Starting phenix.real_space_refine on Sat Jul 4 05:49:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v01_26925/07_2026/7v01_26925_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v01_26925/07_2026/7v01_26925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v01_26925/07_2026/7v01_26925_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v01_26925/07_2026/7v01_26925_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v01_26925/07_2026/7v01_26925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v01_26925/07_2026/7v01_26925.map" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.030 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 61 5.49 5 S 51 5.16 5 C 11549 2.51 5 N 3112 2.21 5 O 3719 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18492 Number of models: 1 Model: "" Number of chains: 11 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: "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: "E" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2473 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 8, 'TRANS': 293} Chain breaks: 3 Chain: "F" Number of atoms: 5636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5636 Classifications: {'peptide': 693} Link IDs: {'PTRANS': 7, 'TRANS': 685} Chain breaks: 3 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': 2, 'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna2p': 10, 'rna3p': 19} Chain: "H" Number of atoms: 2386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2386 Classifications: {'peptide': 297} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 287} Chain breaks: 1 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: "U" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 522 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 8, 'rna3p_pur': 5, 'rna3p_pyr': 8} Link IDs: {'rna2p': 12, 'rna3p': 12} Chain breaks: 1 Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.67, per 1000 atoms: 0.20 Number of scatterers: 18492 At special positions: 0 Unit cell: (96.21, 118.659, 186.006, 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 51 16.00 P 61 15.00 O 3719 8.00 N 3112 7.00 C 11549 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 410 " - pdb=" SG CYS F 426 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.69 Conformation dependent library (CDL) restraints added in 547.7 milliseconds 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3988 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 26 sheets defined 48.9% alpha, 16.0% beta 8 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 47 through 63 removed outlier: 3.532A pdb=" N ILE A 51 " --> pdb=" O PRO A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 73 removed outlier: 3.991A pdb=" N HIS A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 161 through 178 removed outlier: 3.743A pdb=" N ASN A 178 " --> pdb=" O HIS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'B' and resid 47 through 62 removed outlier: 3.763A pdb=" N ILE B 51 " --> pdb=" O PRO B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 84 removed outlier: 3.537A pdb=" N PHE B 83 " --> pdb=" O VAL B 79 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 184 through 188 Processing helix chain 'C' and resid 47 through 63 removed outlier: 3.570A pdb=" N PHE C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 72 removed outlier: 4.477A pdb=" N HIS C 72 " --> pdb=" O LYS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 83 Processing helix chain 'C' and resid 104 through 115 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 Processing helix chain 'C' and resid 184 through 188 Processing helix chain 'E' and resid 42 through 53 Processing helix chain 'E' and resid 55 through 65 Processing helix chain 'E' and resid 69 through 73 removed outlier: 3.670A pdb=" N ASN E 73 " --> pdb=" O PRO E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 82 removed outlier: 3.576A pdb=" N GLN E 82 " --> pdb=" O TYR E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 130 through 147 removed outlier: 3.522A pdb=" N ILE E 134 " --> pdb=" O PRO E 130 " (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 231 Processing helix chain 'E' and resid 237 through 248 Processing helix chain 'E' and resid 248 through 253 Processing helix chain 'E' and resid 278 through 294 removed outlier: 3.762A pdb=" N ARG E 294 " --> pdb=" O THR E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 296 No H-bonds generated for 'chain 'E' and resid 295 through 296' Processing helix chain 'E' and resid 297 through 303 removed outlier: 3.995A pdb=" N MET E 300 " --> pdb=" O TYR E 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 13 removed outlier: 3.712A pdb=" N LEU F 13 " --> pdb=" O TYR F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 24 removed outlier: 4.407A pdb=" N ILE F 20 " --> pdb=" O ILE F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 31 removed outlier: 4.178A pdb=" N ARG F 30 " --> pdb=" O THR F 27 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY F 31 " --> pdb=" O PHE F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 42 Processing helix chain 'F' and resid 49 through 58 Processing helix chain 'F' and resid 60 through 66 removed outlier: 3.692A pdb=" N LYS F 66 " --> pdb=" O LYS F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 86 removed outlier: 4.388A pdb=" N ILE F 77 " --> pdb=" O ASN F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 122 removed outlier: 4.085A pdb=" N ILE F 120 " --> pdb=" O SER F 116 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN F 122 " --> pdb=" O PHE F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 170 removed outlier: 3.545A pdb=" N TYR F 156 " --> pdb=" O SER F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 176 No H-bonds generated for 'chain 'F' and resid 174 through 176' Processing helix chain 'F' and resid 177 through 190 removed outlier: 3.784A 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 237 Processing helix chain 'F' and resid 239 through 249 Processing helix chain 'F' and resid 261 through 266 Processing helix chain 'F' and resid 273 through 300 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 384 removed outlier: 3.572A pdb=" N THR F 371 " --> pdb=" O GLY F 367 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS F 384 " --> pdb=" O LEU F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 398 removed outlier: 3.508A pdb=" N ASN F 397 " --> pdb=" O ILE F 393 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS F 398 " --> pdb=" O LEU F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 422 Processing helix chain 'F' and resid 423 through 437 removed outlier: 4.143A pdb=" N ARG F 437 " --> pdb=" O SER F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 472 Processing helix chain 'F' and resid 500 through 505 removed outlier: 3.647A pdb=" N ASN F 505 " --> pdb=" O ALA F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 513 through 518 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 550 through 567 Processing helix chain 'F' and resid 567 through 573 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 593 through 612 Processing helix chain 'F' and resid 630 through 636 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 