Starting phenix.real_space_refine on Thu Mar 5 03:23:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v01_26925/03_2026/7v01_26925_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v01_26925/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7v01_26925/03_2026/7v01_26925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v01_26925/03_2026/7v01_26925.map" model { file = "/net/cci-nas-00/data/ceres_data/7v01_26925/03_2026/7v01_26925_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v01_26925/03_2026/7v01_26925_neut.cif" } 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-5986/lib/python3.9/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: 4.56, per 1000 atoms: 0.25 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: 1.57 Conformation dependent library (CDL) restraints added in 698.1 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: 2.30 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: 3.63 Time building geometry restraints manager: 2.11 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: 6.900 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.980 Find NCS groups from input model: 0.150 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: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 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= 0.315 Angle : 0.884 16.419 25751 Z= 0.535 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 covalent geometry : bond 0.00563 (18947) covalent geometry : angle 0.88403 (25749) SS BOND : bond 0.00160 ( 1) SS BOND : angle 1.98932 ( 2) hydrogen bonds : bond 0.18529 ( 846) hydrogen bonds : angle 6.80632 ( 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 : 0.728 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: 0.1922 time to fit residues: 103.1380 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 : 0.690 ------------------------------------------------------------------------------- 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: 10.0000 chunk 77 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 F 560 GLN H 206 GLN I 71 ASN ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 69 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.064130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.049530 restraints weight = 122151.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.051046 restraints weight = 73286.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.052064 restraints weight = 51943.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.052752 restraints weight = 41027.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.053130 restraints weight = 34876.749| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18948 Z= 0.210 Angle : 0.763 14.084 25751 Z= 0.406 Chirality : 0.046 0.302 2849 Planarity : 0.004 0.065 3088 Dihedral : 17.103 177.551 3199 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.95 % Allowed : 9.84 % Favored : 88.21 % 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: -0.67 (0.18), residues: 2086 helix: 0.55 (0.17), residues: 948 sheet: -0.12 (0.29), residues: 309 loop : -1.73 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 405 TYR 0.028 0.002 TYR E 155 PHE 0.042 0.002 PHE I 85 TRP 0.025 0.001 TRP F 339 HIS 0.007 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00429 (18947) covalent geometry : angle 0.76281 (25749) SS BOND : bond 0.00306 ( 1) SS BOND : angle 1.45803 ( 2) hydrogen bonds : bond 0.04854 ( 846) hydrogen bonds : angle 5.45253 ( 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 214 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 177 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.9429 (pt0) cc_final: 0.9191 (pt0) REVERT: C 122 LYS cc_start: 0.9488 (OUTLIER) cc_final: 0.9149 (ptmt) REVERT: E 190 ARG cc_start: 0.8090 (mtm110) cc_final: 0.7278 (ttm110) REVERT: F 163 MET cc_start: 0.8573 (ptp) cc_final: 0.7825 (tpt) REVERT: F 257 MET cc_start: 0.9495 (mtp) cc_final: 0.9175 (mtm) REVERT: F 352 MET cc_start: 0.8822 (mmm) cc_final: 0.8212 (mmm) REVERT: F 624 MET cc_start: 0.4319 (tmm) cc_final: 0.3743 (tpp) REVERT: H 13 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7515 (pttm) REVERT: I 49 ARG cc_start: 0.8297 (mmp-170) cc_final: 0.7932 (mmm160) REVERT: I 58 LEU cc_start: 0.9703 (mt) cc_final: 0.9448 (mt) REVERT: I 104 MET cc_start: 0.8793 (mpp) cc_final: 0.8590 (mpp) REVERT: I 120 PHE cc_start: 0.9756 (t80) cc_final: 0.9451 (t80) REVERT: I 130 LEU cc_start: 0.9274 (mt) cc_final: 0.9069 (mt) REVERT: K 52 MET cc_start: 0.8693 (pmm) cc_final: 0.8403 (pmm) REVERT: K 58 LEU cc_start: 0.9636 (mm) cc_final: 0.9254 (pp) REVERT: K 113 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8398 (pptt) REVERT: K 126 TYR cc_start: 0.8758 (t80) cc_final: 0.8552 (t80) REVERT: K 137 TYR cc_start: 0.8336 (m-10) cc_final: 0.7678 (m-80) outliers start: 37 outliers final: 16 residues processed: 207 average time/residue: 0.1673 time to fit residues: 50.6909 Evaluate side-chains 153 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 E residue 142 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 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 H residue 13 LYS Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 255 TYR 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 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: 0.0040 chunk 142 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 211 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 141 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN E 117 HIS E 196 ASN E 324 GLN ** F 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 HIS ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.063633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.049242 restraints weight = 122715.