: 0.3067 (p0) REVERT: Q 188 MET cc_start: 0.2895 (ppp) cc_final: 0.2378 (mpp) REVERT: Q 257 ARG cc_start: 0.7523 (ttp80) cc_final: 0.7239 (ttp80) outliers start: 70 outliers final: 45 residues processed: 301 average time/residue: 0.4853 time to fit residues: 237.0859 Evaluate side-chains 282 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 225 time to evaluate : 3.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 762 LEU Chi-restraints excluded: chain I residue 902 VAL Chi-restraints excluded: chain I residue 909 LEU Chi-restraints excluded: chain I residue 910 THR Chi-restraints excluded: chain I residue 924 LEU Chi-restraints excluded: chain I residue 971 VAL Chi-restraints excluded: chain I residue 1050 TYR Chi-restraints excluded: chain I residue 1174 PHE Chi-restraints excluded: chain I residue 1182 GLN Chi-restraints excluded: chain I residue 1313 PHE Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 252 ASN Chi-restraints excluded: chain K residue 305 MET Chi-restraints excluded: chain K residue 316 GLU Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain L residue 1676 LEU Chi-restraints excluded: chain L residue 1677 LYS Chi-restraints excluded: chain L residue 1720 PHE Chi-restraints excluded: chain L residue 1851 THR Chi-restraints excluded: chain L residue 1954 ILE Chi-restraints excluded: chain L residue 1958 GLU Chi-restraints excluded: chain L residue 2052 CYS Chi-restraints excluded: chain L residue 2076 TYR Chi-restraints excluded: chain L residue 2152 VAL Chi-restraints excluded: chain L residue 2257 ARG Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 208 MET Chi-restraints excluded: chain M residue 283 MET Chi-restraints excluded: chain M residue 324 LYS Chi-restraints excluded: chain M residue 353 LEU Chi-restraints excluded: chain M residue 362 GLU Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 920 LEU Chi-restraints excluded: chain N residue 935 HIS Chi-restraints excluded: chain N residue 945 ARG Chi-restraints excluded: chain O residue 469 MET Chi-restraints excluded: chain O residue 470 ILE Chi-restraints excluded: chain O residue 530 HIS Chi-restraints excluded: chain O residue 615 MET Chi-restraints excluded: chain O residue 631 THR Chi-restraints excluded: chain O residue 661 TYR Chi-restraints excluded: chain O residue 677 VAL Chi-restraints excluded: chain P residue 337 VAL Chi-restraints excluded: chain P residue 441 MET Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain R residue 46 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 224 optimal weight: 0.8980 chunk 360 optimal weight: 8.9990 chunk 220 optimal weight: 2.9990 chunk 171 optimal weight: 0.0010 chunk 250 optimal weight: 0.8980 chunk 378 optimal weight: 10.0000 chunk 348 optimal weight: 0.8980 chunk 301 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 232 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 HIS ** K 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L2268 ASN M 177 HIS ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 662 GLN ** O 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 362 HIS ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2190 moved from start: 0.8677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 35402 Z= 0.196 Angle : 0.688 14.845 48811 Z= 0.357 Chirality : 0.042 0.254 5491 Planarity : 0.005 0.060 5406 Dihedral : 23.476 176.362 6573 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.39 % Favored : 95.58 % Rotamer: Outliers : 1.76 % Allowed : 24.58 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3552 helix: 0.60 (0.11), residues: 2200 sheet: -0.69 (0.43), residues: 150 loop : -1.78 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP P 320 HIS 0.017 0.001 HIS L2004 PHE 0.046 0.002 PHE N 906 TYR 0.043 0.001 TYR O 941 ARG 0.008 0.001 ARG N 945 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 244 time to evaluate : 3.420 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.4082 (mmm) cc_final: 0.2813 (ptp) REVERT: D 59 MET cc_start: 0.0683 (tpp) cc_final: 0.0231 (tpp) REVERT: H 59 MET cc_start: -0.2556 (ttm) cc_final: -0.3107 (ttm) REVERT: I 797 MET cc_start: -0.2030 (mtm) cc_final: -0.2702 (mtt) REVERT: I 878 MET cc_start: 0.0393 (tpt) cc_final: -0.0068 (tpt) REVERT: I 886 MET cc_start: 0.0347 (mtt) cc_final: -0.0401 (ttt) REVERT: I 915 GLN cc_start: -0.0233 (mp10) cc_final: -0.1535 (pm20) REVERT: I 1112 MET cc_start: 0.0812 (mmm) cc_final: -0.1942 (mtp) REVERT: I 1150 PHE cc_start: 0.0577 (t80) cc_final: -0.0210 (m-80) REVERT: I 1174 PHE cc_start: 0.3481 (OUTLIER) cc_final: 0.1678 (t80) REVERT: I 1182 GLN cc_start: -0.0783 (OUTLIER) cc_final: -0.2436 (tm-30) REVERT: I 1305 MET cc_start: 0.3097 (ppp) cc_final: 0.2459 (mmt) REVERT: I 1317 MET cc_start: 0.3136 (tpt) cc_final: 0.2192 (ttp) REVERT: J 43 MET cc_start: -0.2177 (OUTLIER) cc_final: -0.3110 (mmt) REVERT: J 79 ARG cc_start: 0.1040 (OUTLIER) cc_final: -0.0684 (tpp-160) REVERT: J 141 PHE cc_start: -0.1523 (OUTLIER) cc_final: -0.1929 (m-80) REVERT: J 338 ILE cc_start: 0.1301 (OUTLIER) cc_final: 0.1033 (tp) REVERT: K 84 LYS cc_start: 0.7395 (mttt) cc_final: 0.6358 (pttp) REVERT: K 123 MET cc_start: 0.0009 (tpp) cc_final: -0.1051 (tpt) REVERT: K 190 MET cc_start: 0.4688 (mmm) cc_final: 0.4222 (mmm) REVERT: K 316 GLU cc_start: -0.3193 (OUTLIER) cc_final: -0.3516 (mt-10) REVERT: L 1702 MET cc_start: 0.0035 (mmp) cc_final: -0.1605 (tpt) REVERT: L 2057 ARG cc_start: 0.7931 (mmp80) cc_final: 0.6433 (ttp80) REVERT: M 53 ARG cc_start: 0.3707 (ttp-170) cc_final: 0.2937 (ptp90) REVERT: M 208 MET cc_start: -0.2516 (tpt) cc_final: -0.3166 (tpt) REVERT: M 324 LYS cc_start: -0.0381 (OUTLIER) cc_final: -0.1157 (tmtt) REVERT: N 498 MET cc_start: 0.1033 (mtp) cc_final: -0.0398 (tpt) REVERT: O 469 MET cc_start: 0.5379 (OUTLIER) cc_final: 0.3492 (mmm) REVERT: O 687 ARG cc_start: 0.5439 (mtt180) cc_final: 0.5164 (ttt-90) REVERT: P 352 MET cc_start: 0.4111 (tpt) cc_final: 0.1606 (ttm) REVERT: P 366 MET cc_start: -0.1877 (ptp) cc_final: -0.2683 (ttp) REVERT: P 472 ASN cc_start: 0.3274 (p0) cc_final: 0.2967 (p0) REVERT: Q 188 MET cc_start: 0.2711 (ppp) cc_final: 0.2418 (mpp) REVERT: Q 195 ARG cc_start: 0.4951 (mtt180) cc_final: 0.4589 (ttm170) outliers start: 56 outliers final: 41 residues processed: 293 average time/residue: 0.4982 time to fit residues: 234.8655 Evaluate side-chains 275 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 225 time to evaluate : 3.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 472 HIS Chi-restraints excluded: chain I residue 762 LEU Chi-restraints excluded: chain I residue 902 VAL Chi-restraints excluded: chain I residue 909 LEU Chi-restraints excluded: chain I residue 910 THR Chi-restraints excluded: chain I residue 924 LEU Chi-restraints excluded: chain I residue 971 VAL Chi-restraints excluded: chain I residue 1050 TYR Chi-restraints excluded: chain I residue 1174 PHE Chi-restraints excluded: chain I residue 1182 GLN Chi-restraints excluded: chain I residue 1313 PHE Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 305 MET Chi-restraints excluded: chain K residue 316 GLU Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain L residue 1676 LEU Chi-restraints excluded: chain L residue 1720 PHE Chi-restraints excluded: chain L residue 1850 ASP Chi-restraints excluded: chain L residue 1851 THR Chi-restraints excluded: chain L residue 1954 ILE Chi-restraints excluded: chain L residue 2052 CYS Chi-restraints excluded: chain L residue 2076 TYR Chi-restraints excluded: chain L residue 2152 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 324 LYS Chi-restraints excluded: chain M residue 353 LEU Chi-restraints excluded: chain M residue 362 GLU Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 920 LEU Chi-restraints excluded: chain N residue 927 LEU Chi-restraints excluded: chain N residue 935 HIS Chi-restraints excluded: chain N residue 945 ARG Chi-restraints excluded: chain O residue 469 MET Chi-restraints excluded: chain O residue 530 HIS Chi-restraints excluded: chain O residue 631 THR Chi-restraints excluded: chain O residue 661 TYR Chi-restraints excluded: chain O residue 677 VAL Chi-restraints excluded: chain P residue 337 VAL Chi-restraints excluded: chain P residue 443 SER Chi-restraints excluded: chain Q residue 215 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 239 optimal weight: 0.1980 chunk 321 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 277 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 301 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 310 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 935 HIS ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 432 ASN ** Q 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.129230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.105745 restraints weight = 174920.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.108082 restraints weight = 85568.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.109477 restraints weight = 51520.591| |-----------------------------------------------------------------------------| r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4220 r_free = 0.4220 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4220 r_free = 0.4220 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2929 moved from start: 0.9242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 35402 Z= 0.252 Angle : 0.750 14.419 48811 Z= 0.387 Chirality : 0.043 0.256 5491 Planarity : 0.005 0.086 5406 Dihedral : 23.464 177.592 6573 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 24.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.04 % Allowed : 24.46 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3552 helix: 0.43 (0.11), residues: 2208 sheet: -0.61 (0.43), residues: 149 loop : -1.85 (0.18), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 56 HIS 0.011 0.001 HIS M 322 PHE 0.043 0.002 PHE N 906 TYR 0.037 0.002 TYR O 941 ARG 0.014 0.001 ARG O 882 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7165.29 seconds wall clock time: 130 minutes 54.70 seconds (7854.70 seconds total)