Starting phenix.real_space_refine on Mon Jul 22 23:27:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzz_26923/07_2024/7uzz_26923.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzz_26923/07_2024/7uzz_26923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzz_26923/07_2024/7uzz_26923.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzz_26923/07_2024/7uzz_26923.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzz_26923/07_2024/7uzz_26923.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzz_26923/07_2024/7uzz_26923.cif" } resolution = 4.45 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= -0.001 sd= 0.038 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: 5 Type Number sf(0) Gaussians P 30 5.49 5 S 55 5.16 5 C 12617 2.51 5 N 3365 2.21 5 O 3900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I GLU 19": "OE1" <-> "OE2" Residue "I GLU 128": "OE1" <-> "OE2" Residue "K GLU 128": "OE1" <-> "OE2" Residue "D ARG 129": "NH1" <-> "NH2" Residue "D ARG 191": "NH1" <-> "NH2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C ARG 191": "NH1" <-> "NH2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 191": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 19967 Number of models: 1 Model: "" Number of chains: 11 Chain: "G" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 644 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 3, 'rna3p_pur': 11, 'rna3p_pyr': 8} Link IDs: {'rna2p': 10, 'rna3p': 19} Chain: "J" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 871 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain breaks: 2 Chain: "I" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 995 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "K" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 995 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "E" Number of atoms: 2398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2398 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 8, 'TRANS': 284} Chain breaks: 4 Chain: "D" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1578 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 4, 'TRANS': 194} Chain breaks: 1 Chain: "C" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1628 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "A" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1628 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "B" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1523 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 187} Chain breaks: 2 Chain: "H" Number of atoms: 2378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2378 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 286} Chain breaks: 1 Chain: "F" Number of atoms: 5329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 654, 5329 Classifications: {'peptide': 654} Link IDs: {'PTRANS': 7, 'TRANS': 646} Chain breaks: 6 Time building chain proxies: 10.91, per 1000 atoms: 0.55 Number of scatterers: 19967 At special positions: 0 Unit cell: (94.0808, 119.739, 211.682, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 P 30 15.00 O 3900 8.00 N 3365 7.00 C 12617 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS F 407 " - pdb=" SG CYS F 423 " distance=1.76 Simple disulfide: pdb=" SG CYS F 410 " - pdb=" SG CYS F 426 " distance=2.01 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: 8.06 Conformation dependent library (CDL) restraints added in 3.7 seconds 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4466 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 25 sheets defined 48.3% alpha, 16.7% beta 0 base pairs and 3 stacking pairs defined. Time for finding SS restraints: 5.83 Creating SS restraints... Processing helix chain 'J' and resid 17 through 24 removed outlier: 4.235A pdb=" N VAL J 21 " --> pdb=" O ALA J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 61 removed outlier: 3.812A pdb=" N LEU J 48 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASN J 50 " --> pdb=" O SER J 46 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU J 51 " --> pdb=" O LYS J 47 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE J 61 " --> pdb=" O ARG J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 92 Processing helix chain 'J' and resid 92 through 102 Processing helix chain 'J' and resid 103 through 115 Processing helix chain 'J' and resid 116 through 137 Processing helix chain 'I' and resid 15 through 24 removed outlier: 4.470A pdb=" N GLU I 19 " --> pdb=" O THR I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 47 Processing helix chain 'I' and resid 48 through 65 Processing helix chain 'I' and resid 71 through 92 Processing helix chain 'I' and resid 92 through 102 Processing helix chain 'I' and resid 103 through 115 Processing helix chain 'I' and resid 116 through 137 Processing helix chain 'K' and resid 15 through 24 removed outlier: 4.637A pdb=" N VAL K 21 " --> pdb=" O ALA K 17 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LYS K 22 " --> pdb=" O HIS K 18 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER K 23 " --> pdb=" O GLU K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 47 Processing helix chain 'K' and resid 48 through 65 Processing helix chain 'K' and resid 71 through 92 Processing helix chain 'K' and resid 92 through 102 Processing helix chain 'K' and resid 103 through 115 Processing helix chain 'K' and resid 116 through 137 removed outlier: 3.620A pdb=" N TYR K 137 " --> pdb=" O TYR K 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 53 Processing helix chain 'E' and resid 55 through 65 removed outlier: 3.850A pdb=" N TYR E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 82 Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 130 through 147 Processing helix chain 'E' and resid 150 through 155 removed outlier: 3.603A pdb=" N ILE E 154 " --> pdb=" O LYS E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'E' and resid 211 through 230 Processing helix chain 'E' and resid 231 through 235 removed outlier: 3.944A pdb=" N LYS E 235 " --> pdb=" O VAL E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 246 Processing helix chain 'E' and resid 248 through 255 Processing helix chain 