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.050773 restraints weight = 72527.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.051782 restraints weight = 51152.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.052423 restraints weight = 40289.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.052869 restraints weight = 34309.435| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18948 Z= 0.158 Angle : 0.682 13.306 25751 Z= 0.359 Chirality : 0.044 0.269 2849 Planarity : 0.004 0.058 3088 Dihedral : 16.869 177.107 3191 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.05 % Allowed : 11.11 % Favored : 86.84 % 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: -0.59 (0.18), residues: 2086 helix: 0.67 (0.17), residues: 953 sheet: -0.11 (0.29), residues: 309 loop : -1.75 (0.19), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 405 TYR 0.020 0.001 TYR E 155 PHE 0.042 0.002 PHE F 693 TRP 0.010 0.001 TRP F 339 HIS 0.009 0.001 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00332 (18947) covalent geometry : angle 0.68151 (25749) SS BOND : bond 0.00347 ( 1) SS BOND : angle 1.21475 ( 2) hydrogen bonds : bond 0.04450 ( 846) hydrogen bonds : angle 5.15329 ( 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 194 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.9422 (pt0) cc_final: 0.9191 (pt0) REVERT: C 97 GLN cc_start: 0.9010 (mm-40) cc_final: 0.8765 (mm-40) REVERT: C 122 LYS cc_start: 0.9506 (OUTLIER) cc_final: 0.9191 (ptmt) REVERT: E 56 LEU cc_start: 0.8792 (tt) cc_final: 0.8477 (mt) REVERT: E 68 LYS cc_start: 0.7218 (tptt) cc_final: 0.6913 (mptt) REVERT: E 327 MET cc_start: 0.8330 (pmm) cc_final: 0.8116 (pmm) REVERT: F 41 LEU cc_start: 0.9080 (tp) cc_final: 0.8819 (tp) REVERT: F 160 MET cc_start: 0.9376 (tmm) cc_final: 0.8685 (ptm) REVERT: F 163 MET cc_start: 0.8617 (ptp) cc_final: 0.7802 (tpt) REVERT: F 257 MET cc_start: 0.9514 (OUTLIER) cc_final: 0.9074 (mtm) REVERT: F 352 MET cc_start: 0.8742 (mmm) cc_final: 0.7907 (mmm) REVERT: F 468 MET cc_start: 0.9426 (ptp) cc_final: 0.9164 (ptp) REVERT: F 624 MET cc_start: 0.4467 (tmm) cc_final: 0.3887 (tpp) REVERT: H 226 MET cc_start: 0.9211 (tpp) cc_final: 0.8365 (tpp) REVERT: I 120 PHE cc_start: 0.9744 (t80) cc_final: 0.9381 (t80) REVERT: K 58 LEU cc_start: 0.9581 (mm) cc_final: 0.9199 (pp) REVERT: K 137 TYR cc_start: 0.8569 (m-10) cc_final: 0.8254 (m-80) outliers start: 39 outliers final: 21 residues processed: 188 average time/residue: 0.1704 time to fit residues: 47.3261 Evaluate side-chains 149 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 257 MET 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 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 26 LYS Chi-restraints excluded: chain K residue 71 ASN Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 86 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 96 optimal weight: 6.9990 chunk 177 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 119 optimal weight: 0.6980 chunk 178 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 GLN ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 ASN ** F 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 ASN ** F 731 ASN ** 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 = 0.3558 r_free = 0.3558 target = 0.058727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.045102 restraints weight = 130239.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.046525 restraints weight = 76381.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.047435 restraints weight = 53788.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.047994 restraints weight = 42455.