Starting phenix.real_space_refine on Sat Sep 12 22:10:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v01_26925/09_2026/7v01_26925_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v01_26925/09_2026/7v01_26925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v01_26925/09_2026/7v01_26925_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v01_26925/09_2026/7v01_26925_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v01_26925/09_2026/7v01_26925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v01_26925/09_2026/7v01_26925.map" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 61 5.49 5 S 51 5.16 5 C 11549 2.51 5 N 3112 2.21 5 O 3719 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18492 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1628 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "B" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1523 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 187} Chain breaks: 2 Chain: "C" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1628 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "E" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2473 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 8, 'TRANS': 293} Chain breaks: 3 Chain: "F" Number of atoms: 5636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5636 Classifications: {'peptide': 693} Link IDs: {'PTRANS': 7, 'TRANS': 685} Chain breaks: 3 Chain: "G" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 644 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 2, 'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna2p': 10, 'rna3p': 19} Chain: "H" Number of atoms: 2386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2386 Classifications: {'peptide': 297} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 287} Chain breaks: 1 Chain: "I" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 995 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "K" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 995 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "U" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 522 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 8, 'rna3p_pur': 5, 'rna3p_pyr': 8} Link IDs: {'rna2p': 12, 'rna3p': 12} Chain breaks: 1 Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.98, per 1000 atoms: 0.22 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: 1.60 Conformation dependent library (CDL) restraints added in 728.1 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: 2.08 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: 3.56 Time building geometry restraints manager: 2.13 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: 25449 3.28 - 6.57: 267 6.57 - 9.85: 25 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=" N3 U G 12 " pdb=" C4 U G 12 " pdb=" O4 U G 12 " ideal model delta sigma weight residual 119.40 112.90 6.50 7.00e-01 2.04e+00 8.63e+01 angle pdb=" O4 U G 12 " pdb=" C4 U G 12 " pdb=" C5 U G 12 " ideal model delta sigma weight residual 125.90 131.44 -5.54 6.00e-01 2.78e+00 8.52e+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: 2423 0.074 - 0.149: 389 0.149 - 0.223: 30 0.223 - 0.297: 5 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 1.90e+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: 4.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.310 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 18948 Z= 0.351 Angle : 0.899 16.419 25751 Z= 0.601 Chirality : 0.054 0.371 2849 Planarity : 0.005 0.094 3088 Dihedral : 15.848 178.878 7482 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.47 % Allowed : 0.58 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.17), residues: 2086 helix: -0.01 (0.16), residues: 926 sheet: -0.42 (0.28), residues: 321 loop : -1.75 (0.19), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.001 ARG C 78 TYR 0.055 0.002 TYR K 86 PHE 0.102 0.003 PHE F 540 TRP 0.041 0.002 TRP F 339 HIS 0.007 0.001 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.35 (18947) covalent geometry : angle 0.89899 / 0.60 (25749) SS BOND : bond 0.00160 / 0.08 ( 1) SS BOND : angle 1.98932 / 1.12 ( 2) hydrogen bonds : bond 0.18529 / 12.96 ( 846) hydrogen bonds : angle 6.80632 / 4.73 ( 2401) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 375 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 137 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6563 (ttm170) REVERT: E 119 MET cc_start: 0.7312 (tpp) cc_final: 0.6996 (tpp) REVERT: E 186 MET cc_start: 0.6058 (mmm) cc_final: 0.5677 (mmm) REVERT: E 289 LEU cc_start: 0.7281 (mt) cc_final: 0.6797 (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: 0.8111 (tp) REVERT: I 58 LEU cc_start: 0.9499 (mt) cc_final: 0.9083 (mt) REVERT: I 81 LEU cc_start: 0.9526 (tp) cc_final: 0.9092 (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: 0.9118 (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: 0.9006 (mm-30) REVERT: K 137 TYR cc_start: 0.7843 (m-10) cc_final: 0.7468 (m-10) outliers start: 9 outliers final: 2 residues processed: 383 average time/residue: 0.1854 time to fit residues: 100.4585 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 : 0.714 ------------------------------------------------------------------------------- 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: 20.0000 chunk 77 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 174 HIS ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 ASN E 54 ASN E 61 ASN ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 ASN ** F 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 549 ASN F 560 GLN H 206 GLN I 71 ASN ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN K 69 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.064798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.050020 restraints weight = 121834.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.051588 restraints weight = 73114.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.052596 restraints weight = 52000.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.053284 restraints weight = 41305.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.053677 restraints weight = 35111.513| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18948 Z= 0.214 Angle : 0.805 13.788 25751 Z= 0.432 Chirality : 0.050 0.511 2849 Planarity : 0.005 0.075 3088 Dihedral : 17.246 178.240 3199 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.05 % Allowed : 9.42 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.18), residues: 2086 helix: 0.43 (0.17), residues: 928 sheet: -0.12 (0.28), residues: 316 loop : -1.75 (0.19), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 240 TYR 0.043 0.002 TYR E 155 PHE 0.052 0.002 PHE I 85 TRP 0.026 0.002 TRP F 339 HIS 0.014 0.002 HIS K 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.21 (18947) covalent geometry : angle 0.80515 / 0.43 (25749) SS BOND : bond 0.00392 / 0.21 ( 1) SS BOND : angle 1.46160 / 0.82 ( 2) hydrogen bonds : bond 0.05546 / 3.83 ( 846) hydrogen bonds : angle 5.68182 / 3.95 ( 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 222 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 183 time to evaluate : 0.756 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: C 122 LYS cc_start: 0.9513 (OUTLIER) cc_final: 0.9167 (ptmt) REVERT: E 190 ARG cc_start: 0.8048 (mtm110) cc_final: 0.7350 (ttm110) REVERT: F 163 MET cc_start: 0.8555 (ptp) cc_final: 0.7756 (tpt) REVERT: F 184 TRP cc_start: 0.6694 (m100) cc_final: 0.6468 (m100) REVERT: F 257 MET cc_start: 0.9501 (mtp) cc_final: 0.9181 (mtm) REVERT: F 352 MET cc_start: 0.8908 (mmm) cc_final: 0.8223 (mmm) REVERT: F 624 MET cc_start: 0.4886 (tmm) cc_final: 0.4174 (tpp) REVERT: H 258 MET cc_start: -0.2510 (mmm) cc_final: -0.2738 (mmt) REVERT: I 49 ARG cc_start: 0.8436 (mmp-170) cc_final: 0.8122 (mmm160) REVERT: I 58 LEU cc_start: 0.9722 (mt) cc_final: 0.9480 (mt) REVERT: I 104 MET cc_start: 0.8900 (mpp) cc_final: 0.8625 (mpp) REVERT: I 120 PHE cc_start: 0.9758 (t80) cc_final: 0.9450 (t80) REVERT: K 85 PHE cc_start: 0.9483 (m-80) cc_final: 0.9160 (m-80) REVERT: K 113 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8494 (pptt) REVERT: K 120 PHE cc_start: 0.9470 (t80) cc_final: 0.9269 (t80) REVERT: K 137 TYR cc_start: 0.8322 (m-10) cc_final: 0.7727 (m-80) outliers start: 39 outliers final: 19 residues processed: 213 average time/residue: 0.1622 time to fit residues: 50.6999 Evaluate side-chains 151 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 412 ARG Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 558 SER Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain F residue 696 LYS Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 255 TYR Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 91 ARG 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: 0.5980 chunk 142 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 0.3980 chunk 76 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 HIS E 196 ASN E 324 GLN ** F 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 735 ASN H 206 GLN ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 HIS K 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.064416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.050041 restraints weight = 121935.