removed outlier: 3.664A pdb=" N ASN F 703 " --> pdb=" O ALA F 699 " (cutoff:3.500A) Processing helix chain 'F' and resid 705 through 719 Processing helix chain 'F' and resid 722 through 734 Processing helix chain 'F' and resid 735 through 750 Processing helix chain 'H' and resid 31 through 47 Processing helix chain 'H' and resid 100 through 106 Processing helix chain 'H' and resid 110 through 121 Processing helix chain 'H' and resid 136 through 140 removed outlier: 3.514A pdb=" N THR H 139 " --> pdb=" O ALA H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 183 Processing helix chain 'H' and resid 190 through 194 removed outlier: 3.724A pdb=" N GLY H 194 " --> pdb=" O ARG H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 213 Processing helix chain 'H' and resid 231 through 236 Processing helix chain 'H' and resid 256 through 260 Processing helix chain 'I' and resid 15 through 24 Processing helix chain 'I' and resid 44 through 47 Processing helix chain 'I' and resid 48 through 65 removed outlier: 3.809A pdb=" N SER I 65 " --> pdb=" O ILE I 61 " (cutoff:3.500A) 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 removed outlier: 3.864A pdb=" N ILE I 107 " --> pdb=" O LEU I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 137 Processing helix chain 'K' and resid 15 through 24 Processing helix chain 'K' and resid 44 through 47 Processing helix chain 'K' and resid 48 through 65 removed outlier: 3.809A pdb=" N SER K 65 " --> pdb=" O ILE K 61 " (cutoff:3.500A) 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 removed outlier: 3.865A pdb=" N ILE K 107 " --> pdb=" O LEU K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 116 through 137 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.504A pdb=" N VAL A 203 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS A 6 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N THR A 201 " --> pdb=" O LYS A 6 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N SER A 8 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE A 199 " --> pdb=" O SER A 8 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N THR A 10 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR A 197 " --> pdb=" O THR A 10 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLU A 12 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LYS A 195 " --> pdb=" O GLU A 12 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 37 through 38 removed outlier: 3.787A pdb=" N LEU A 43 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 119 through 124 removed outlier: 3.551A pdb=" N LYS A 122 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A 139 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.577A pdb=" N PHE B 102 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.522A pdb=" N VAL B 156 " --> pdb=" O SER B 3 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER B 3 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LYS B 4 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR B 10 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASP B 196 " --> pdb=" O THR B 10 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU B 12 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N PHE B 194 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 119 through 124 Processing sheet with id=AA8, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.556A pdb=" N ILE C 46 " --> pdb=" O ALA C 101 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.556A pdb=" N ILE C 46 " --> pdb=" O ALA C 101 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER C 3 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS C 4 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR C 10 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ASP C 196 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU C 12 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.723A 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 124 removed outlier: 3.818A pdb=" N ARG C 141 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 158 through 160 Processing sheet with id=AB3, first strand: chain 'E' and resid 19 through 24 removed outlier: 4.859A pdb=" N GLN E 22 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 31 through 32 removed outlier: 3.679A pdb=" N LYS E 37 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR E 95 " --> pdb=" O MET E 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 184 through 193 removed outlier: 6.861A pdb=" N MET E 186 " --> pdb=" O ASP E 178 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASP E 178 " --> pdb=" O MET E 186 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU E 188 " --> pdb=" O LYS E 176 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N GLN E 175 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N THR E 315 " --> pdb=" O GLN E 175 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR E 321 " --> pdb=" O ASN E 316 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 307 through 311 removed outlier: 6.258A pdb=" N LEU F 307 " --> pdb=" O LEU F 318 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU F 318 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR F 309 " --> pdb=" O TYR F 316 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY F 311 " --> pdb=" O HIS F 314 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU F 254 " --> pdb=" O GLU F 355 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 450 through 452 removed outlier: 3.692A pdb=" N LYS F 456 " --> pdb=" O MET F 452 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 578 through 584 removed outlier: 6.734A pdb=" N PHE F 589 " --> pdb=" O ILE F 581 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER F 583 " --> pdb=" O ASP F 587 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASP F 587 " --> pdb=" O SER F 583 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE F 625 " --> pdb=" O LEU F 526 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL F 528 " --> pdb=" O GLY F 623 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY F 623 " --> pdb=" O VAL F 528 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG F 530 " --> pdb=" O GLY F 621 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 63 through 65 removed outlier: 3.825A pdb=" N VAL H 7 " --> pdb=" O ILE H 203 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE H 203 " --> pdb=" O VAL H 7 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 58 through 59 Processing sheet with id=AC2, first strand: chain 'H' and resid 71 through 73 Processing sheet with id=AC3, first strand: chain 'H' and resid 125 through 131 Processing sheet with id=AC4, first strand: chain 'H' and resid 273 through 274 Processing sheet with id=AC5, first strand: chain 'H' and resid 243 through 246 Processing sheet with id=AC6, first strand: chain 'H' and resid 281 through 284 Processing sheet with id=AC7, first strand: chain 'I' and resid 25 through 26 removed outlier: 3.543A pdb=" N LYS I 26 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 25 through 26 removed outlier: 3.543A pdb=" N LYS K 26 " --> pdb=" O VAL K 38 " (cutoff:3.500A) 833 hydrogen bonds defined for protein. 