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.048411 restraints weight = 36405.674| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 18948 Z= 0.342 Angle : 0.838 12.856 25751 Z= 0.443 Chirality : 0.049 0.335 2849 Planarity : 0.005 0.055 3088 Dihedral : 16.971 177.539 3191 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.11 % Allowed : 12.84 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.01 (0.18), residues: 2086 helix: 0.38 (0.16), residues: 944 sheet: -0.53 (0.28), residues: 331 loop : -1.96 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 241 TYR 0.023 0.002 TYR E 155 PHE 0.035 0.003 PHE K 105 TRP 0.031 0.003 TRP E 89 HIS 0.015 0.002 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00711 (18947) covalent geometry : angle 0.83836 (25749) SS BOND : bond 0.01885 ( 1) SS BOND : angle 1.31512 ( 2) hydrogen bonds : bond 0.04882 ( 846) hydrogen bonds : angle 5.53505 ( 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 196 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 137 time to evaluate : 0.884 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: C 122 LYS cc_start: 0.9516 (OUTLIER) cc_final: 0.9157 (ptmt) REVERT: E 40 MET cc_start: 0.8566 (mmp) cc_final: 0.8269 (mmp) REVERT: E 117 HIS cc_start: 0.7130 (t70) cc_final: 0.6686 (t70) REVERT: E 289 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6767 (mt) REVERT: E 327 MET cc_start: 0.8602 (pmm) cc_final: 0.8374 (pmm) REVERT: F 1 MET cc_start: 0.7330 (mmt) cc_final: 0.6946 (mmt) REVERT: F 163 MET cc_start: 0.8997 (ptp) cc_final: 0.8239 (tpt) REVERT: F 257 MET cc_start: 0.9430 (OUTLIER) cc_final: 0.8845 (mtm) REVERT: F 352 MET cc_start: 0.8828 (mmm) cc_final: 0.7800 (mmm) REVERT: F 463 TYR cc_start: 0.8732 (OUTLIER) cc_final: 0.8142 (p90) REVERT: F 624 MET cc_start: 0.5084 (tmm) cc_final: 0.4744 (tpp) REVERT: F 697 MET cc_start: 0.4839 (mmm) cc_final: 0.4526 (mmm) REVERT: I 41 ASN cc_start: 0.8992 (m-40) cc_final: 0.8444 (m-40) REVERT: I 52 MET cc_start: 0.9573 (pmm) cc_final: 0.9349 (pmm) REVERT: I 96 ASP cc_start: 0.9433 (OUTLIER) cc_final: 0.9089 (m-30) REVERT: K 72 GLU cc_start: 0.9375 (OUTLIER) cc_final: 0.9037 (pm20) REVERT: K 137 TYR cc_start: 0.8859 (m-10) cc_final: 0.8328 (m-80) outliers start: 59 outliers final: 33 residues processed: 183 average time/residue: 0.1608 time to fit residues: 43.7839 Evaluate side-chains 152 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 113 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 122 LYS Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain F residue 155 ASN Chi-restraints excluded: chain F residue 257 MET 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 551 ILE 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 14 THR Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 255 TYR Chi-restraints excluded: chain H residue 304 VAL 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 55 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 71 ASN Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 86 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 12 optimal weight: 10.0000 chunk 122 optimal weight: 0.3980 chunk 191 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 203 optimal weight: 7.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN B 113 GLN C 113 GLN C 161 GLN ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 722 ASN H 17 HIS H 129 GLN ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 71 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.060567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.046775 restraints weight = 126257.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.048292 restraints weight = 73667.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.049245 restraints weight = 51389.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.049881 restraints weight = 40368.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.050277 restraints weight = 34166.641| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18948 Z= 0.144 Angle : 0.653 12.931 25751 Z= 0.347 Chirality : 0.044 0.316 2849 Planarity : 0.004 0.053 3088 Dihedral : 16.772 178.871 3191 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.53 % Allowed : 14.00 % Favored : 83.47 % 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: -0.58 (0.18), residues: 2086 helix: 0.80 (0.17), residues: 940 sheet: -0.42 (0.29), residues: 333 loop : -1.77 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 279 TYR 0.021 0.001 TYR I 126 PHE 0.022 0.001 PHE E 62 TRP 0.036 0.002 TRP H 52 HIS 0.005 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00298 (18947) covalent geometry : angle 0.65240 (25749) SS BOND : bond 0.00446 ( 1) SS BOND : angle 1.58022 ( 2) hydrogen bonds : bond 0.03934 ( 846) hydrogen bonds : angle 5.09403 ( 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 178 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 130 time to evaluate : 0.738 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: A 3 SER cc_start: 0.8853 (OUTLIER) cc_final: 0.8025 (m) REVERT: A 54 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.7028 (mmtm) REVERT: A 113 GLN cc_start: 0.9478 (pt0) cc_final: 0.9165 (pt0) REVERT: C 122 LYS cc_start: 0.9503 (OUTLIER) cc_final: 0.9157 (ptmt) REVERT: E 40 MET cc_start: 0.8531 (mmp) cc_final: 0.8211 (mmp) REVERT: E 68 LYS cc_start: 0.7310 (tptt) cc_final: 0.6904 (mptt) REVERT: E 117 HIS cc_start: 0.7387 (t70) cc_final: 0.6837 (t70) REVERT: E 125 ASN cc_start: 0.9196 (OUTLIER) cc_final: 0.8978 (t0) REVERT: E 289 LEU cc_start: 0.6998 (mm) cc_final: 0.6780 (tp) REVERT: F 41 LEU cc_start: 0.9126 (tp) cc_final: 0.8895 (tp) REVERT: F 47 PHE