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.051607 restraints weight = 71868.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.052583 restraints weight = 50462.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.053267 restraints weight = 39894.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.053716 restraints weight = 33787.929| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18948 Z= 0.166 Angle : 0.722 12.817 25751 Z= 0.383 Chirality : 0.048 0.485 2849 Planarity : 0.004 0.076 3088 Dihedral : 16.989 178.364 3191 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.05 % Allowed : 11.68 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.18), residues: 2086 helix: 0.50 (0.17), residues: 935 sheet: -0.20 (0.29), residues: 311 loop : -1.75 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 279 TYR 0.027 0.002 TYR E 155 PHE 0.035 0.002 PHE F 693 TRP 0.018 0.001 TRP F 339 HIS 0.006 0.001 HIS I 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (18947) covalent geometry : angle 0.72145 / 0.38 (25749) SS BOND : bond 0.00312 / 0.16 ( 1) SS BOND : angle 1.22095 / 0.69 ( 2) hydrogen bonds : bond 0.05007 / 3.42 ( 846) hydrogen bonds : angle 5.37207 / 3.74 ( 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 179 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 140 time to evaluate : 0.751 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: A 113 GLN cc_start: 0.9419 (pt0) cc_final: 0.9110 (pt0) REVERT: C 72 HIS cc_start: 0.7999 (p90) cc_final: 0.7762 (p90) REVERT: C 122 LYS cc_start: 0.9508 (OUTLIER) cc_final: 0.9194 (ptmt) REVERT: E 56 LEU cc_start: 0.8768 (tt) cc_final: 0.8367 (mt) REVERT: E 327 MET cc_start: 0.8222 (pmm) cc_final: 0.8006 (pmm) REVERT: F 41 LEU cc_start: 0.9163 (tp) cc_final: 0.8843 (tp) REVERT: F 163 MET cc_start: 0.8562 (ptp) cc_final: 0.7793 (tpt) REVERT: F 257 MET cc_start: 0.9507 (OUTLIER) cc_final: 0.9191 (mtt) REVERT: F 352 MET cc_start: 0.8782 (mmm) cc_final: 0.8268 (mmm) REVERT: F 624 MET cc_start: 0.4199 (tmm) cc_final: 0.3654 (tpp) REVERT: H 206 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8926 (pp30) REVERT: H 258 MET cc_start: -0.2528 (mmm) cc_final: -0.2760 (mmt) REVERT: I 58 LEU cc_start: 0.9687 (mt) cc_final: 0.9451 (mt) REVERT: I 85 PHE cc_start: 0.9565 (m-80) cc_final: 0.9110 (m-80) REVERT: I 104 MET cc_start: 0.8837 (mpp) cc_final: 0.8610 (mpp) REVERT: I 120 PHE cc_start: 0.9738 (t80) cc_final: 0.9386 (t80) REVERT: K 113 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8441 (pptt) REVERT: K 120 PHE cc_start: 0.9543 (t80) cc_final: 0.9176 (t80) REVERT: K 126 TYR cc_start: 0.8846 (t80) cc_final: 0.8500 (t80) REVERT: K 130 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8730 (mm) REVERT: K 137 TYR cc_start: 0.8314 (m-10) cc_final: 0.7574 (m-80) outliers start: 39 outliers final: 18 residues processed: 169 average time/residue: 0.1559 time to fit residues: 39.5806 Evaluate side-chains 146 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 142 LEU Chi-restraints excluded: chain F residue 257 MET 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 F residue 735 ASN Chi-restraints excluded: chain H residue 206 GLN 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 18 HIS Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain K residue 130 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 96 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 113 GLN E 54 ASN ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3620 r_free = 0.3620 target = 0.061335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.047201 restraints weight = 127177.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.048693 restraints weight = 75382.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.049668 restraints weight = 53246.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.050245 restraints weight = 41891.