2361 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 3.32 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3874 1.33 - 1.45: 4726 1.45 - 1.57: 10139 1.57 - 1.70: 118 1.70 - 1.82: 90 Bond restraints: 18947 Sorted by residual: bond pdb=" C4 ATP F 802 " pdb=" C5 ATP F 802 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 6.99e+01 bond pdb=" C5 ATP F 802 " pdb=" C6 ATP F 802 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.71e+01 bond pdb=" C5 ATP F 802 " pdb=" N7 ATP F 802 " ideal model delta sigma weight residual 1.387 1.333 0.054 1.00e-02 1.00e+04 2.97e+01 bond pdb=" C4 ATP F 802 " pdb=" N9 ATP F 802 " ideal model delta sigma weight residual 1.374 1.330 0.044 1.00e-02 1.00e+04 1.97e+01 bond pdb=" C8 ATP F 802 " pdb=" N7 ATP F 802 " ideal model delta sigma weight residual 1.310 1.352 -0.042 1.00e-02 1.00e+04 1.76e+01 ... (remaining 18942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 25454 3.28 - 6.57: 264 6.57 - 9.85: 23 9.85 - 13.14: 3 13.14 - 16.42: 5 Bond angle restraints: 25749 Sorted by residual: angle pdb=" PB ATP F 802 " pdb=" O3B ATP F 802 " pdb=" PG ATP F 802 " ideal model delta sigma weight residual 139.87 123.45 16.42 1.00e+00 1.00e+00 2.70e+02 angle pdb=" PA ATP F 802 " pdb=" O3A ATP F 802 " pdb=" PB ATP F 802 " ideal model delta sigma weight residual 136.83 121.94 14.89 1.00e+00 1.00e+00 2.22e+02 angle pdb=" CA PHE F 540 " pdb=" CB PHE F 540 " pdb=" CG PHE F 540 " ideal model delta sigma weight residual 113.80 99.01 14.79 1.00e+00 1.00e+00 2.19e+02 angle pdb=" C4' A U 25 " pdb=" C3' A U 25 " pdb=" O3' A U 25 " ideal model delta sigma weight residual 113.00 97.76 15.24 1.50e+00 4.44e-01 1.03e+02 angle pdb=" O3' U U 28 " pdb=" C3' U U 28 " pdb=" C2' U U 28 " ideal model delta sigma weight residual 109.50 124.01 -14.51 1.50e+00 4.44e-01 9.36e+01 ... (remaining 25744 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 11156 35.78 - 71.55: 277 71.55 - 107.33: 33 107.33 - 143.10: 3 143.10 - 178.88: 4 Dihedral angle restraints: 11473 sinusoidal: 5268 harmonic: 6205 Sorted by residual: dihedral pdb=" O4' U U 17 " pdb=" C1' U U 17 " pdb=" N1 U U 17 " pdb=" C2 U U 17 " ideal model delta sinusoidal sigma weight residual -128.00 48.98 -176.98 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U U 10 " pdb=" C1' U U 10 " pdb=" N1 U U 10 " pdb=" C2 U U 10 " ideal model delta sinusoidal sigma weight residual 232.00 75.77 156.23 1 1.70e+01 3.46e-03 6.36e+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 7.04 -135.04 1 1.70e+01 3.46e-03 5.67e+01 ... (remaining 11470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2472 0.074 - 0.149: 337 0.149 - 0.223: 32 0.223 - 0.297: 6 0.297 - 0.371: 2 Chirality restraints: 2849 Sorted by residual: chirality pdb=" P G U 29 " pdb=" OP1 G U 29 " pdb=" OP2 G U 29 " pdb=" O5' G U 29 " both_signs ideal model delta sigma weight residual True 2.41 -2.78 -0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" C3' A U 25 " pdb=" C4' A U 25 " pdb=" O3' A U 25 " pdb=" C2' A U 25 " both_signs ideal model delta sigma weight residual False -2.48 -2.83 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" C1' G G 21 " pdb=" O4' G G 21 " pdb=" C2' G G 21 " pdb=" N9 G G 21 " both_signs ideal model delta sigma weight residual False 2.44 2.16 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 2846 not shown) Planarity restraints: 3088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 540 " -0.061 2.00e-02 2.50e+03 4.57e-02 3.65e+01 pdb=" CG PHE F 540 " 0.102 2.00e-02 2.50e+03 pdb=" CD1 PHE F 540 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE F 540 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE F 540 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE F 540 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE F 540 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY E 14 " 0.063 5.00e-02 4.00e+02 9.41e-02 1.42e+01 pdb=" N PRO E 15 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO E 15 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO E 15 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 43 " 0.059 5.00e-02 4.00e+02 8.68e-02 1.20e+01 pdb=" N PRO A 44 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 44 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 44 " 0.048 5.00e-02 4.00e+02 ... (remaining 3085 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 66 2.44 - 3.05: 12282 3.05 - 3.67: 27339 3.67 - 4.28: 40610 4.28 - 4.90: 65946 Nonbonded interactions: 146243 Sorted by model distance: nonbonded pdb=" ND2 ASN B 57 " pdb=" O2 C G 8 " model vdw 1.822 3.120 nonbonded pdb=" OG SER B 86 " pdb=" O2' G G 5 " model vdw 2.070 3.040 nonbonded pdb=" OH TYR B 2 " pdb=" OE1 GLN H 45 " model vdw 2.177 3.040 nonbonded pdb=" OG SER I 46 " pdb=" OP2 U U 9 " model vdw 2.182 3.040 nonbonded pdb=" O2' G U 21 " pdb=" O5' C U 22 " model vdw 2.211 3.040 ... (remaining 146238 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 21 \ 4)) selection = chain 'B' selection = (chain 'C' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 21 \ 4)) } ncs_group { reference = chain 'I' selection = chain 'K' } 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: 5.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.140 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 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 : 0.006 0.090 18948 Z= 0.343 Angle : 0.884 16.419 25751 Z= 0.582 Chirality : 0.052 0.371 2849 Planarity : 0.005 0.094 3088 Dihedral : 15.848 178.878 7482 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.47 % Allowed : 0.58 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.17), residues: 2086 helix: -0.01 (0.16), residues: 926 sheet: -0.42 (0.28), residues: 321 loop : -1.75 (0.19), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.001 ARG C 78 TYR 0.055 0.002 TYR K 86 PHE 0.102 0.003 PHE F 540 TRP 0.041 0.002 TRP F 339 HIS 0.007 0.001 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.34 (18947) covalent geometry : angle 0.88404 / 0.58 (25749) SS BOND : bond 0.00160 / 0.08 ( 1) SS BOND : angle 1.98932 / 1.12 ( 2) hydrogen bonds : bond 0.18529 / 12.96 ( 846) hydrogen bonds : angle 6.80632 / 4.73 ( 2401) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 375 time to evaluate : 0.672 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: C 137 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6567 (ttm170) REVERT: E 119 MET cc_start: 0.7312 (tpp) cc_final: 0.6999 (tpp) REVERT: E 289 LEU cc_start: 0.7281 (mt) cc_final: 0.6794 (tt) REVERT: F 163 MET cc_start: 0.7443 (ptp) cc_final: 0.7050 (tpt) REVERT: F 588 LEU cc_start: 0.8293 (tp) cc_final: 0.8052 (tp) REVERT: F 697 MET cc_start: 0.7188 (mmm) cc_final: 0.6916 (mmm) REVERT: H 258 MET cc_start: -0.0037 (mmm) cc_final: -0.0583 (mmt) REVERT: I 43 LEU cc_start: 0.8394 (tp) cc_final: 0.8112 (tp) REVERT: I 58 LEU cc_start: 0.9499 (mt) cc_final: 0.9086 (mt) REVERT: I 81 LEU cc_start: 0.9526 (tp) cc_final: 0.9093 (tp) REVERT: I 84 LYS cc_start: 0.9569 (mmtm) cc_final: 0.9265 (mmmt) REVERT: I 120 PHE cc_start: 0.9357 (t80) cc_final: 0.9117 (t80) REVERT: K 75 ILE cc_start: 0.9334 (mm) cc_final: 0.8728 (mm) REVERT: K 77 GLU cc_start: 0.9211 (mm-30) cc_final: 0.9007 (mm-30) REVERT: K 87 TYR cc_start: 0.8289 (t80) cc_final: 0.6884 (t80) REVERT: K 137 TYR cc_start: 0.7843 (m-10) cc_final: 0.7469 (m-10) outliers start: 9 outliers final: 2 residues processed: 383 average time/residue: 0.1565 time to fit residues: 85.0123 Evaluate side-chains 168 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 165 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 384 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 174 HIS ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 ASN E 54 ASN E 61 ASN ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 ASN ** F 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 549 ASN H 206 GLN I 71 ASN ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN K 69 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.064758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.050057 restraints weight = 121747.