'E' and resid 278 through 290 Processing helix chain 'D' and resid 47 through 63 removed outlier: 3.836A pdb=" N ILE D 51 " --> pdb=" O PRO D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 73 Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 104 through 114 Processing helix chain 'D' and resid 161 through 179 Processing helix chain 'C' and resid 47 through 63 removed outlier: 3.648A pdb=" N ILE C 51 " --> pdb=" O PRO C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.544A pdb=" N LYS C 108 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 161 through 178 removed outlier: 3.551A pdb=" N ASN C 178 " --> pdb=" O HIS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 188 Processing helix chain 'A' and resid 47 through 63 removed outlier: 3.579A pdb=" N ILE A 51 " --> pdb=" O PRO A 47 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 72 Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 162 through 179 Processing helix chain 'B' and resid 47 through 62 removed outlier: 3.618A pdb=" N ILE B 51 " --> pdb=" O PRO B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 104 through 115 Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 161 through 178 removed outlier: 3.651A pdb=" N ASN B 178 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 47 removed outlier: 3.507A pdb=" N LEU H 35 " --> pdb=" O THR H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 93 removed outlier: 3.523A pdb=" N LYS H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 107 Processing helix chain 'H' and resid 110 through 121 Processing helix chain 'H' and resid 136 through 141 removed outlier: 3.969A pdb=" N ASP H 140 " --> pdb=" O ALA H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 184 removed outlier: 4.210A pdb=" N TYR H 184 " --> pdb=" O THR H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'H' and resid 205 through 213 Processing helix chain 'H' and resid 231 through 236 Processing helix chain 'F' and resid 2 through 13 removed outlier: 3.763A pdb=" N LEU F 13 " --> pdb=" O TYR F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 23 removed outlier: 3.977A pdb=" N ILE F 20 " --> pdb=" O ILE F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 42 Processing helix chain 'F' and resid 49 through 58 Processing helix chain 'F' and resid 60 through 67 removed outlier: 4.156A pdb=" N LYS F 66 " --> pdb=" O LYS F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 86 removed outlier: 3.884A pdb=" N ILE F 77 " --> pdb=" O ASN F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 123 removed outlier: 4.426A pdb=" N ILE F 120 " --> pdb=" O SER F 116 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN F 122 " --> pdb=" O PHE F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 170 removed outlier: 4.088A pdb=" N TYR F 156 " --> pdb=" O SER F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 190 removed outlier: 3.566A pdb=" N GLN F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 227 Processing helix chain 'F' and resid 231 through 236 Processing helix chain 'F' and resid 239 through 249 Processing helix chain 'F' and resid 261 through 267 Processing helix chain 'F' and resid 273 through 300 removed outlier: 3.585A pdb=" N SER F 280 " --> pdb=" O LYS F 276 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE F 283 " --> pdb=" O ARG F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 305 No H-bonds generated for 'chain 'F' and resid 303 through 305' Processing helix chain 'F' and resid 322 through 344 Processing helix chain 'F' and resid 358 through 363 Processing helix chain 'F' and resid 367 through 386 removed outlier: 3.973A pdb=" N THR F 371 " --> pdb=" O GLY F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 398 removed outlier: 3.514A pdb=" N HIS F 398 " --> pdb=" O LEU F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 439 removed outlier: 4.171A pdb=" N ARG F 437 " --> pdb=" O SER F 433 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASP F 438 " --> pdb=" O ASN F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 473 Processing helix chain 'F' and resid 536 through 541 Processing helix chain 'F' and resid 550 through 573 removed outlier: 4.677A pdb=" N LEU F 569 " --> pdb=" O PHE F 565 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ASN F 570 " --> pdb=" O LYS F 566 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU F 573 " --> pdb=" O LEU F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 576 No H-bonds generated for 'chain 'F' and resid 574 through 576' Processing helix chain 'F' and resid 594 through 612 Processing helix chain 'F' and resid 630 through 636 removed outlier: 4.235A pdb=" N PHE F 636 " --> pdb=" O SER F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 665 through 670 Processing helix chain 'F' and resid 674 through 686 Processing helix chain 'F' and resid 690 through 703 Processing helix chain 'F' and resid 705 through 719 Processing helix chain 'F' and resid 722 through 735 Processing helix chain 'F' and resid 735 through 750 Processing sheet with id=AA1, first strand: chain 'J' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'I' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'E' and resid 158 through 160 removed outlier: 4.271A pdb=" N ASN E 256 " --> pdb=" O VAL E 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 23 through 24 removed outlier: 7.069A pdb=" N HIS E 117 " --> pdb=" O GLU E 191 " (cutoff:3.500A) removed outlier: 9.412A pdb=" N ILE E 193 " --> pdb=" O HIS E 117 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LYS E 176 " --> pdb=" O MET E 186 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU E 188 " --> pdb=" O TYR E 174 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N TYR E 174 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG E 190 " --> pdb=" O ALA E 172 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA E 172 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLN E 175 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N THR E 315 " --> pdb=" O GLN E 175 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 29 through 31 removed outlier: 3.776A pdb=" N ILE E 30 " --> pdb=" O TYR E 