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.050681 restraints weight = 35956.241| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 18948 Z= 0.304 Angle : 0.772 13.473 25751 Z= 0.411 Chirality : 0.048 0.493 2849 Planarity : 0.005 0.055 3088 Dihedral : 16.807 179.169 3189 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.37 % Allowed : 12.42 % Favored : 85.21 % 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: -0.83 (0.18), residues: 2086 helix: 0.48 (0.16), residues: 933 sheet: -0.31 (0.29), residues: 320 loop : -1.83 (0.19), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 711 TYR 0.027 0.002 TYR K 133 PHE 0.040 0.002 PHE E 62 TRP 0.026 0.003 TRP E 89 HIS 0.027 0.002 HIS K 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.30 (18947) covalent geometry : angle 0.77198 / 0.41 (25749) SS BOND : bond 0.01226 / 0.65 ( 1) SS BOND : angle 1.09734 / 0.58 ( 2) hydrogen bonds : bond 0.04848 / 3.44 ( 846) hydrogen bonds : angle 5.48422 / 3.82 ( 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 177 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 132 time to evaluate : 0.599 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: C 122 LYS cc_start: 0.9498 (OUTLIER) cc_final: 0.9185 (ptmt) REVERT: E 117 HIS cc_start: 0.7240 (t70) cc_final: 0.6819 (t70) REVERT: E 327 MET cc_start: 0.8359 (pmm) cc_final: 0.8126 (pmm) REVERT: F 41 LEU cc_start: 0.9275 (tp) cc_final: 0.9072 (tp) REVERT: F 163 MET cc_start: 0.8787 (ptp) cc_final: 0.8564 (ptm) REVERT: F 352 MET cc_start: 0.8796 (mmm) cc_final: 0.8492 (mmm) REVERT: F 463 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.8145 (p90) REVERT: F 624 MET cc_start: 0.4553 (tmm) cc_final: 0.4179 (tpp) REVERT: H 13 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7628 (pttm) REVERT: H 226 MET cc_start: 0.9366 (tpp) cc_final: 0.8293 (tpp) REVERT: I 96 ASP cc_start: 0.9077 (m-30) cc_final: 0.8742 (m-30) REVERT: I 120 PHE cc_start: 0.9746 (t80) cc_final: 0.9339 (t80) REVERT: K 18 HIS cc_start: 0.7899 (OUTLIER) cc_final: 0.7360 (t70) REVERT: K 49 ARG cc_start: 0.8569 (ppt170) cc_final: 0.8205 (ppt170) REVERT: K 113 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8406 (pptt) REVERT: K 120 PHE cc_start: 0.9459 (t80) cc_final: 0.9152 (t80) REVERT: K 126 TYR cc_start: 0.9004 (t80) cc_final: 0.8587 (t80) REVERT: K 130 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8609 (mm) REVERT: K 137 TYR cc_start: 0.8508 (m-10) cc_final: 0.7810 (m-80) outliers start: 45 outliers final: 28 residues processed: 168 average time/residue: 0.1538 time to fit residues: 38.4739 Evaluate side-chains 152 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain F residue 182 LEU 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 23 LEU Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 228 LYS 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 71 ASN Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 18 HIS Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain K residue 130 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 12 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 192 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 HIS F 731 ASN F 735 ASN H 206 GLN ** 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 = 0.3631 r_free = 0.3631 target = 0.061637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.047617 restraints weight = 123284.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.049088 restraints weight = 72459.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.050066 restraints weight = 50807.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.050711 restraints weight = 39920.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.051140 restraints weight = 33857.826| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18948 Z= 0.187 Angle : 0.675 13.066 25751 Z= 0.362 Chirality : 0.046 0.465 2849 Planarity : 0.004 0.055 3088 Dihedral : 16.723 179.605 3189 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.32 % Allowed : 13.95 % Favored : 83.74 % 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: -0.64 (0.18), residues: 2086 helix: 0.66 (0.17), residues: 929 sheet: -0.25 (0.29), residues: 319 loop : -1.73 (0.19), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 711 TYR 0.022 0.001 TYR E 155 PHE 0.029 0.002 PHE E 62 TRP 0.011 0.001 TRP F 339 HIS 0.012 0.001 HIS K 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.19 (18947) covalent geometry : angle 0.67503 / 0.36 (25749) SS BOND : bond 0.00648 / 0.34 ( 1) SS BOND : angle 1.31846 / 0.71 ( 2) hydrogen bonds : bond 0.04331 / 2.99 ( 846) hydrogen bonds : angle 5.24162 / 3.66 ( 