cc_start: 0.8027 (m-80) cc_final: 0.7115 (m-80) REVERT: F 160 MET cc_start: 0.9414 (tmm) cc_final: 0.8832 (ptm) REVERT: F 163 MET cc_start: 0.8862 (ptp) cc_final: 0.8045 (tpt) REVERT: F 257 MET cc_start: 0.9422 (mtp) cc_final: 0.8908 (mtm) REVERT: F 262 ILE cc_start: 0.9497 (OUTLIER) cc_final: 0.9291 (pt) REVERT: F 352 MET cc_start: 0.8723 (mmm) cc_final: 0.7842 (mmm) REVERT: F 463 TYR cc_start: 0.8692 (OUTLIER) cc_final: 0.8093 (p90) REVERT: F 624 MET cc_start: 0.4590 (tmm) cc_final: 0.4314 (tpp) REVERT: H 187 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.8790 (tt) REVERT: H 226 MET cc_start: 0.9208 (tpp) cc_final: 0.8675 (tpp) REVERT: I 41 ASN cc_start: 0.9136 (m-40) cc_final: 0.8592 (m-40) REVERT: I 52 MET cc_start: 0.9601 (OUTLIER) cc_final: 0.9227 (pmm) REVERT: I 96 ASP cc_start: 0.9403 (OUTLIER) cc_final: 0.9075 (m-30) REVERT: K 49 ARG cc_start: 0.8480 (ppt170) cc_final: 0.8168 (ptm-80) REVERT: K 72 GLU cc_start: 0.9353 (OUTLIER) cc_final: 0.8907 (pm20) REVERT: K 137 TYR cc_start: 0.8906 (m-10) cc_final: 0.8372 (m-10) outliers start: 48 outliers final: 22 residues processed: 170 average time/residue: 0.1567 time to fit residues: 39.7037 Evaluate side-chains 146 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER 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 E residue 125 ASN Chi-restraints excluded: chain E residue 178 ASP 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 499 TYR Chi-restraints excluded: chain F residue 567 TYR Chi-restraints excluded: chain F residue 570 ASN 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 33 ASP Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 99 HIS 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 48 LEU Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 71 ASN Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR 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: 6.9990 chunk 163 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 199 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 HIS ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 ASN ** F 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 ASN ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 71 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.057854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.044603 restraints weight = 127624.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.046004 restraints weight = 74271.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.046910 restraints weight = 51956.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.047500 restraints weight = 40791.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.047855 restraints weight = 34723.466| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.5684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 18948 Z= 0.311 Angle : 0.761 12.977 25751 Z= 0.404 Chirality : 0.046 0.337 2849 Planarity : 0.004 0.051 3088 Dihedral : 16.768 179.639 3191 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.47 % Allowed : 14.05 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.86 (0.18), residues: 2086 helix: 0.62 (0.17), residues: 942 sheet: -0.78 (0.27), residues: 360 loop : -1.92 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 711 TYR 0.030 0.002 TYR E 78 PHE 0.021 0.002 PHE E 243 TRP 0.022 0.002 TRP H 52 HIS 0.005 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00644 (18947) covalent geometry : angle 0.76072 (25749) SS BOND : bond 0.01511 ( 1) SS BOND : angle 1.43989 ( 2) hydrogen bonds : bond 0.04372 ( 846) hydrogen bonds : angle 5.42484 ( 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 182 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 116 time to evaluate : 0.716 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: A 54 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7269 (mmtm) REVERT: B 201 THR cc_start: 0.9263 (OUTLIER) cc_final: 0.8939 (m) REVERT: C 122 LYS cc_start: 0.9511 (OUTLIER) cc_final: 0.9167 (ptmt) REVERT: E 40 MET cc_start: 0.8551 (mmp) cc_final: 0.8194 (mmp) REVERT: E 117 HIS cc_start: 0.7244 (t70) cc_final: 0.6644 (t70) REVERT: E 289 LEU cc_start: 0.7064 (mm) cc_final: 0.6592 (mt) REVERT: E 300 MET cc_start: 0.3866 (ppp) cc_final: 0.2944 (ppp) REVERT: F 163 MET cc_start: 0.9106 (ptp) cc_final: 0.8905 (ptm) REVERT: F 257 MET cc_start: 0.9432 (OUTLIER) cc_final: 0.8767 (mtm) REVERT: F 352 MET cc_start: 0.8664 (mmm) cc_final: 0.7693 (mmm) REVERT: F 463 TYR cc_start: 0.8780 (OUTLIER) cc_final: 0.8133 (p90) REVERT: F 697 MET cc_start: 0.3956 (mmm) cc_final: 0.3726 (mmm) REVERT: H 187 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9147 (tt) REVERT: H 226 MET cc_start: 0.9376 (tpp) cc_final: 0.8440 (tpp) REVERT: I 52 MET cc_start: 0.9596 (OUTLIER) cc_final: 0.9266 (pmm) REVERT: I 96 ASP cc_start: 0.9368 (OUTLIER) cc_final: 0.9035 (m-30) REVERT: I 130 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9258 (mm) REVERT: K 72 GLU cc_start: 0.9351 (OUTLIER) cc_final: 0.8920 (pm20) REVERT: K 137 TYR cc_start: 