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.051612 restraints weight = 72963.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.052616 restraints weight = 51701.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.053255 restraints weight = 40976.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.053706 restraints weight = 35105.300| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 18948 Z= 0.210 Angle : 0.790 14.472 25751 Z= 0.427 Chirality : 0.048 0.264 2849 Planarity : 0.005 0.071 3088 Dihedral : 17.289 178.139 3199 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.95 % Allowed : 9.68 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.18), residues: 2086 helix: 0.45 (0.17), residues: 928 sheet: -0.21 (0.28), residues: 326 loop : -1.77 (0.19), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 240 TYR 0.029 0.002 TYR E 155 PHE 0.051 0.002 PHE I 85 TRP 0.026 0.002 TRP F 339 HIS 0.014 0.002 HIS K 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.21 (18947) covalent geometry : angle 0.79032 / 0.43 (25749) SS BOND : bond 0.00414 / 0.22 ( 1) SS BOND : angle 1.45702 / 0.82 ( 2) hydrogen bonds : bond 0.05612 / 3.85 ( 846) hydrogen bonds : angle 5.69681 / 3.96 ( 2401) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 0.664 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: C 122 LYS cc_start: 0.9506 (OUTLIER) cc_final: 0.9134 (ptmt) REVERT: E 186 MET cc_start: 0.5293 (mmt) cc_final: 0.4765 (mmt) REVERT: E 190 ARG cc_start: 0.8042 (mtm110) cc_final: 0.7333 (ttm110) REVERT: F 163 MET cc_start: 0.8554 (ptp) cc_final: 0.7755 (tpt) REVERT: F 184 TRP cc_start: 0.6689 (m100) cc_final: 0.6464 (m100) REVERT: F 257 MET cc_start: 0.9509 (mtp) cc_final: 0.9181 (mtm) REVERT: F 352 MET cc_start: 0.8878 (mmm) cc_final: 0.8171 (mmm) REVERT: F 624 MET cc_start: 0.4900 (tmm) cc_final: 0.4186 (tpp) REVERT: I 49 ARG cc_start: 0.8403 (mmp-170) cc_final: 0.8107 (mmm160) REVERT: I 58 LEU cc_start: 0.9716 (mt) cc_final: 0.9471 (mt) REVERT: I 120 PHE cc_start: 0.9760 (t80) cc_final: 0.9454 (t80) REVERT: K 85 PHE cc_start: 0.9479 (m-80) cc_final: 0.9137 (m-80) REVERT: K 91 ARG cc_start: 0.7713 (tpp80) cc_final: 0.7229 (tpp80) REVERT: K 113 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8505 (pptt) REVERT: K 137 TYR cc_start: 0.8339 (m-10) cc_final: 0.7772 (m-80) outliers start: 37 outliers final: 17 residues processed: 208 average time/residue: 0.1536 time to fit residues: 47.2169 Evaluate side-chains 149 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 412 ARG Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 558 SER Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain F residue 696 LYS Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 255 TYR Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 113 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 560 GLN F 735 ASN ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.062500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.048334 restraints weight = 124744.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.049758 restraints weight = 75542.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.050700 restraints weight = 54064.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.051326 restraints weight = 43074.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.051723 restraints weight = 36852.739| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 18948 Z= 0.264 Angle : 0.758 13.345 25751 Z= 0.407 Chirality : 0.047 0.377 2849 Planarity : 0.005 0.157 3088 Dihedral : 17.126 177.190 3191 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.21 % Allowed : 11.53 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.18), residues: 2086 helix: 0.52 (0.17), residues: 927 sheet: -0.34 (0.28), residues: 333 loop : -1.81 (0.19), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG F 711 TYR 0.026 0.002 TYR E 155 PHE 0.046 0.002 PHE F 693 TRP 0.016 0.002 TRP F 339 HIS 0.010 0.001 HIS I 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.26 (18947) covalent geometry : angle 0.75843 / 0.41 (25749) SS BOND : bond 0.00878 / 0.46 ( 1) SS BOND : angle 1.16553 / 0.63 ( 2) hydrogen bonds : bond 0.05049 / 3.49 ( 846) hydrogen bonds : angle 5.51806 / 3.83 ( 2401) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 0.583 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 113 GLN cc_start: 0.9440 (pt0) cc_final: 0.9152 (pt0) REVERT: C 122 LYS cc_start: 0.9483 (OUTLIER) cc_final: 0.9168 (ptmt) REVERT: E 56 LEU cc_start: 0.8763 (tt) cc_final: 0.8365 (mt) REVERT: E 117 HIS cc_start: 0.7347 (t70) cc_final: 0.6801 (t70) REVERT: E 327 MET cc_start: 0.8299 (pmm) cc_final: 0.8071 (pmm) REVERT: F 41 LEU cc_start: 0.9215 (tp) cc_final: 0.8941 (tp) REVERT: F 163 MET cc_start: 0.8712 (ptp) cc_final: 0.7930 (tpt) REVERT: F 352 MET cc_start: 0.8780 (mmm) cc_final: 0.8538 (mmm) REVERT: F 624 MET cc_start: 0.4497 (tmm) cc_final: 0.3899 (tpp) REVERT: I 120 PHE cc_start: 0.9745 (t80) cc_final: 0.9369 (t80) REVERT: K 113 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8406 (pptt) REVERT: K 120 PHE cc_start: 0.9487 (t80) cc_final: 0.9249 (t80) REVERT: K 126 TYR cc_start: 0.8898 (t80) cc_final: 0.8536 (t80) REVERT: K 130 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8596 (mm) REVERT: K 137 TYR cc_start: 0.8436 (m-10) cc_final: 0.7820 (m-80) outliers start: 42 outliers final: 21 residues processed: 176 average time/residue: 0.1451 time to fit residues: 37.7737 Evaluate side-chains 145 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 499 TYR Chi-restraints excluded: chain F residue 558 SER Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain F residue 735 ASN Chi-restraints excluded: chain H residue 255 TYR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain K residue 130 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 96 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 87 optimal weight: 0.2980 chunk 119 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 158 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 GLN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.062620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.048386 restraints weight = 125666.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.049893 restraints weight = 73442.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.050869 restraints weight = 51525.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.051502 restraints weight = 40594.