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 96 through 103 removed outlier: 5.815A pdb=" N LEU D 96 " --> pdb=" O ASN D 155 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASN D 155 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ILE D 98 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE D 153 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASP D 100 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL D 151 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY D 9 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N SER D 3 " --> pdb=" O VAL D 156 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LYS D 4 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N THR D 201 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LYS D 6 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ILE D 199 " --> pdb=" O LYS D 6 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N SER D 8 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR D 197 " --> pdb=" O SER D 8 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 119 through 124 Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 98 Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 98 removed outlier: 6.869A pdb=" N LYS C 4 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N THR C 10 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASP C 196 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLU C 12 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N PHE C 194 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 119 through 127 Processing sheet with id=AB2, first strand: chain 'A' and resid 37 through 38 removed outlier: 3.629A pdb=" N LEU A 43 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE A 103 " --> pdb=" O PRO A 44 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 46 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N VAL A 151 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA A 101 " --> pdb=" O ASP A 149 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ASP A 149 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N PHE A 103 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N GLU A 147 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LYS A 4 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N THR A 201 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS A 6 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE A 199 " --> pdb=" O LYS A 6 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N SER A 8 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR A 197 " --> pdb=" O SER A 8 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 119 through 124 Processing sheet with id=AB4, first strand: chain 'B' and resid 45 through 46 removed outlier: 3.620A pdb=" N ILE B 46 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE B 102 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 45 through 46 removed outlier: 3.620A pdb=" N ILE B 46 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE B 102 " --> pdb=" O ASP B 149 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER B 3 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LYS B 4 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR B 10 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ASP B 196 " --> pdb=" O THR B 10 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLU B 12 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N PHE B 194 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 119 through 127 Processing sheet with id=AB7, first strand: chain 'H' and resid 58 through 59 removed outlier: 3.609A pdb=" N GLY H 160 " --> pdb=" O TYR H 65 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 58 through 59 Processing sheet with id=AB9, first strand: chain 'H' and resid 71 through 73 Processing sheet with id=AC1, first strand: chain 'H' and resid 125 through 131 Processing sheet with id=AC2, first strand: chain 'H' and resid 239 through 240 removed outlier: 3.601A pdb=" N SER H 219 " --> pdb=" O PHE H 274 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 243 through 248 removed outlier: 3.763A pdb=" N SER H 267 " --> pdb=" O THR H 244 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLY H 248 " --> pdb=" O SER H 263 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N SER H 263 " --> pdb=" O GLY H 248 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 283 through 284 Processing sheet with id=AC5, first strand: chain 'F' and resid 307 through 311 removed outlier: 6.578A pdb=" N TYR F 316 " --> pdb=" O LEU F 308 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N THR F 310 " --> pdb=" O HIS F 314 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N HIS F 314 " --> pdb=" O THR F 310 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 450 through 452 removed outlier: 3.551A pdb=" N LYS F 456 " --> pdb=" O MET F 452 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE F 441 " --> pdb=" O ILE F 461 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE F 478 " --> pdb=" O THR F 492 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 578 through 584 removed outlier: 7.122A pdb=" N ILE F 578 " --> pdb=" O ALA F 593 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ALA F 593 " --> pdb=" O ILE F 578 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ALA F 580 " --> pdb=" O ILE F 591 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE F 591 " --> pdb=" O ALA F 580 " (cutoff:3.500A) 953 hydrogen bonds defined for protein. 