0.9062 (m-10) cc_final: 0.8556 (m-10) outliers start: 66 outliers final: 41 residues processed: 171 average time/residue: 0.1486 time to fit residues: 38.4685 Evaluate side-chains 158 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 107 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 257 MET 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 478 ILE Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 499 TYR Chi-restraints excluded: chain F residue 540 PHE Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 558 SER 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 13 LYS Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 255 TYR Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 16 PHE 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 52 MET Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 71 ASN Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 97 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 140 optimal weight: 8.9990 chunk 149 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 26 optimal weight: 0.0670 chunk 166 optimal weight: 0.7980 chunk 190 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 199 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 ASN F 165 HIS F 400 HIS H 87 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.059902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.046235 restraints weight = 126775.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.047754 restraints weight = 73203.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.048722 restraints weight = 50703.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.049329 restraints weight = 39627.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.049742 restraints weight = 33645.575| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.5770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18948 Z= 0.127 Angle : 0.643 12.809 25751 Z= 0.340 Chirality : 0.044 0.312 2849 Planarity : 0.004 0.049 3088 Dihedral : 16.553 178.909 3191 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.84 % Allowed : 14.89 % Favored : 82.26 % 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: -0.47 (0.18), residues: 2086 helix: 0.88 (0.17), residues: 946 sheet: -0.46 (0.29), residues: 333 loop : -1.67 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 711 TYR 0.024 0.001 TYR E 78 PHE 0.028 0.001 PHE E 62 TRP 0.027 0.002 TRP E 89 HIS 0.004 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00263 (18947) covalent geometry : angle 0.64297 (25749) SS BOND : bond 0.00294 ( 1) SS BOND : angle 1.51634 ( 2) hydrogen bonds : bond 0.03745 ( 846) hydrogen bonds : angle 5.00766 ( 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 178 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 124 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 MET cc_start: 0.9425 (mtp) cc_final: 0.9211 (mtp) REVERT: B 201 THR cc_start: 0.9253 (OUTLIER) cc_final: 0.9041 (m) REVERT: C 97 GLN cc_start: 0.8881 (mm-40) cc_final: 0.8497 (mm-40) REVERT: C 122 LYS cc_start: 0.9510 (OUTLIER) cc_final: 0.9168 (ptmt) REVERT: E 40 MET cc_start: 0.8483 (mmp) cc_final: 0.8027 (mmp) REVERT: E 68 LYS cc_start: 0.7413 (tptt) cc_final: 0.6941 (mptt) REVERT: E 125 ASN cc_start: 0.9219 (OUTLIER) cc_final: 0.8971 (t0) REVERT: E 289 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6440 (mm) REVERT: F 160 MET cc_start: 0.9473 (tmm) cc_final: 0.8934 (ptm) REVERT: F 163 MET cc_start: 0.8973 (ptp) cc_final: 0.8171 (tpt) REVERT: F 257 MET cc_start: 0.9424 (OUTLIER) cc_final: 0.8779 (mtm) REVERT: F 296 LEU cc_start: 0.9906 (OUTLIER) cc_final: 0.9627 (mt) REVERT: F 352 MET cc_start: 0.8700 (mmm) cc_final: 0.7950 (mmm) REVERT: F 427 GLU cc_start: 0.9375 (OUTLIER) cc_final: 0.8845 (pp20) REVERT: F 463 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.8079 (p90) REVERT: F 624 MET cc_start: 0.5782 (tmm) cc_final: 0.5567 (tpp) REVERT: H 187 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.8942 (tt) REVERT: H 226 MET cc_start: 0.9328 (tpp) cc_final: 0.8550 (tpp) REVERT: I 52 MET cc_start: 0.9551 (OUTLIER) cc_final: 0.9214 (pmm) REVERT: I 96 ASP cc_start: 0.9348 (OUTLIER) cc_final: 0.9000 (m-30) REVERT: I 130 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9236 (mm) REVERT: K 14 MET cc_start: 0.6252 (OUTLIER) cc_final: 0.5893 (ppp) REVERT: K 49 ARG cc_start: 0.8599 (ppt170) cc_final: 0.8351 (ppt170) REVERT: K 72 GLU cc_start: 0.9331 (OUTLIER) cc_final: 0.8868 (pm20) REVERT: K 97 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8215 (pt0) REVERT: K 126 TYR cc_start: 0.9064 (t80) cc_final: 0.8860 (t80) REVERT: K 137 TYR cc_start: 0.9057 (m-10) cc_final: 0.8618 (m-10) outliers start: 54 outliers final: 26 residues processed: 168 average time/residue: 0.1490 time to fit residues: 37.8846 Evaluate side-chains 150 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 109 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain B residue 126 THR 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 125 ASN Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain F residue 155 ASN Chi-restraints excluded: chain F residue 257 MET 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 427 GLU Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 540 PHE 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 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 187 LEU Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain K residue 14 MET Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 71 ASN Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 97 GLU 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: 1.9990 chunk 171 optimal weight: 6.9990 chunk 212 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 167 optimal weight: 0.0020 overall best weight: 1.