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.051904 restraints weight = 34624.215| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18948 Z= 0.183 Angle : 0.688 13.249 25751 Z= 0.371 Chirality : 0.045 0.289 2849 Planarity : 0.004 0.057 3088 Dihedral : 16.990 177.993 3191 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.11 % Allowed : 12.05 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.18), residues: 2086 helix: 0.60 (0.17), residues: 935 sheet: -0.24 (0.29), residues: 323 loop : -1.81 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 49 TYR 0.021 0.001 TYR E 155 PHE 0.036 0.002 PHE E 62 TRP 0.014 0.001 TRP F 339 HIS 0.007 0.001 HIS K 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 (18947) covalent geometry : angle 0.68749 / 0.37 (25749) SS BOND : bond 0.00535 / 0.28 ( 1) SS BOND : angle 1.28654 / 0.71 ( 2) hydrogen bonds : bond 0.04504 / 3.12 ( 846) hydrogen bonds : angle 5.30282 / 3.70 ( 2401) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.493 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: A 113 GLN cc_start: 0.9420 (pt0) cc_final: 0.9165 (pt0) REVERT: C 122 LYS cc_start: 0.9528 (OUTLIER) cc_final: 0.9197 (ptmt) REVERT: E 117 HIS cc_start: 0.7373 (t70) cc_final: 0.6974 (t70) REVERT: E 289 LEU cc_start: 0.6959 (mm) cc_final: 0.6740 (tp) REVERT: E 327 MET cc_start: 0.8320 (pmm) cc_final: 0.8057 (pmm) REVERT: F 41 LEU cc_start: 0.9216 (tp) cc_final: 0.8971 (tp) REVERT: F 47 PHE cc_start: 0.8271 (m-80) cc_final: 0.7397 (m-80) REVERT: F 163 MET cc_start: 0.8746 (ptp) cc_final: 0.7948 (tpt) REVERT: F 463 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.8195 (p90) REVERT: F 468 MET cc_start: 0.9427 (ptp) cc_final: 0.9176 (ptp) REVERT: F 624 MET cc_start: 0.4439 (tmm) cc_final: 0.3912 (tpp) REVERT: H 13 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7631 (pttm) REVERT: H 226 MET cc_start: 0.9289 (tpp) cc_final: 0.8300 (tpp) REVERT: I 41 ASN cc_start: 0.9111 (t0) cc_final: 0.8889 (m-40) REVERT: I 52 MET cc_start: 0.9565 (pmm) cc_final: 0.9334 (pmm) REVERT: I 96 ASP cc_start: 0.9127 (m-30) cc_final: 0.8801 (m-30) REVERT: I 120 PHE cc_start: 0.9730 (t80) cc_final: 0.9341 (t80) REVERT: K 52 MET cc_start: 0.8791 (pmm) cc_final: 0.8509 (pmm) REVERT: K 113 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8401 (pptt) REVERT: K 120 PHE cc_start: 0.9508 (t80) cc_final: 0.9186 (t80) REVERT: K 126 TYR cc_start: 0.8969 (t80) cc_final: 0.8557 (t80) REVERT: K 130 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8588 (mm) REVERT: K 137 TYR cc_start: 0.8551 (m-10) cc_final: 0.8243 (m-80) outliers start: 40 outliers final: 21 residues processed: 168 average time/residue: 0.1472 time to fit residues: 36.6381 Evaluate side-chains 143 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 558 SER Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 255 TYR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain K residue 130 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 12 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 191 optimal weight: 6.9990 chunk 142 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 192 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 3 optimal weight: 0.0970 chunk 203 optimal weight: 4.9990 overall best weight: 1.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 113 GLN ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 722 ASN F 735 ASN ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.062076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.047999 restraints weight = 125251.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.049480 restraints weight = 73549.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.050449 restraints weight = 51628.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.051065 restraints weight = 40727.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.051481 restraints weight = 34878.526| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18948 Z= 0.175 Angle : 0.665 13.135 25751 Z= 0.357 Chirality : 0.045 0.295 2849 Planarity : 0.004 0.055 3088 Dihedral : 16.843 179.764 3191 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.21 % Allowed : 13.37 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.18), residues: 2086 helix: 0.74 (0.17), residues: 927 sheet: -0.23 (0.29), residues: 323 loop : -1.70 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 242 TYR 0.017 0.001 TYR E 155 PHE 0.039 0.002 PHE E 62 TRP 0.037 0.002 TRP E 89 HIS 0.007 0.001 HIS K 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 (18947) covalent geometry : angle 0.66533 / 0.36 (25749) SS BOND : bond 0.00611 / 0.32 ( 1) SS BOND : angle 1.21781 / 0.66 ( 2) hydrogen bonds : bond 0.04248 / 2.91 ( 846) hydrogen bonds : angle 5.19557 / 3.62 ( 2401) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 0.675 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: A 113 GLN cc_start: 0.9418 (pt0) cc_final: 0.9147 (pt0) REVERT: C 122 LYS cc_start: 0.9526 (OUTLIER) cc_final: 0.9207 (ptmt) REVERT: E 56 LEU cc_start: 0.8782 (tt) cc_final: 0.8473 (mt) REVERT: E 117 HIS cc_start: 0.7384 (t70) cc_final: 0.6876 (t70) REVERT: F 41 LEU cc_start: 0.9245 (tp) cc_final: 0.9014 (tp) REVERT: F 47 PHE cc_start: 0.8245 (m-80) cc_final: 0.7429 (m-80) REVERT: F 160 MET cc_start: 0.9404 (tmm) cc_final: 0.8794 (ptm) REVERT: F 163 MET cc_start: 0.8732 (ptp) cc_final: 0.7857 (tpt) REVERT: F 257 MET cc_start: 0.9504 (mtm) cc_final: 0.9209 (mtm) REVERT: F 352 MET cc_start: 0.8988 (mmm) cc_final: 0.8359 (mmm) REVERT: F 463 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.8153 (p90) REVERT: F 624 MET cc_start: 0.4539 (tmm) cc_final: 0.4133 (tpp) REVERT: H 13 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7574 (pttm) REVERT: H 226 MET cc_start: 0.9374 (tpp) cc_final: 0.8436 (tpp) REVERT: I 41 ASN cc_start: 0.9170 (t0) cc_final: 0.8942 (m-40) REVERT: I 52 MET cc_start: 0.9541 (pmm) cc_final: 0.9281 (pmm) REVERT: I 85 PHE cc_start: 0.9626 (m-80) cc_final: 0.9401 (m-80) REVERT: I 96 ASP cc_start: 0.9105 (m-30) cc_final: 0.8780 (m-30) REVERT: I 120 PHE cc_start: 0.9720 (t80) cc_final: 0.9321 (t80) REVERT: I 124 CYS cc_start: 0.9293 (m) cc_final: 0.9045 (m) REVERT: K 113 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8428 (pptt) REVERT: K 120 PHE cc_start: 0.9511 (t80) cc_final: 0.9189 (t80) REVERT: K 130 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8865 (mm) REVERT: K 137 TYR cc_start: 0.8651 (m-10) cc_final: 0.8437 (m-80) outliers start: 42 outliers final: 27 residues processed: 162 average time/residue: 0.1533 time to fit residues: 37.6775 Evaluate side-chains 148 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 499 TYR Chi-restraints excluded: chain F residue 558 SER Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 255 TYR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain K residue 130 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 20 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 163 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 139 optimal weight: 0.0770 chunk 189 optimal weight: 0.9980 chunk 80 optimal weight: 0.0970 chunk 109 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 113 GLN ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 HIS F 165 HIS F 471 GLN ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.062919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.048827 restraints weight = 122252.