2769 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 3 stacking parallelities Total time for adding SS restraints: 6.16 Time building geometry restraints manager: 8.86 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: 4491 1.33 - 1.45: 4694 1.45 - 1.57: 11049 1.57 - 1.69: 59 1.69 - 1.81: 97 Bond restraints: 20390 Sorted by residual: bond pdb=" N GLY H 186 " pdb=" CA GLY H 186 " ideal model delta sigma weight residual 1.442 1.469 -0.027 7.70e-03 1.69e+04 1.21e+01 bond pdb=" N ILE F 149 " pdb=" CA ILE F 149 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.12e-02 7.97e+03 1.04e+01 bond pdb=" N ILE B 139 " pdb=" CA ILE B 139 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.19e-02 7.06e+03 9.63e+00 bond pdb=" N ILE E 30 " pdb=" CA ILE E 30 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.53e+00 bond pdb=" N ILE B 91 " pdb=" CA ILE B 91 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.32e+00 ... (remaining 20385 not shown) Histogram of bond angle deviations from ideal: 98.69 - 105.83: 382 105.83 - 112.97: 10923 112.97 - 120.11: 7917 120.11 - 127.25: 8157 127.25 - 134.38: 167 Bond angle restraints: 27546 Sorted by residual: angle pdb=" C SER H 185 " pdb=" N GLY H 186 " pdb=" CA GLY H 186 " ideal model delta sigma weight residual 122.69 115.86 6.83 1.04e+00 9.25e-01 4.31e+01 angle pdb=" N VAL H 285 " pdb=" CA VAL H 285 " pdb=" C VAL H 285 " ideal model delta sigma weight residual 111.77 105.75 6.02 1.04e+00 9.25e-01 3.36e+01 angle pdb=" C4' C G 8 " pdb=" C3' C G 8 " pdb=" O3' C G 8 " ideal model delta sigma weight residual 113.00 104.98 8.02 1.50e+00 4.44e-01 2.86e+01 angle pdb=" N THR C 131 " pdb=" CA THR C 131 " pdb=" C THR C 131 " ideal model delta sigma weight residual 114.62 108.70 5.92 1.14e+00 7.69e-01 2.70e+01 angle pdb=" C CYS F 426 " pdb=" CA CYS F 426 " pdb=" CB CYS F 426 " ideal model delta sigma weight residual 110.88 103.25 7.63 1.57e+00 4.06e-01 2.36e+01 ... (remaining 27541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.31: 12033 33.31 - 66.62: 223 66.62 - 99.93: 29 99.93 - 133.24: 3 133.24 - 166.55: 1 Dihedral angle restraints: 12289 sinusoidal: 5352 harmonic: 6937 Sorted by residual: dihedral pdb=" O4' C G 10 " pdb=" C1' C G 10 " pdb=" N1 C G 10 " pdb=" C2 C G 10 " ideal model delta sinusoidal sigma weight residual -160.00 -45.68 -114.32 1 1.50e+01 4.44e-03 6.02e+01 dihedral pdb=" O4' C G 2 " pdb=" C1' C G 2 " pdb=" N1 C G 2 " pdb=" C2 C G 2 " ideal model delta sinusoidal sigma weight residual -128.00 -7.64 -120.36 1 1.70e+01 3.46e-03 5.00e+01 dihedral pdb=" O4' U G 14 " pdb=" C1' U G 14 " pdb=" N1 U G 14 " pdb=" C2 U G 14 " ideal model delta sinusoidal sigma weight residual -160.00 -61.07 -98.93 1 1.50e+01 4.44e-03 4.93e+01 ... (remaining 12286 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2245 0.062 - 0.125: 639 0.125 - 0.187: 128 0.187 - 0.250: 13 0.250 - 0.312: 5 Chirality restraints: 3030 Sorted by residual: chirality pdb=" P G G 15 " pdb=" OP1 G G 15 " pdb=" OP2 G G 15 " pdb=" O5' G G 15 " both_signs ideal model delta sigma weight residual True 2.41 -2.72 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" P G G 21 " pdb=" OP1 G G 21 " pdb=" OP2 G G 21 " pdb=" O5' G G 21 " both_signs ideal model delta sigma weight residual True 2.41 -2.72 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA CYS F 426 " pdb=" N CYS F 426 " pdb=" C CYS F 426 " pdb=" CB CYS F 426 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 3027 not shown) Planarity restraints: 3415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS H 17 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C HIS H 17 " 0.060 2.00e-02 2.50e+03 pdb=" O HIS H 17 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE H 18 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 46 " 0.053 5.00e-02 4.00e+02 8.04e-02 1.03e+01 pdb=" N PRO C 47 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO C 47 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 47 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL J 55 " 0.014 2.00e-02 2.50e+03 2.71e-02 7.32e+00 pdb=" C VAL J 55 " -0.047 2.00e-02 2.50e+03 pdb=" O VAL J 55 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN J 56 " 0.016 2.00e-02 2.50e+03 ... (remaining 3412 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 1 2.12 - 2.81: 5768 2.81 - 3.51: 27755 3.51 - 4.20: 44994 4.20 - 4.90: 78263 Nonbonded interactions: 156781 Sorted by model distance: nonbonded pdb=" N7 A G 20 " pdb=" ND2 ASN C 57 " model vdw 1.424 2.600 nonbonded pdb=" O2 C G 8 " pdb=" ND2 ASN B 57 " model vdw 2.126 2.520 nonbonded pdb=" C8 A G 20 " pdb=" ND2 ASN C 57 " model vdw 2.132 3.340 nonbonded pdb=" O PHE K 98 " pdb=" OG1 THR K 102 " model vdw 2.173 2.440 nonbonded pdb=" N GLY C 48 " pdb=" OD1 ASP C 100 " model vdw 2.196 2.520 ... (remaining 156776 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' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 20 \ 8)) selection = (chain 'B' and resid 2 through 208) selection = (chain 'C' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 20 \ 8)) selection = (chain 'D' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 20 \ 8)) } ncs_group { reference = (chain 'I' and (resid 17 through 61 or resid 74 through 139)) selection = chain 'J' selection = (chain 'K' and (resid 17 through 61 or resid 74 through 139)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 55.580 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 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 : 0.008 0.075 20390 Z= 0.551 Angle : 0.984 9.772 27546 Z= 0.681 Chirality : 0.061 0.312 3030 Planarity : 0.005 0.080 3415 Dihedral : 13.195 166.549 7817 Min Nonbonded Distance : 1.424 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.96 % Favored : 95.00 % Rotamer: Outliers : 0.75 % Allowed : 1.74 % Favored : 97.51 % 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: -0.66 (0.16), residues: 2320 helix: 0.65 (0.15), residues: 1030 sheet: 0.18 (0.27), residues: 371 loop : -1.99 (0.17), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 339 HIS 0.013 0.002 HIS H 291 PHE 0.022 0.002 PHE E 92 TYR 0.029 0.002 TYR F 191 ARG 0.011 0.001 ARG D 137 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 352 time to evaluate : 2.264 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 81 LEU cc_start: 0.9506 (tp) cc_final: 0.8177 (tt) REVERT: J 104 MET cc_start: 0.9132 (tpp) cc_final: 0.8674 (tpp) REVERT: J 120 PHE cc_start: 0.8616 (t80) cc_final: 0.8398 (t80) REVERT: J 127 PHE cc_start: 0.8819 (t80) cc_final: 0.8449 (t80) REVERT: I 66 ASN cc_start: 0.9233 (m-40) cc_final: 0.8816 (p0) REVERT: I 77 GLU cc_start: 0.9302 (mm-30) cc_final: 0.9056 (mt-10) REVERT: I 86 TYR cc_start: 0.8556 (m-80) cc_final: 0.8156 (m-80) REVERT: K 52 MET cc_start: 0.9392 (mtt) cc_final: 0.8536 (tpt) REVERT: K 76 ASP cc_start: 0.9210 (m-30) cc_final: 0.8227 (m-30) REVERT: K 