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 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** ** K 18 HIS ** 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 = 0.3578 r_free = 0.3578 target = 0.058993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.045481 restraints weight = 127885.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.046950 restraints weight = 73827.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.047891 restraints weight = 51263.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.048464 restraints weight = 40078.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.048873 restraints weight = 34196.036| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.5960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18948 Z= 0.171 Angle : 0.651 12.942 25751 Z= 0.345 Chirality : 0.044 0.304 2849 Planarity : 0.004 0.048 3088 Dihedral : 16.498 178.841 3191 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.42 % Allowed : 15.37 % Favored : 82.21 % 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: -0.48 (0.18), residues: 2086 helix: 0.91 (0.17), residues: 945 sheet: -0.60 (0.29), residues: 350 loop : -1.67 (0.20), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 91 TYR 0.020 0.001 TYR E 78 PHE 0.028 0.001 PHE K 120 TRP 0.042 0.002 TRP E 89 HIS 0.007 0.001 HIS H 87 Details of bonding type rmsd covalent geometry : bond 0.00357 (18947) covalent geometry : angle 0.65098 (25749) SS BOND : bond 0.00725 ( 1) SS BOND : angle 1.12334 ( 2) hydrogen bonds : bond 0.03821 ( 846) hydrogen bonds : angle 5.02713 ( 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 159 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 113 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.8961 (m) REVERT: C 97 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8510 (mm-40) REVERT: C 122 LYS cc_start: 0.9517 (OUTLIER) cc_final: 0.9190 (ptmt) REVERT: E 40 MET cc_start: 0.8370 (mmp) cc_final: 0.8076 (mmp) REVERT: E 68 LYS cc_start: 0.7455 (tptt) cc_final: 0.7002 (mptt) REVERT: E 117 HIS cc_start: 0.7220 (t70) cc_final: 0.6721 (t70) REVERT: E 289 LEU cc_start: 0.6401 (OUTLIER) cc_final: 0.6063 (mm) REVERT: F 8 MET cc_start: 0.8924 (ptp) cc_final: 0.8478 (ptp) REVERT: F 160 MET cc_start: 0.9485 (tmm) cc_final: 0.8906 (ptm) REVERT: F 163 MET cc_start: 0.8979 (ptp) cc_final: 0.8172 (tpt) REVERT: F 257 MET cc_start: 0.9418 (OUTLIER) cc_final: 0.8753 (mtm) REVERT: F 296 LEU cc_start: 0.9912 (OUTLIER) cc_final: 0.9635 (mt) REVERT: F 352 MET cc_start: 0.8692 (mmm) cc_final: 0.7879 (mmm) REVERT: F 427 GLU cc_start: 0.9396 (OUTLIER) cc_final: 0.8827 (pp20) REVERT: F 463 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.8052 (p90) REVERT: H 187 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.8932 (tt) REVERT: H 226 MET cc_start: 0.9341 (tpp) cc_final: 0.8775 (tpp) REVERT: I 52 MET cc_start: 0.9557 (OUTLIER) cc_final: 0.9230 (pmm) REVERT: I 96 ASP cc_start: 0.9348 (OUTLIER) cc_final: 0.9003 (m-30) REVERT: K 72 GLU cc_start: 0.9318 (OUTLIER) cc_final: 0.8826 (pm20) REVERT: K 97 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8152 (pt0) REVERT: K 137 TYR cc_start: 0.9121 (m-10) cc_final: 0.8668 (m-10) outliers start: 46 outliers final: 28 residues processed: 148 average time/residue: 0.1496 time to fit residues: 33.6707 Evaluate side-chains 149 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 109 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain F residue 257 MET 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 427 GLU Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 540 PHE 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 13 LYS 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 I residue 52 MET Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain K residue 71 ASN Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 97 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 118 optimal weight: 0.9980 chunk 210 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 137 optimal weight: 0.3980 chunk 39 optimal weight: 5.9990 chunk 173 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 203 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.059625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.046107 restraints weight = 126682.