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.050375 restraints weight = 71707.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.051355 restraints weight = 50136.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.052001 restraints weight = 39388.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.052416 restraints weight = 33458.347| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18948 Z= 0.125 Angle : 0.628 13.036 25751 Z= 0.335 Chirality : 0.044 0.286 2849 Planarity : 0.003 0.053 3088 Dihedral : 16.676 179.207 3191 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.32 % Allowed : 14.11 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.18), residues: 2086 helix: 0.84 (0.17), residues: 936 sheet: -0.17 (0.29), residues: 309 loop : -1.63 (0.19), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 190 TYR 0.017 0.001 TYR H 184 PHE 0.026 0.001 PHE E 62 TRP 0.018 0.001 TRP E 89 HIS 0.007 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (18947) covalent geometry : angle 0.62820 / 0.33 (25749) SS BOND : bond 0.00232 / 0.12 ( 1) SS BOND : angle 1.25646 / 0.70 ( 2) hydrogen bonds : bond 0.03911 / 2.66 ( 846) hydrogen bonds : angle 4.98806 / 3.47 ( 2401) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 129 time to evaluate : 0.698 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: A 3 SER cc_start: 0.8818 (OUTLIER) cc_final: 0.7996 (m) REVERT: A 113 GLN cc_start: 0.9425 (pt0) cc_final: 0.9135 (pt0) REVERT: B 201 THR cc_start: 0.9253 (OUTLIER) cc_final: 0.8985 (m) REVERT: C 113 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8884 (pp30) REVERT: C 122 LYS cc_start: 0.9520 (OUTLIER) cc_final: 0.9205 (ptmt) REVERT: E 56 LEU cc_start: 0.8771 (tt) cc_final: 0.8469 (mt) REVERT: E 68 LYS cc_start: 0.7292 (tptt) cc_final: 0.6911 (mptt) REVERT: E 125 ASN cc_start: 0.9069 (OUTLIER) cc_final: 0.8820 (t0) REVERT: F 41 LEU cc_start: 0.9218 (tp) cc_final: 0.8971 (tp) REVERT: F 47 PHE cc_start: 0.8294 (m-80) cc_final: 0.7513 (m-80) REVERT: F 163 MET cc_start: 0.8687 (ptp) cc_final: 0.7899 (tpt) REVERT: F 257 MET cc_start: 0.9487 (mtm) cc_final: 0.9255 (mtm) REVERT: F 352 MET cc_start: 0.8832 (mmm) cc_final: 0.8453 (mmm) REVERT: F 624 MET cc_start: 0.4070 (tmm) cc_final: 0.3644 (tpp) REVERT: H 13 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7468 (pttm) REVERT: H 226 MET cc_start: 0.9370 (tpp) cc_final: 0.8529 (tpp) REVERT: I 41 ASN cc_start: 0.9157 (t0) cc_final: 0.8929 (m-40) REVERT: I 52 MET cc_start: 0.9572 (pmm) cc_final: 0.9307 (pmm) REVERT: I 85 PHE cc_start: 0.9639 (m-80) cc_final: 0.9427 (m-80) REVERT: I 96 ASP cc_start: 0.9104 (m-30) cc_final: 0.8784 (m-30) REVERT: I 120 PHE cc_start: 0.9692 (t80) cc_final: 0.9323 (t80) REVERT: I 124 CYS cc_start: 0.9278 (m) cc_final: 0.9023 (m) REVERT: I 130 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9180 (mm) REVERT: K 52 MET cc_start: 0.8743 (pmm) cc_final: 0.8061 (pmm) REVERT: K 72 GLU cc_start: 0.9386 (OUTLIER) cc_final: 0.9105 (pm20) REVERT: K 97 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8381 (pt0) REVERT: K 113 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8445 (pptt) REVERT: K 120 PHE cc_start: 0.9520 (t80) cc_final: 0.9180 (t80) REVERT: K 126 TYR cc_start: 0.8931 (t80) cc_final: 0.8509 (t80) REVERT: K 130 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8675 (mm) REVERT: K 137 TYR cc_start: 0.8674 (m-10) cc_final: 0.8044 (m-10) outliers start: 44 outliers final: 22 residues processed: 168 average time/residue: 0.1407 time to fit residues: 36.2307 Evaluate side-chains 150 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 255 TYR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain K residue 130 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 140 optimal weight: 0.3980 chunk 149 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 184 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 199 optimal weight: 0.6980 chunk 209 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 97 GLN ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.062501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.048466 restraints weight = 124389.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.049986 restraints weight = 72440.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.050959 restraints weight = 50549.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.051597 restraints weight = 39655.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.052020 restraints weight = 33709.882| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 18948 Z= 0.135 Angle : 0.623 13.011 25751 Z= 0.332 Chirality : 0.043 0.285 2849 Planarity : 0.003 0.050 3088 Dihedral : 16.559 179.411 3191 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.32 % Allowed : 14.63 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.18), residues: 2086 helix: 0.89 (0.17), residues: 938 sheet: -0.34 (0.29), residues: 332 loop : -1.58 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 91 TYR 0.023 0.001 TYR I 126 PHE 0.017 0.001 PHE E 62 TRP 0.015 0.001 TRP E 89 HIS 0.006 0.001 HIS C 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (18947) covalent geometry : angle 0.62344 / 0.33 (25749) SS BOND : bond 0.00352 / 0.19 ( 1) SS BOND : angle 1.00596 / 0.56 ( 2) hydrogen bonds : bond 0.03915 / 2.69 ( 846) hydrogen bonds : angle 4.96526 / 3.47 ( 2401) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 121 time to evaluate : 0.818 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: A 3 SER cc_start: 0.8761 (OUTLIER) cc_final: 0.7924 (m) REVERT: A 113 GLN cc_start: 0.9421 (pt0) cc_final: 0.9126 (pt0) REVERT: B 201 THR cc_start: 0.9250 (OUTLIER) cc_final: 0.8985 (m) REVERT: C 113 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8773 (pp30) REVERT: C 122 LYS cc_start: 0.9529 (OUTLIER) cc_final: 0.9227 (ptmt) REVERT: E 56 LEU cc_start: 0.8793 (tt) cc_final: 0.8519 (mt) REVERT: E 68 LYS cc_start: 0.7311 (tptt) cc_final: 0.6932 (mptt) REVERT: F 41 LEU cc_start: 0.9259 (tp) cc_final: 0.9032 (tp) REVERT: F 47 PHE cc_start: 0.8292 (m-80) cc_final: 0.7545 (m-80) REVERT: F 160 MET cc_start: 0.9393 (tmm) cc_final: 0.8687 (ptm) REVERT: F 163 MET cc_start: 0.8693 (ptp) cc_final: 0.7836 (tpt) REVERT: F 257 MET cc_start: 0.9481 (mtm) cc_final: 0.9275 (mtm) REVERT: F 352 MET cc_start: 0.8826 (mmm) cc_final: 0.8418 (mmm) REVERT: F 624 MET cc_start: 0.4000 (tmm) cc_final: 0.3595 (tpp) REVERT: H 13 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7398 (pttm) REVERT: H 187 LEU cc_start: 0.9299 (mt) cc_final: 0.8993 (tt) REVERT: H 226 MET cc_start: 0.9382 (tpp) cc_final: 0.8584 (tpp) REVERT: I 41 ASN cc_start: 0.9170 (t0) cc_final: 0.8931 (m-40) REVERT: I 52 MET cc_start: 0.9560 (pmm) cc_final: 0.9341 (pmm) REVERT: I 85 PHE cc_start: 0.9668 (m-80) cc_final: 0.9434 (m-80) REVERT: I 96 ASP cc_start: 0.9117 (m-30) cc_final: 0.8791 (m-30) REVERT: I 120 PHE cc_start: 0.9695 (t80) cc_final: 0.9314 (t80) REVERT: I 124 CYS cc_start: 0.9269 (m) cc_final: 0.9003 (m) REVERT: I 130 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9166 (mm) REVERT: K 52 MET cc_start: 0.8489 (pmm) cc_final: 0.8117 (pmm) REVERT: K 72 GLU cc_start: 0.9394 (OUTLIER) cc_final: 0.9098 (pm20) REVERT: K 97 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8320 (pt0) REVERT: K 113 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8454 (pptt) REVERT: K 120 PHE cc_start: 0.9503 (t80) cc_final: 0.9183 (t80) REVERT: K 130 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8891 (mm) REVERT: K 137 TYR cc_start: 0.8646 (m-10) cc_final: 0.8051 (m-10) outliers start: 44 outliers final: 27 residues processed: 158 average time/residue: 0.1357 time to fit residues: 32.4575 Evaluate side-chains 156 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 65 TYR Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 567 TYR Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 255 TYR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain K residue 130 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 7 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 171 optimal weight: 8.9990 chunk 212 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 180 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 167 optimal weight: 0.0470 overall best weight: 0.7878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 471 GLN H 17 HIS ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 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 = 0.3661 r_free = 0.3661 target = 0.062568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.048549 restraints weight = 123589.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.050086 restraints weight = 72281.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.051063 restraints weight = 50627.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.051708 restraints weight = 39652.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.052116 restraints weight = 33646.328| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18948 Z= 0.127 Angle : 0.617 12.925 25751 Z= 0.328 Chirality : 0.043 0.283 2849 Planarity : 0.003 0.049 3088 Dihedral : 16.476 179.308 3191 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.21 % Allowed : 14.68 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.18), residues: 2086 helix: 0.95 (0.17), residues: 940 sheet: -0.32 (0.29), residues: 332 loop : -1.57 (0.19), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 91 TYR 0.019 0.001 TYR K 126 PHE 0.023 0.001 PHE E 62 TRP 0.012 0.001 TRP E 89 HIS 0.003 0.001 HIS F 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (18947) covalent geometry : angle 0.61696 / 0.33 (25749) SS BOND : bond 0.00295 / 0.16 ( 1) SS BOND : angle 0.94067 / 0.52 ( 2) hydrogen bonds : bond 0.03776 / 2.58 ( 846) hydrogen bonds : angle 4.88929 / 3.42 ( 2401) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 0.715 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: A 3 SER cc_start: 0.8726 (OUTLIER) cc_final: 0.7897 (m) REVERT: A 113 GLN cc_start: 0.9421 (pt0) cc_final: 0.9129 (pt0) REVERT: B 201 THR cc_start: 0.9245 (OUTLIER) cc_final: 0.8987 (m) REVERT: C 122 LYS cc_start: 0.9523 (OUTLIER) cc_final: 0.9197 (ptmt) REVERT: E 56 LEU cc_start: 0.8797 (tt) cc_final: 0.8586 (mt) REVERT: E 68 LYS cc_start: 0.7277 (tptt) cc_final: 0.6924 (mptt) REVERT: F 41 LEU cc_start: 0.9258 (tp) cc_final: 0.9031 (tp) REVERT: F 47 PHE cc_start: 0.8290 (m-80) cc_final: 0.7534 (m-80) REVERT: F 160 MET cc_start: 0.9393 (tmm) cc_final: 0.8720 (ptm) REVERT: F 163 MET cc_start: 0.8703 (ptp) cc_final: 0.7860 (tpt) REVERT: F 257 MET cc_start: 0.9477 (mtm) cc_final: 0.9102 (mtm) REVERT: F 352 MET cc_start: 0.8752 (mmm) cc_final: 0.8039 (mmm) REVERT: F 463 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.8134 (p90) REVERT: F 624 MET cc_start: 0.4068 (tmm) cc_final: 0.3654 (tpp) REVERT: H 13 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7353 (pttm) REVERT: H 187 LEU cc_start: 0.9312 (mt) cc_final: 0.9007 (tt) REVERT: H 226 MET cc_start: 0.9391 (tpp) cc_final: 0.8640 (tpp) REVERT: I 41 ASN cc_start: 0.9172 (t0) cc_final: 0.8944 (m-40) REVERT: I 52 MET cc_start: 0.9568 (OUTLIER) cc_final: 0.9224 (pmm) REVERT: I 85 PHE cc_start: 0.9671 (m-80) cc_final: 0.9448 (m-80) REVERT: I 96 ASP cc_start: 0.9113 (m-30) cc_final: 0.8785 (m-30) REVERT: I 120 PHE cc_start: 0.9686 (t80) cc_final: 0.9326 (t80) REVERT: I 124 CYS cc_start: 0.9282 (m) cc_final: 0.9036 (m) REVERT: K 72 GLU cc_start: 0.9383 (OUTLIER) cc_final: 0.9070 (pm20) REVERT: K 97 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8327 (pt0) REVERT: K 113 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8448 (pptt) REVERT: K 120 PHE cc_start: 0.9476 (t80) cc_final: 0.9187 (t80) REVERT: K 137 TYR cc_start: 0.8692 (m-10) cc_final: 0.8121 (m-10) outliers start: 42 outliers final: 22 residues processed: 161 average time/residue: 0.1400 time to fit residues: 34.5936 Evaluate side-chains 149 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 65 TYR Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 567 TYR Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 113 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 118 optimal weight: 0.8980 chunk 210 optimal weight: 0.9990 chunk 153 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 203 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 28 optimal weight: 0.0770 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 113 GLN ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.061757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.047766 restraints weight = 124561.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.049304 restraints weight = 73052.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.050293 restraints weight = 50989.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.050887 restraints weight = 39818.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.051326 restraints weight = 34046.156| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18948 Z= 0.145 Angle : 0.652 17.094 25751 Z= 0.341 Chirality : 0.044 0.378 2849 Planarity : 0.003 0.048 3088 Dihedral : 16.429 179.483 3191 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.00 % Allowed : 15.47 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.18), residues: 2086 helix: 0.97 (0.17), residues: 939 sheet: -0.33 (0.28), residues: 344 loop : -1.58 (0.20), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 91 TYR 0.015 0.001 TYR I 123 PHE 0.019 0.001 PHE I 16 TRP 0.028 0.002 TRP H 52 HIS 0.003 0.001 HIS I 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (18947) covalent geometry : angle 0.65206 / 0.34 (25749) SS BOND : bond 0.00526 / 0.28 ( 1) SS BOND : angle 0.77197 / 0.41 ( 2) hydrogen bonds : bond 0.03785 / 2.60 ( 846) hydrogen bonds : angle 4.90166 / 3.43 ( 2401) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.735 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: A 3 SER cc_start: 0.8754 (OUTLIER) cc_final: 0.7931 (m) REVERT: A 113 GLN cc_start: 0.9440 (pt0) cc_final: 0.9150 (pt0) REVERT: B 201 THR cc_start: 0.9240 (OUTLIER) cc_final: 0.8966 (m) REVERT: C 122 LYS cc_start: 0.9514 (OUTLIER) cc_final: 0.9167 (ptmt) REVERT: E 56 LEU cc_start: 0.8796 (tt) cc_final: 0.8579 (mt) REVERT: E 68 LYS cc_start: 0.7339 (tptt) cc_final: 0.6990 (mptt) REVERT: F 41 LEU cc_start: 0.9286 (tp) cc_final: 0.9064 (tp) REVERT: F 47 PHE cc_start: 0.8247 (m-80) cc_final: 0.7462 (m-80) REVERT: F 160 MET cc_start: 0.9410 (tmm) cc_final: 0.8759 (ptm) REVERT: F 163 MET cc_start: 0.8755 (ptp) cc_final: 0.7897 (tpt) REVERT: F 257 MET cc_start: 0.9476 (mtm) cc_final: 0.9099 (mtm) REVERT: F 352 MET cc_start: 0.8723 (mmm) cc_final: 0.7995 (mmm) REVERT: F 463 TYR cc_start: 0.8705 (OUTLIER) cc_final: 0.8162 (p90) REVERT: F 624 MET cc_start: 0.4279 (tmm) cc_final: 0.3981 (tpp) REVERT: H 13 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7427 (pttm) REVERT: H 187 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8881 (tt) REVERT: H 226 MET cc_start: 0.9413 (tpp) cc_final: 0.8659 (tpp) REVERT: I 41 ASN cc_start: 0.9205 (t0) cc_final: 0.8982 (m-40) REVERT: I 85 PHE cc_start: 0.9674 (m-80) cc_final: 0.9463 (m-80) REVERT: I 96 ASP cc_start: 0.9115 (m-30) cc_final: 0.8790 (m-30) REVERT: I 120 PHE cc_start: 0.9650 (t80) cc_final: 0.9285 (t80) REVERT: K 72 GLU cc_start: 0.9398 (OUTLIER) cc_final: 0.9085 (pm20) REVERT: K 97 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8385 (pt0) REVERT: K 113 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8461 (pptt) REVERT: K 120 PHE cc_start: 0.9524 (t80) cc_final: 0.9174 (t80) REVERT: K 137 TYR cc_start: 0.8764 (m-10) cc_final: 0.8194 (m-10) outliers start: 38 outliers final: 23 residues processed: 153 average time/residue: 0.1344 time to fit residues: 31.1904 Evaluate side-chains 149 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 65 TYR Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 567 TYR Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 113 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 182 optimal weight: 7.9990 chunk 2 optimal weight: 0.0000 chunk 28 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 206 optimal weight: 0.7980 overall best weight: 1.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 40 GLN ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 HIS ** F 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 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 = 0.3626 r_free = 0.3626 target = 0.060993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.047241 restraints weight = 124047.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.048733 restraints weight = 72316.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.049684 restraints weight = 50360.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.050313 restraints weight = 39459.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.050697 restraints weight = 33438.787| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18948 Z= 0.166 Angle : 0.667 13.901 25751 Z= 0.351 Chirality : 0.045 0.325 2849 Planarity : 0.003 0.050 3088 Dihedral : 16.401 179.435 3191 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.95 % Allowed : 15.68 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.18), residues: 2086 helix: 1.01 (0.17), residues: 935 sheet: -0.36 (0.29), residues: 344 loop : -1.53 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 91 TYR 0.015 0.001 TYR H 184 PHE 0.019 0.001 PHE I 16 TRP 0.034 0.002 TRP H 52 HIS 0.003 0.001 HIS I 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 (18947) covalent geometry : angle 0.66696 / 0.35 (25749) SS BOND : bond 0.00689 / 0.36 ( 1) SS BOND : angle 0.72009 / 0.38 ( 2) hydrogen bonds : bond 0.03797 / 2.60 ( 846) hydrogen bonds : angle 4.98488 / 3.50 ( 2401) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 SER cc_start: 0.8815 (OUTLIER) cc_final: 0.8005 (m) REVERT: A 113 GLN cc_start: 0.9445 (pt0) cc_final: 0.9131 (pt0) REVERT: B 201 THR cc_start: 0.9220 (OUTLIER) cc_final: 0.8923 (m) REVERT: C 122 LYS cc_start: 0.9510 (OUTLIER) cc_final: 0.9164 (ptmt) REVERT: E 68 LYS cc_start: 0.7363 (tptt) cc_final: 0.7008 (mptt) REVERT: E 117 HIS cc_start: 0.7303 (t70) cc_final: 0.6865 (t70) REVERT: F 8 MET cc_start: 0.9130 (ptp) cc_final: 0.8855 (mpp) REVERT: F 47 PHE cc_start: 0.8254 (m-80) cc_final: 0.7465 (m-80) REVERT: F 160 MET cc_start: 0.9414 (tmm) cc_final: 0.8810 (ptm) REVERT: F 163 MET cc_start: 0.8811 (ptp) cc_final: 0.7946 (tpt) REVERT: F 257 MET cc_start: 0.9469 (mtm) cc_final: 0.9062 (mtm) REVERT: F 352 MET cc_start: 0.8709 (mmm) cc_final: 0.7946 (mmm) REVERT: F 452 MET cc_start: 0.9078 (tpp) cc_final: 0.8801 (tpp) REVERT: F 463 TYR cc_start: 0.8676 (OUTLIER) cc_final: 0.8071 (p90) REVERT: F 624 MET cc_start: 0.4349 (tmm) cc_final: 0.4043 (tpp) REVERT: H 13 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7466 (pttm) REVERT: H 179 MET cc_start: 0.9435 (mmm) cc_final: 0.9146 (mmm) REVERT: H 187 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.8918 (tt) REVERT: H 226 MET cc_start: 0.9425 (tpp) cc_final: 0.8731 (tpp) REVERT: I 49 ARG cc_start: 0.8517 (mmp-170) cc_final: 0.7797 (mmp-170) REVERT: I 96 ASP cc_start: 0.9103 (m-30) cc_final: 0.8771 (m-30) REVERT: K 72 GLU cc_start: 0.9393 (OUTLIER) cc_final: 0.9083 (pm20) REVERT: K 113 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8447 (pptt) REVERT: K 120 PHE cc_start: 0.9522 (t80) cc_final: 0.9247 (t80) REVERT: K 137 TYR cc_start: 0.8879 (m-10) cc_final: 0.8341 (m-10) outliers start: 37 outliers final: 26 residues processed: 145 average time/residue: 0.1418 time to fit residues: 31.0767 Evaluate side-chains 142 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 65 TYR Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 567 TYR Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 113 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 72 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 163 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 202 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 206 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.060273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.046145 restraints weight = 127555.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.047614 restraints weight = 74854.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.048577 restraints weight = 52526.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.049177 restraints weight = 41288.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.049576 restraints weight = 35204.670| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18948 Z= 0.208 Angle : 0.701 14.944 25751 Z= 0.371 Chirality : 0.044 0.310 2849 Planarity : 0.004 0.052 3088 Dihedral : 16.388 179.704 3189 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.11 % Allowed : 16.00 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.18), residues: 2086 helix: 0.90 (0.17), residues: 944 sheet: -0.42 (0.29), residues: 342 loop : -1.63 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 78 TYR 0.018 0.001 TYR E 78 PHE 0.018 0.002 PHE C 63 TRP 0.031 0.002 TRP H 52 HIS 0.009 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.21 (18947) covalent geometry : angle 0.70119 / 0.37 (25749) SS BOND : bond 0.00918 / 0.48 ( 1) SS BOND : angle 0.86481 / 0.46 ( 2) hydrogen bonds : bond 0.03861 / 2.64 ( 846) hydrogen bonds : angle 5.06947 / 3.58 ( 2401) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3252.01 seconds wall clock time: 57 minutes 17.43 seconds (3437.43 seconds total)