83 ILE cc_start: 0.9634 (mt) cc_final: 0.9030 (mt) REVERT: K 120 PHE cc_start: 0.9405 (t80) cc_final: 0.9143 (t80) REVERT: E 252 VAL cc_start: 0.7452 (OUTLIER) cc_final: 0.7120 (t) REVERT: C 17 LEU cc_start: 0.9078 (tt) cc_final: 0.8854 (mm) REVERT: C 40 GLN cc_start: 0.9204 (tt0) cc_final: 0.8973 (pt0) REVERT: A 17 LEU cc_start: 0.7175 (tp) cc_final: 0.6857 (tp) REVERT: F 159 LEU cc_start: 0.9084 (tp) cc_final: 0.8824 (mm) REVERT: F 317 LEU cc_start: 0.8988 (mp) cc_final: 0.8742 (tp) REVERT: F 318 LEU cc_start: 0.8244 (tp) cc_final: 0.7895 (tp) REVERT: F 420 ASP cc_start: 0.7497 (m-30) cc_final: 0.7141 (t70) REVERT: F 495 TRP cc_start: 0.7838 (m-90) cc_final: 0.7001 (m100) REVERT: F 624 MET cc_start: 0.8276 (ttm) cc_final: 0.7868 (ttp) outliers start: 16 outliers final: 2 residues processed: 365 average time/residue: 0.4003 time to fit residues: 205.9205 Evaluate side-chains 176 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 173 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 1.9990 chunk 178 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 184 optimal weight: 0.9980 chunk 71 optimal weight: 0.0060 chunk 112 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 214 optimal weight: 6.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 37 GLN I 37 GLN ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 ASN K 56 ASN ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 ASN D 110 HIS D 138 GLN D 198 ASN C 18 HIS C 135 ASN C 174 HIS A 72 HIS A 110 HIS ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN H 137 GLN H 214 GLN F 14 HIS ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 560 GLN F 685 GLN F 722 ASN F 735 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20390 Z= 0.176 Angle : 0.565 9.065 27546 Z= 0.309 Chirality : 0.041 0.199 3030 Planarity : 0.004 0.060 3415 Dihedral : 12.456 164.633 3005 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.49 % Favored : 96.47 % Rotamer: Outliers : 0.28 % Allowed : 1.46 % Favored : 98.26 % 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: 0.13 (0.17), residues: 2320 helix: 1.18 (0.15), residues: 1082 sheet: 0.47 (0.27), residues: 385 loop : -1.54 (0.19), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 184 HIS 0.010 0.001 HIS A 72 PHE 0.033 0.002 PHE F 589 TYR 0.033 0.002 TYR K 59 ARG 0.006 0.001 ARG F 702 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 205 time to evaluate : 2.430 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 81 LEU cc_start: 0.9303 (tp) cc_final: 0.8628 (tt) REVERT: J 85 PHE cc_start: 0.8159 (m-80) cc_final: 0.7338 (m-80) REVERT: J 104 MET cc_start: 0.8521 (tpp) cc_final: 0.8310 (tpp) REVERT: J 127 PHE cc_start: 0.8995 (t80) cc_final: 0.8542 (t80) REVERT: I 27 ASN cc_start: 0.6553 (t0) cc_final: 0.6305 (t0) REVERT: I 52 MET cc_start: 0.8617 (tpt) cc_final: 0.8045 (tpt) REVERT: I 66 ASN cc_start: 0.9311 (m-40) cc_final: 0.8879 (p0) REVERT: I 80 TYR cc_start: 0.8327 (m-80) cc_final: 0.7903 (m-80) REVERT: I 86 TYR cc_start: 0.8744 (m-80) cc_final: 0.8410 (m-80) REVERT: K 52 MET cc_start: 0.9285 (mtt) cc_final: 0.8351 (tpt) REVERT: K 76 ASP cc_start: 0.9060 (m-30) cc_final: 0.8761 (m-30) REVERT: K 120 PHE cc_start: 0.9262 (t80) cc_final: 0.8989 (t80) REVERT: E 260 LEU cc_start: 0.8438 (mm) cc_final: 0.8193 (mm) REVERT: D 113 GLN cc_start: 0.8958 (mt0) cc_final: 0.8687 (pt0) REVERT: D 181 LEU cc_start: 0.9155 (pp) cc_final: 0.8229 (mp) REVERT: C 17 LEU cc_start: 0.9303 (tt) cc_final: 0.8896 (mm) REVERT: C 40 GLN cc_start: 0.9337 (tt0) cc_final: 0.9117 (pt0) REVERT: A 17 LEU cc_start: 0.7347 (tp) cc_final: 0.6775 (tp) REVERT: A 82 LEU cc_start: 0.8953 (mt) cc_final: 0.8661 (mt) REVERT: B 96 LEU cc_start: 0.9205 (tp) cc_final: 0.8634 (pp) REVERT: B 115 ASP cc_start: 0.7203 (t0) cc_final: 0.6953 (t0) REVERT: H 208 LEU cc_start: 0.9720 (tt) cc_final: 0.9217 (mt) REVERT: F 13 LEU cc_start: 0.9304 (mt) cc_final: 0.9093 (mp) REVERT: F 160 MET cc_start: 0.8951 (mtm) cc_final: 0.8736 (mtp) REVERT: F 257 MET cc_start: 0.7993 (mpp) cc_final: 0.7644 (mpp) REVERT: F 363 MET cc_start: 0.8534 (mtp) cc_final: 0.8213 (mmm) REVERT: F 624 MET cc_start: 0.8084 (ttm) cc_final: 0.7429 (tmm) outliers start: 6 outliers final: 0 residues processed: 210 average time/residue: 0.3757 time to fit residues: 116.1698 Evaluate side-chains 151 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 178 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 214 optimal weight: 9.9990 chunk 231 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 37 GLN ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN D 114 ASN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 114 ASN A 113 GLN ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 GLN ** F 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 HIS F 375 ASN ** F 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20390 Z= 0.270 Angle : 0.594 7.508 27546 Z= 0.326 Chirality : 0.040 0.198 3030 Planarity : 0.004 0.034 3415 Dihedral : 12.384 177.002 3005 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.28 % Favored : 96.68 % Rotamer: Outliers : 0.14 % Allowed : 2.63 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.17), residues: 2320 helix: 1.25 (0.16), residues: 1077 sheet: 0.31 (0.26), residues: 411 loop : -1.54 (0.19), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 184 HIS 0.006 0.001 HIS H 17 PHE 0.018 0.002 PHE F 725 TYR 0.028 0.002 TYR J 123 ARG 0.005 0.001 ARG C 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 154 time to evaluate : 2.285 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 104 MET cc_start: 0.8785 (tpp) cc_final: 0.8220 (tpp) REVERT: J 120 PHE cc_start: 0.8769 (t80) cc_final: 0.8502 (t80) REVERT: J 127 PHE cc_start: 0.8891 (t80) cc_final: 0.8546 (t80) REVERT: I 14 MET cc_start: 0.8633 (tpt) cc_final: 0.8311 (tpp) REVERT: I 52 MET cc_start: 0.8377 (tpt) cc_final: 0.7707 (tpt) REVERT: I 66 ASN cc_start: 0.9236 (m-40) cc_final: 0.8680 (p0) REVERT: I 80 TYR cc_start: 0.8441 (m-80) cc_final: 0.8157 (m-80) REVERT: I 86 TYR cc_start: 0.8758 (m-80) cc_final: 0.8436 (m-80) REVERT: K 14 MET cc_start: 0.7050 (pmm) cc_final: 0.6656 (pmm) REVERT: K 52 MET cc_start: 0.9070 (mtt) cc_final: 0.8090 (tpt) REVERT: K 76 ASP cc_start: 0.9030 (m-30) cc_final: 0.8783 (m-30) REVERT: K 85 PHE cc_start: 0.9439 (m-10) cc_final: 0.9108 (m-80) REVERT: E 300 MET cc_start: 0.1618 (mtt) cc_final: 0.1337 (mtt) REVERT: C 17 LEU cc_start: 0.9558 (tt) cc_final: 0.8895 (mm) REVERT: A 17 LEU cc_start: 0.8043 (tp) cc_final: 0.7766 (tp) REVERT: B 115 ASP cc_start: 0.7722 (t0) cc_final: 0.7409 (t0) REVERT: F 352 MET cc_start: 0.8233 (mpp) cc_final: 0.7687 (mpp) REVERT: F 624 MET cc_start: 0.8096 (ttm) cc_final: 0.7439 (tmm) REVERT: F 634 MET cc_start: 0.8452 (mmp) cc_final: 0.8212 (mmm) outliers start: 3 outliers final: 0 residues processed: 157 average time/residue: 0.3766 time to fit residues: 87.4079 Evaluate side-chains 120 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 228 optimal weight: 9.9990 chunk 112 optimal weight: 0.8980 chunk 204 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 37 GLN J 56 ASN ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 ASN ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN ** F 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20390 Z= 0.156 Angle : 0.508 7.731 27546 Z= 0.277 Chirality : 0.039 0.237 3030 Planarity : 0.003 0.045 3415 Dihedral : 12.194 178.171 3005 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.19 % Favored : 96.77 % Rotamer: Outliers : 0.05 % Allowed : 2.07 % Favored : 97.88 % 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: 0.32 (0.17), residues: 2320 helix: 1.40 (0.16), residues: 1077 sheet: 0.38 (0.26), residues: 420 loop : -1.49 (0.19), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP F 184 HIS 0.008 0.001 HIS E 17 PHE 0.017 0.001 PHE I 98 TYR 0.032 0.001 TYR K 59 ARG 0.008 0.000 ARG J 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 154 time to evaluate : 2.321 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 104 MET cc_start: 0.8658 (tpp) cc_final: 0.8063 (tpp) REVERT: J 120 PHE cc_start: 0.8720 (t80) cc_final: 0.8407 (t80) REVERT: J 127 PHE cc_start: 0.8852 (t80) cc_final: 0.8535 (t80) REVERT: I 14 MET cc_start: 0.8495 (tpt) cc_final: 0.8216 (tpp) REVERT: I 64 ASN cc_start: 0.8660 (m110) cc_final: 0.8324 (m110) REVERT: I 66 ASN cc_start: 0.9197 (m-40) cc_final: 0.8683 (p0) REVERT: I 80 TYR cc_start: 0.8359 (m-80) cc_final: 0.8009 (m-80) REVERT: I 86 TYR cc_start: 0.8695 (m-80) cc_final: 0.8357 (m-80) REVERT: K 14 MET cc_start: 0.6742 (pmm) cc_final: 0.6265 (pmm) REVERT: K 52 MET cc_start: 0.9279 (mtt) cc_final: 0.8157 (tpt) REVERT: K 76 ASP cc_start: 0.8969 (m-30) cc_final: 0.8740 (m-30) REVERT: K 85 PHE cc_start: 0.9468 (m-10) cc_final: 0.9092 (m-80) REVERT: E 300 MET cc_start: 0.1641 (mtt) cc_final: 0.1352 (mtt) REVERT: C 17 LEU cc_start: 0.9504 (tt) cc_final: 0.8817 (mm) REVERT: A 17 LEU cc_start: 0.8263 (tp) cc_final: 0.7978 (tp) REVERT: B 115 ASP cc_start: 0.7564 (t0) cc_final: 0.7237 (t0) REVERT: H 10 LEU cc_start: 0.9026 (mt) cc_final: 0.8811 (mt) REVERT: H 208 LEU cc_start: 0.9721 (tt) cc_final: 0.9217 (mt) REVERT: F 160 MET cc_start: 0.9194 (mtm) cc_final: 0.8685 (mpp) REVERT: F 624 MET cc_start: 0.6845 (ttm) cc_final: 0.6535 (tmm) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.3732 time to fit residues: 86.8567 Evaluate side-chains 123 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 chunk 169 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 194 optimal weight: 0.8980 chunk 157 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 37 GLN ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 HIS A 138 GLN ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 HIS ** F 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20390 Z= 0.154 Angle : 0.494 6.879 27546 Z= 0.269 Chirality : 0.039 0.248 3030 Planarity : 0.003 0.070 3415 Dihedral : 11.966 171.747 3005 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.15 % Favored : 96.81 % Rotamer: Outliers : 0.09 % Allowed : 1.83 % Favored : 98.07 % 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: 0.44 (0.17), residues: 2320 helix: 1.44 (0.16), residues: 1079 sheet: 0.52 (0.26), residues: 411 loop : -1.36 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 184 HIS 0.003 0.001 HIS H 291 PHE 0.020 0.001 PHE I 98 TYR 0.026 0.001 TYR J 123 ARG 0.011 0.000 ARG I 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 2.194 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: symmetry clash revert: symmetry clash REVERT: J 104 MET cc_start: 0.8677 (tpp) cc_final: 0.7940 (tpp) REVERT: J 120 PHE cc_start: 0.8672 (t80) cc_final: 0.8441 (t80) REVERT: J 127 PHE cc_start: 0.8904 (t80) cc_final: 0.8563 (t80) REVERT: I 14 MET cc_start: 0.8497 (tpt) cc_final: 0.8222 (tpp) REVERT: I 52 MET cc_start: 0.8873 (mtm) cc_final: 0.8501 (mtt) REVERT: I 64 ASN cc_start: 0.8653 (m110) cc_final: 0.8330 (m-40) REVERT: I 66 ASN cc_start: 0.9237 (m-40) cc_final: 0.8716 (p0) REVERT: I 80 TYR cc_start: 0.8558 (m-80) cc_final: 0.8134 (m-80) REVERT: I 86 TYR cc_start: 0.8762 (m-80) cc_final: 0.8372 (m-80) REVERT: K 14 MET cc_start: 0.7240 (pmm) cc_final: 0.6476 (pmm) REVERT: K 52 MET cc_start: 0.9190 (mtt) cc_final: 0.8367 (tpt) REVERT: K 76 ASP cc_start: 0.8934 (m-30) cc_final: 0.8723 (m-30) REVERT: K 112 ILE cc_start: 0.9259 (pt) cc_final: 0.9018 (pt) REVERT: E 251 ASP cc_start: 0.9406 (p0) cc_final: 0.9001 (p0) REVERT: E 300 MET cc_start: 0.1789 (mtt) cc_final: 0.1450 (mtt) REVERT: C 17 LEU cc_start: 0.9494 (tt) cc_final: 0.8777 (mm) REVERT: B 115 ASP cc_start: 0.7554 (t0) cc_final: 0.7278 (t0) REVERT: H 10 LEU cc_start: 0.8523 (mt) cc_final: 0.8181 (mt) REVERT: H 208 LEU cc_start: 0.9719 (tt) cc_final: 0.9240 (mt) REVERT: F 160 MET cc_start: 0.9250 (mtm) cc_final: 0.8626 (mtp) REVERT: F 352 MET cc_start: 0.8015 (mpp) cc_final: 0.7778 (mpp) REVERT: F 624 MET cc_start: 0.6975 (ttm) cc_final: 0.6531 (tmm) outliers start: 2 outliers final: 1 residues processed: 151 average time/residue: 0.3577 time to fit residues: 80.7370 Evaluate side-chains 117 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 0.7980 chunk 205 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 228 optimal weight: 0.8980 chunk 189 optimal weight: 0.2980 chunk 105 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 