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.047598 restraints weight = 73077.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.048544 restraints weight = 50670.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.049166 restraints weight = 39664.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.049565 restraints weight = 33552.713| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.6113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18948 Z= 0.133 Angle : 0.640 12.789 25751 Z= 0.335 Chirality : 0.043 0.299 2849 Planarity : 0.004 0.096 3088 Dihedral : 16.329 178.576 3191 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.37 % Allowed : 15.68 % Favored : 81.95 % 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: -0.34 (0.18), residues: 2086 helix: 0.99 (0.17), residues: 943 sheet: -0.42 (0.30), residues: 336 loop : -1.59 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 319 TYR 0.021 0.001 TYR K 126 PHE 0.033 0.001 PHE K 120 TRP 0.042 0.002 TRP E 89 HIS 0.005 0.001 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00278 (18947) covalent geometry : angle 0.63995 (25749) SS BOND : bond 0.00393 ( 1) SS BOND : angle 1.11043 ( 2) hydrogen bonds : bond 0.03582 ( 846) hydrogen bonds : angle 4.87939 ( 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 166 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 121 time to evaluate : 0.796 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: A 68 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.7330 (tmtt) REVERT: B 201 THR cc_start: 0.9226 (OUTLIER) cc_final: 0.9003 (m) REVERT: C 97 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8451 (mm-40) REVERT: C 122 LYS cc_start: 0.9509 (OUTLIER) cc_final: 0.9187 (ptmt) REVERT: E 40 MET cc_start: 0.8303 (mmp) cc_final: 0.7980 (mmp) REVERT: E 68 LYS cc_start: 0.7542 (tptt) cc_final: 0.7079 (mptt) REVERT: E 117 HIS cc_start: 0.7353 (t70) cc_final: 0.6867 (t70) REVERT: E 289 LEU cc_start: 0.6482 (OUTLIER) cc_final: 0.6257 (tp) REVERT: F 163 MET cc_start: 0.9043 (ptp) cc_final: 0.8795 (ptm) REVERT: F 257 MET cc_start: 0.9416 (OUTLIER) cc_final: 0.8893 (mtm) REVERT: F 296 LEU cc_start: 0.9903 (OUTLIER) cc_final: 0.9644 (mt) REVERT: F 352 MET cc_start: 0.8669 (mmm) cc_final: 0.7584 (tpp) REVERT: F 427 GLU cc_start: 0.9369 (OUTLIER) cc_final: 0.8805 (pp20) REVERT: F 463 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.8098 (p90) REVERT: F 624 MET cc_start: 0.6328 (OUTLIER) cc_final: 0.4385 (mpp) REVERT: H 187 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9002 (tt) REVERT: H 226 MET cc_start: 0.9329 (tpp) cc_final: 0.8807 (tpp) REVERT: I 52 MET cc_start: 0.9540 (OUTLIER) cc_final: 0.9193 (pmm) REVERT: I 96 ASP cc_start: 0.9357 (OUTLIER) cc_final: 0.9025 (m-30) REVERT: K 72 GLU cc_start: 0.9312 (OUTLIER) cc_final: 0.8831 (pm20) REVERT: K 97 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8315 (pt0) REVERT: K 137 TYR cc_start: 0.9081 (m-10) cc_final: 0.8727 (m-10) outliers start: 45 outliers final: 26 residues processed: 152 average time/residue: 0.1510 time to fit residues: 34.7099 Evaluate side-chains 155 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 115 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain B residue 126 THR 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 178 ASP Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain F residue 155 ASN Chi-restraints excluded: chain F residue 257 MET 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 427 GLU Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 540 PHE 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 F residue 624 MET Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 52 TRP 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 I residue 52 MET Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain K residue 71 ASN Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 97 GLU 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: 2.9990 chunk 28 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 210 optimal weight: 0.1980 chunk 24 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 206 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 ASN F 165 HIS ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.059147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.045786 restraints weight = 127035.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.047199 restraints weight = 72839.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.048137 restraints weight = 50609.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.048731 restraints weight = 39604.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.049132 restraints weight = 33600.701| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.6271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18948 Z= 0.150 Angle : 0.658 12.785 25751 Z= 0.344 Chirality : 0.043 0.292 2849 Planarity : 0.004 0.057 3088 Dihedral : 16.206 178.922 3191 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.26 % Allowed : 16.00 % Favored : 81.74 % 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: 0.96 (0.17), residues: 945 sheet: -0.40 (0.30), residues: 340 loop : -1.57 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 319 TYR 0.020 0.001 TYR I 123 PHE 0.018 0.001 PHE I 16 TRP 0.038 0.002 TRP E 89 HIS 0.005 0.001 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00316 (18947) covalent geometry : angle 0.65755 (25749) SS BOND : bond 0.00609 ( 1) SS BOND : angle 0.98566 ( 2) hydrogen bonds : bond 0.03677 ( 846) hydrogen bonds : angle 4.88726 ( 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 158 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 115 time to evaluate : 0.643 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: A 68 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.7358 (tmtt) REVERT: B 201 THR cc_start: 0.9212 (OUTLIER) cc_final: 0.8968 (m) REVERT: C 97 GLN cc_start: 0.8835 (mm-40) cc_final: 0.8459 (mm-40) REVERT: C 122 LYS cc_start: 0.9512 (OUTLIER) cc_final: 0.9196 (ptmt) REVERT: E 40 MET cc_start: 0.8306 (mmp) cc_final: 0.7985 (mmp) REVERT: E 68 LYS cc_start: 0.7637 (tptt) cc_final: 0.7156 (mptt) REVERT: E 117 HIS cc_start: 0.7337 (t70) cc_final: 0.6814 (t70) REVERT: E 289 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.6248 (tp) REVERT: F 160 MET cc_start: 0.9521 (tmm) cc_final: 0.8875 (ptm) REVERT: F 163 MET cc_start: 0.9037 (ptp) cc_final: 0.8762 (ptm) REVERT: F 257 MET cc_start: 0.9440 (OUTLIER) cc_final: 0.8881 (mtm) REVERT: F 296 LEU cc_start: 0.9912 (OUTLIER) cc_final: 0.9642 (mt) REVERT: F 352 MET cc_start: 0.8612 (mmm) cc_final: 0.7855 (mmm) REVERT: F 427 GLU cc_start: 0.9397 (OUTLIER) cc_final: 0.8796 (pp20) REVERT: F 463 TYR cc_start: 0.8852 (OUTLIER) cc_final: 0.8154 (p90) REVERT: F 624 MET cc_start: 0.6546 (tpp) cc_final: 0.4809 (mpp) REVERT: H 187 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.8994 (tt) REVERT: H 226 MET cc_start: 0.9325 (tpp) cc_final: 0.8794 (tpp) REVERT: I 52 MET cc_start: 0.9537 (OUTLIER) cc_final: 0.9177 (pmm) REVERT: I 96 ASP cc_start: 0.9341 (OUTLIER) cc_final: 0.8974 (m-30) REVERT: K 72 GLU cc_start: 0.9308 (OUTLIER) cc_final: 0.8778 (pm20) REVERT: K 73 GLU cc_start: 0.9661 (pm20) cc_final: 0.9238 (pm20) REVERT: K 97 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8359 (pt0) REVERT: K 137 TYR cc_start: 0.9088 (m-10) cc_final: 0.8711 (m-10) outliers start: 43 outliers final: 27 residues processed: 148 average time/residue: 0.1601 time to fit residues: 35.6992 Evaluate side-chains 151 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain F residue 257 MET 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 427 GLU Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 540 PHE 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 33 ASP Chi-restraints excluded: chain H residue 52 TRP 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 I residue 52 MET Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain K residue 71 ASN Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 97 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 72 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 163 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 157 optimal weight: 3.9990 chunk 206 optimal weight: 0.7980 chunk 80 optimal weight: 0.4980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 471 GLN ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN ** I 64 ASN ** 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 = 0.3589 r_free = 0.3589 target = 0.059176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.045877 restraints weight = 127285.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.047288 restraints weight = 72927.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.048212 restraints weight = 50057.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.048795 restraints weight = 39112.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.049209 restraints weight = 33272.293| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.6368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18948 Z= 0.142 Angle : 0.658 12.681 25751 Z= 0.345 Chirality : 0.043 0.294 2849 Planarity : 0.004 0.061 3088 Dihedral : 16.169 179.053 3191 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.26 % Allowed : 16.32 % Favored : 81.42 % 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: -0.32 (0.18), residues: 2086 helix: 0.96 (0.17), residues: 939 sheet: -0.39 (0.29), residues: 341 loop : -1.51 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 319 TYR 0.015 0.001 TYR H 184 PHE 0.038 0.001 PHE E 62 TRP 0.034 0.002 TRP E 89 HIS 0.010 0.001 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00299 (18947) covalent geometry : angle 0.65780 (25749) SS BOND : bond 0.00538 ( 1) SS BOND : angle 0.97661 ( 2) hydrogen bonds : bond 0.03633 ( 846) hydrogen bonds : angle 4.89021 ( 2401) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3480.21 seconds wall clock time: 61 minutes 21.14 seconds (3681.14 seconds total)