37 GLN ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 GLN ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20390 Z= 0.147 Angle : 0.487 7.612 27546 Z= 0.264 Chirality : 0.038 0.241 3030 Planarity : 0.003 0.058 3415 Dihedral : 11.785 157.767 3005 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.41 % Favored : 96.55 % Rotamer: Outliers : 0.14 % Allowed : 1.22 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.18), residues: 2320 helix: 1.54 (0.16), residues: 1080 sheet: 0.61 (0.26), residues: 396 loop : -1.27 (0.19), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 184 HIS 0.003 0.001 HIS H 291 PHE 0.027 0.001 PHE F 565 TYR 0.024 0.001 TYR J 123 ARG 0.010 0.000 ARG E 64 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 2.338 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: symmetry clash revert: symmetry clash REVERT: J 120 PHE cc_start: 0.8660 (t80) cc_final: 0.8451 (t80) REVERT: I 64 ASN cc_start: 0.8661 (m110) cc_final: 0.8346 (m-40) REVERT: I 66 ASN cc_start: 0.9220 (m-40) cc_final: 0.8738 (p0) REVERT: I 86 TYR cc_start: 0.8647 (m-80) cc_final: 0.8268 (m-80) REVERT: K 52 MET cc_start: 0.9247 (mtt) cc_final: 0.8406 (tpt) REVERT: K 112 ILE cc_start: 0.9276 (pt) cc_final: 0.9039 (pt) REVERT: E 300 MET cc_start: 0.1997 (mtt) cc_final: 0.1651 (mtt) REVERT: D 102 PHE cc_start: 0.8172 (t80) cc_final: 0.7841 (t80) REVERT: C 17 LEU cc_start: 0.9517 (tt) cc_final: 0.8862 (mm) REVERT: B 115 ASP cc_start: 0.7534 (t0) cc_final: 0.7261 (t0) REVERT: H 10 LEU cc_start: 0.8537 (mt) cc_final: 0.8263 (mt) REVERT: H 208 LEU cc_start: 0.9714 (tt) cc_final: 0.9244 (mt) REVERT: F 160 MET cc_start: 0.9270 (mtm) cc_final: 0.8578 (mtp) REVERT: F 624 MET cc_start: 0.6996 (ttm) cc_final: 0.6518 (tmm) outliers start: 3 outliers final: 1 residues processed: 140 average time/residue: 0.3966 time to fit residues: 84.1784 Evaluate side-chains 108 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 166 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 192 optimal weight: 0.0980 chunk 127 optimal weight: 0.8980 chunk 227 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 37 GLN I 56 ASN ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 GLN ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.5440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 20390 Z= 0.140 Angle : 0.488 8.035 27546 Z= 0.265 Chirality : 0.039 0.263 3030 Planarity : 0.003 0.037 3415 Dihedral : 11.685 148.518 3005 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.02 % Favored : 96.94 % Rotamer: Outliers : 0.05 % Allowed : 0.94 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.18), residues: 2320 helix: 1.62 (0.16), residues: 1066 sheet: 0.62 (0.26), residues: 402 loop : -1.20 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP F 184 HIS 0.004 0.001 HIS B 18 PHE 0.023 0.001 PHE K 85 TYR 0.033 0.001 TYR K 59 ARG 0.008 0.000 ARG E 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 2.318 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: symmetry clash REVERT: J 120 PHE cc_start: 0.8637 (t80) cc_final: 0.8434 (t80) REVERT: J 127 PHE cc_start: 0.8885 (t80) cc_final: 0.8537 (t80) REVERT: I 64 ASN cc_start: 0.8636 (m110) cc_final: 0.8374 (m-40) REVERT: I 66 ASN cc_start: 0.9109 (m-40) cc_final: 0.8692 (p0) REVERT: I 86 TYR cc_start: 0.8637 (m-80) cc_final: 0.8266 (m-80) REVERT: K 52 MET cc_start: 0.9244 (mtt) cc_final: 0.8485 (tpt) REVERT: K 76 ASP cc_start: 0.9164 (m-30) cc_final: 0.8801 (m-30) REVERT: K 112 ILE cc_start: 0.9302 (pt) cc_final: 0.9059 (pt) REVERT: E 300 MET cc_start: 0.2003 (mtt) cc_final: 0.1644 (mtt) REVERT: D 102 PHE cc_start: 0.8132 (t80) cc_final: 0.7874 (t80) REVERT: B 115 ASP cc_start: 0.7499 (t0) cc_final: 0.7245 (t0) REVERT: H 10 LEU cc_start: 0.8362 (mt) cc_final: 0.8064 (mt) REVERT: H 208 LEU cc_start: 0.9709 (tt) cc_final: 0.9253 (mt) REVERT: F 352 MET cc_start: 0.8163 (mpp) cc_final: 0.7911 (mpp) REVERT: F 624 MET cc_start: 0.7000 (ttm) cc_final: 0.6518 (tmm) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.3621 time to fit residues: 75.1928 Evaluate side-chains 107 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 37 GLN I 56 ASN ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 ASN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN A 138 GLN ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN B 193 GLN H 183 GLN H 288 ASN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.6200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20390 Z= 0.290 Angle : 0.633 9.218 27546 Z= 0.344 Chirality : 0.041 0.178 3030 Planarity : 0.004 0.052 3415 Dihedral : 12.048 142.151 3005 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 24.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.61 % Favored : 95.34 % Rotamer: Outliers : 0.05 % Allowed : 1.27 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.17), residues: 2320 helix: 1.12 (0.16), residues: 1082 sheet: 0.49 (0.28), residues: 387 loop : -1.36 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP F 184 HIS 0.008 0.002 HIS F 230 PHE 0.020 0.002 PHE K 85 TYR 0.028 0.002 TYR K 59 ARG 0.009 0.001 ARG E 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 2.689 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: J 127 PHE cc_start: 0.9152 (t80) cc_final: 0.8714 (t80) REVERT: I 64 ASN cc_start: 0.9048 (m110) cc_final: 0.8563 (m110) REVERT: I 66 ASN cc_start: 0.9144 (m-40) cc_final: 0.8812 (p0) REVERT: I 85 PHE cc_start: 0.9228 (m-10) cc_final: 0.8984 (m-80) REVERT: I 86 TYR cc_start: 0.8758 (m-80) cc_final: 0.8413 (m-80) REVERT: K 52 MET cc_start: 0.9228 (mtt) cc_final: 0.8328 (tpt) REVERT: K 76 ASP cc_start: 0.9030 (m-30) cc_final: 0.8681 (m-30) REVERT: E 44 ASN cc_start: 0.9268 (t0) cc_final: 0.9067 (t0) REVERT: B 115 ASP cc_start: 0.7867 (t0) cc_final: 0.7603 (t0) REVERT: H 28 MET cc_start: 0.9258 (pmm) cc_final: 0.8946 (pmm) REVERT: H 208 LEU cc_start: 0.9679 (tt) cc_final: 0.9201 (mt) REVERT: F 352 MET cc_start: 0.8394 (mpp) cc_final: 0.8026 (mpp) REVERT: F 571 HIS cc_start: 0.8083 (t70) cc_final: 0.7795 (t-90) outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.3669 time to fit residues: 69.5360 Evaluate side-chains 101 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 10.0000 chunk 198 optimal weight: 7.9990 chunk 211 optimal weight: 0.0980 chunk 127 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 166 optimal weight: 0.0370 chunk 65 optimal weight: 10.0000 chunk 191 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 139 optimal weight: 20.0000 chunk 224 optimal weight: 1.9990 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 37 GLN I 56 ASN ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 324 GLN D 114 ASN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN A 138 GLN ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN H 207 GLN H 288 ASN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.6236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 20390 Z= 0.155 Angle : 0.526 11.079 27546 Z= 0.283 Chirality : 0.040 0.185 3030 Planarity : 0.003 0.053 3415 Dihedral : 11.873 142.923 3005 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.05 % Allowed : 0.71 % Favored : 99.25 % 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: 0.41 (0.18), residues: 2320 helix: 1.29 (0.16), residues: 1077 sheet: 0.58 (0.27), residues: 381 loop : -1.16 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP F 184 HIS 0.009 0.001 HIS I 18 PHE 0.019 0.001 PHE K 85 TYR 0.061 0.001 TYR I 87 ARG 0.012 0.001 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 2.320 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: J 81 LEU cc_start: 0.9345 (tt) cc_final: 0.8510 (tt) REVERT: J 127 PHE cc_start: 0.8900 (t80) cc_final: 0.8457 (t80) REVERT: I 52 MET cc_start: 0.7403 (tpt) cc_final: 0.6605 (tpt) REVERT: I 64 ASN cc_start: 0.8651 (m110) cc_final: 0.8385 (m-40) REVERT: I 66 ASN cc_start: 0.9136 (m-40) cc_final: 0.8831 (p0) REVERT: I 86 TYR cc_start: 0.8697 (m-80) cc_final: 0.8264 (m-80) REVERT: K 52 MET cc_start: 0.9319 (mtt) cc_final: 0.8603 (tpt) REVERT: K 76 ASP cc_start: 0.9101 (m-30) cc_final: 0.8763 (m-30) REVERT: D 102 PHE cc_start: 0.8300 (t80) cc_final: 0.7943 (t80) REVERT: H 28 MET cc_start: 0.9336 (pmm) cc_final: 0.9053 (pmm) REVERT: H 208 LEU cc_start: 0.9667 (tt) cc_final: 0.9245 (mt) REVERT: F 259 MET cc_start: 0.8702 (tpt) cc_final: 0.8040 (tpt) REVERT: F 352 MET cc_start: 0.8285 (mpp) cc_final: 0.7983 (mpp) REVERT: F 571 HIS cc_start: 0.7950 (t70) cc_final: 0.7679 (t-90) REVERT: F 624 MET cc_start: 0.7009 (ttm) cc_final: 0.6492 (tmm) outliers start: 1 outliers final: 1 residues processed: 127 average time/residue: 0.3517 time to fit residues: 68.9094 Evaluate side-chains 101 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 0.4980 chunk 106 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 235 optimal weight: 6.9990 chunk 216 optimal weight: 0.4980 chunk 187 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 114 optimal weight: 0.0020 chunk 148 optimal weight: 1.9990 chunk 199 optimal weight: 0.8980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 37 GLN ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 GLN ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.6306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20390 Z= 0.135 Angle : 0.522 14.787 27546 Z= 0.278 Chirality : 0.040 0.257 3030 Planarity : 0.003 0.068 3415 Dihedral : 11.770 137.982 3005 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.05 % Allowed : 0.19 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.18), residues: 2320 helix: 1.32 (0.16), residues: 1090 sheet: 0.77 (0.28), residues: 382 loop : -1.12 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP F 184 HIS 0.003 0.000 HIS E 117 PHE 0.031 0.001 PHE J 85 TYR 0.042 0.001 TYR I 87 ARG 0.008 0.000 ARG H 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 2.533 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: J 127 PHE cc_start: 0.8878 (t80) cc_final: 0.8591 (t80) REVERT: I 64 ASN cc_start: 0.8604 (m110) cc_final: 0.8336 (m110) REVERT: I 66 ASN cc_start: 0.9131 (m-40) cc_final: 0.8830 (p0) REVERT: I 86 TYR cc_start: 0.8624 (m-80) cc_final: 0.8257 (m-80) REVERT: I 127 PHE cc_start: 0.9062 (t80) cc_final: 0.8846 (t80) REVERT: K 52 MET cc_start: 0.9328 (mtt) cc_final: 0.8587 (tpt) REVERT: K 76 ASP cc_start: 0.9096 (m-30) cc_final: 0.8738 (m-30) REVERT: D 102 PHE cc_start: 0.8171 (t80) cc_final: 0.7680 (t80) REVERT: H 28 MET cc_start: 0.9332 (pmm) cc_final: 0.9092 (pmm) REVERT: H 208 LEU cc_start: 0.9677 (tt) cc_final: 0.9278 (mt) REVERT: F 259 MET cc_start: 0.8699 (tpt) cc_final: 0.8000 (tpt) REVERT: F 352 MET cc_start: 0.8226 (mpp) cc_final: 0.7886 (mpp) REVERT: F 571 HIS cc_start: 0.7809 (t70) cc_final: 0.7534 (t-90) REVERT: F 624 MET cc_start: 0.6928 (ttm) cc_final: 0.6417 (tmm) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.3515 time to fit residues: 67.7908 Evaluate side-chains 98 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 0.0570 chunk 172 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 10 optimal weight: 0.3980 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 37 GLN ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 GLN ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.038067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.030079 restraints weight = 213510.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.030969 restraints weight = 138066.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.031594 restraints weight = 100918.010| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.6390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 20390 Z= 0.128 Angle : 0.503 10.005 27546 Z= 0.272 Chirality : 0.039 0.180 3030 Planarity : 0.003 0.089 3415 Dihedral : 11.704 136.301 3005 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.05 % Allowed : 0.24 % Favored : 99.72 % 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 (0.18), residues: 2320 helix: 1.37 (0.16), residues: 1090 sheet: 0.79 (0.28), residues: 387 loop : -1.12 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP F 184 HIS 0.003 0.000 HIS E 117 PHE 0.022 0.001 PHE J 85 TYR 0.035 0.001 TYR I 87 ARG 0.013 0.000 ARG K 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3253.30 seconds wall clock time: 60 minutes 26.38 seconds (3626.38 seconds total)