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 169 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 0.790 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: 0.9532 (OUTLIER) cc_final: 0.9211 (ptmt) REVERT: E 56 LEU cc_start: 0.8809 (tt) cc_final: 0.8609 (mt) REVERT: E 68 LYS cc_start: 0.7179 (tptt) cc_final: 0.6813 (mptt) REVERT: E 117 HIS cc_start: 0.7364 (t70) cc_final: 0.6883 (t70) REVERT: E 327 MET cc_start: 0.8365 (pmm) cc_final: 0.8111 (pmm) REVERT: F 1 MET cc_start: 0.7335 (mmt) cc_final: 0.6943 (mmt) REVERT: F 160 MET cc_start: 0.9408 (tmm) cc_final: 0.8807 (ptm) REVERT: F 163 MET cc_start: 0.8708 (ptp) cc_final: 0.7877 (tpt) REVERT: F 463 TYR cc_start: 0.8689 (OUTLIER) cc_final: 0.8198 (p90) REVERT: F 624 MET cc_start: 0.4533 (tmm) cc_final: 0.4156 (tpp) REVERT: H 13 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7525 (pttm) REVERT: H 226 MET cc_start: 0.9400 (tpp) cc_final: 0.8460 (tpp) REVERT: I 52 MET cc_start: 0.9556 (pmm) cc_final: 0.9294 (pmm) REVERT: I 96 ASP cc_start: 0.9098 (m-30) cc_final: 0.8762 (m-30) REVERT: I 120 PHE cc_start: 0.9733 (t80) cc_final: 0.9330 (t80) REVERT: I 124 CYS cc_start: 0.9290 (m) cc_final: 0.9067 (m) REVERT: K 49 ARG cc_start: 0.8550 (ppt170) cc_final: 0.8283 (ppt170) REVERT: K 79 GLU cc_start: 0.9302 (OUTLIER) cc_final: 0.9090 (pm20) REVERT: K 97 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8226 (pt0) REVERT: K 113 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8443 (pptt) REVERT: K 120 PHE cc_start: 0.9497 (t80) cc_final: 0.9170 (t80) REVERT: K 126 TYR cc_start: 0.8989 (t80) cc_final: 0.8572 (t80) REVERT: K 130 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8548 (mm) REVERT: K 137 TYR cc_start: 0.8479 (m-10) cc_final: 0.8215 (m-80) outliers start: 44 outliers final: 24 residues processed: 163 average time/residue: 0.1540 time to fit residues: 37.8902 Evaluate side-chains 146 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 345 THR 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 597 ILE Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 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 45 THR Chi-restraints excluded: chain I residue 48 LEU 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 44 THR Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain K residue 130 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 20 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 189 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 199 optimal weight: 0.0030 chunk 66 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 overall best weight: 1.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.061372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.047399 restraints weight = 123883.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.048901 restraints weight = 72858.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.049874 restraints weight = 51185.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.050491 restraints weight = 40226.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.050897 restraints weight = 34293.116| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18948 Z= 0.171 Angle : 0.667 11.409 25751 Z= 0.352 Chirality : 0.046 0.450 2849 Planarity : 0.003 0.051 3088 Dihedral : 16.581 179.343 3189 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.37 % Allowed : 14.63 % Favored : 83.00 % 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: -0.53 (0.18), residues: 2086 helix: 0.78 (0.17), residues: 934 sheet: -0.25 (0.29), residues: 319 loop : -1.69 (0.19), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 190 TYR 0.018 0.001 TYR E 78 PHE 0.026 0.001 PHE E 62 TRP 0.026 0.002 TRP E 89 HIS 0.005 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (18947) covalent geometry : angle 0.66701 / 0.35 (25749) SS BOND : bond 0.00664 / 0.35 ( 1) SS BOND : angle 1.30555 / 0.70 ( 2) hydrogen bonds : bond 0.04074 / 2.80 ( 846) hydrogen bonds : angle 5.12758 / 3.58 ( 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 171 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 126 time to evaluate : 0.768 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: 0.8882 (OUTLIER) cc_final: 0.8039 (m) REVERT: A 113 GLN cc_start: 0.9414 (OUTLIER) cc_final: 0.9155 (pt0) REVERT: B 201 THR cc_start: 0.9237 (OUTLIER) cc_final: 0.8934 (m) REVERT: C 122 LYS cc_start: 0.9484 (OUTLIER) cc_final: 0.9154 (ptmt) REVERT: E 68 LYS cc_start: 0.7168 (tptt) cc_final: 0.6806 (mptt) REVERT: F 1 MET cc_start: 0.7375 (mmt) cc_final: 0.6981 (mmt) REVERT: F 163 MET cc_start: 0.8758 (ptp) cc_final: 0.8026 (tpt) REVERT: F 257 MET cc_start: 0.9518 (mtm) cc_final: 0.9298 (mtm) REVERT: F 352 MET cc_start: 0.8978 (mmm) cc_final: 0.8477 (mmm) REVERT: F 463 TYR cc_start: 0.8663 (OUTLIER) cc_final: 0.8139 (p90) REVERT: F 624 MET cc_start: 0.4597 (tmm) cc_final: 0.4230 (tpp) REVERT: H 13 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7465 (pttm) REVERT: H 187 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.8799 (tt) REVERT: H 226 MET cc_start: 0.9402 (tpp) cc_final: 0.8546 (tpp) REVERT: I 52 MET cc_start: 0.9547 (pmm) cc_final: 0.9219 (pmm) REVERT: I 96 ASP cc_start: 0.9095 (m-30) cc_final: 0.8764 (m-30) REVERT: I 120 PHE cc_start: 0.9712 (t80) cc_final: 0.9314 (t80) REVERT: I 124 CYS cc_start: 0.9277 (m) cc_final: 0.9023 (m) REVERT: K 49 ARG cc_start: 0.8576 (ppt170) cc_final: 0.8154 (ppt170) REVERT: K 52 MET cc_start: 0.8913 (pmm) cc_final: 0.8627 (pmm) REVERT: K 72 GLU cc_start: 0.9386 (OUTLIER) cc_final: 0.9172 (pm20) REVERT: K 97 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8193 (pt0) REVERT: K 113 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8462 (pptt) REVERT: K 120 PHE cc_start: 0.9500 (t80) cc_final: 0.9176 (t80) REVERT: K 126 TYR cc_start: 0.9026 (t80) cc_final: 0.8592 (t80) REVERT: K 130 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8679 (mm) outliers start: 45 outliers final: 28 residues processed: 164 average time/residue: 0.1429 time to fit residues: 36.1383 Evaluate side-chains 156 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 499 TYR Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 558 SER Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 255 TYR Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain K residue 130 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 140 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 199 optimal weight: 0.8980 chunk 209 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 113 GLN ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 HIS ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.060767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.046894 restraints weight = 126664.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.048400 restraints weight = 74086.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.049367 restraints weight = 51775.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.049993 restraints weight = 40628.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.050394 restraints weight = 34505.770| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18948 Z= 0.181 Angle : 0.648 10.662 25751 Z= 0.346 Chirality : 0.045 0.434 2849 Planarity : 0.003 0.049 3088 Dihedral : 16.473 179.290 3189 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.79 % Allowed : 15.05 % Favored : 82.16 % 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: 0.84 (0.17), residues: 928 sheet: -0.28 (0.29), residues: 320 loop : -1.65 (0.19), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 129 TYR 0.018 0.001 TYR I 123 PHE 0.023 0.001 PHE E 62 TRP 0.025 0.002 TRP H 52 HIS 0.003 0.001 HIS F 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (18947) covalent geometry : angle 0.64830 / 0.35 (25749) SS BOND : bond 0.00776 / 0.41 ( 1) SS BOND : angle 1.20287 / 0.64 ( 2) hydrogen bonds : bond 0.03979 / 2.72 ( 846) hydrogen bonds : angle 5.08049 / 3.54 ( 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 174 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 121 time to evaluate : 0.876 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 3 SER cc_start: 0.8861 (OUTLIER) cc_final: 0.8023 (m) REVERT: A 113 GLN cc_start: 0.9409 (OUTLIER) cc_final: 0.9095 (pt0) REVERT: B 201 THR cc_start: 0.9232 (OUTLIER) cc_final: 0.8926 (m) REVERT: C 122 LYS cc_start: 0.9496 (OUTLIER) cc_final: 0.9174 (ptmt) REVERT: E 40 MET cc_start: 0.8336 (mmp) cc_final: 0.8075 (mmp) REVERT: E 68 LYS cc_start: 0.7200 (tptt) cc_final: 0.6823 (mptt) REVERT: E 117 HIS cc_start: 0.7142 (t70) cc_final: 0.6590 (t70) REVERT: F 1 MET cc_start: 0.7332 (mmt) cc_final: 0.6963 (mmt) REVERT: F 160 MET cc_start: 0.9412 (tmm) cc_final: 0.8831 (ptm) REVERT: F 163 MET cc_start: 0.8796 (ptp) cc_final: 0.7985 (tpt) REVERT: F 352 MET cc_start: 0.8901 (mmm) cc_final: 0.8584 (mmm) REVERT: F 463 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.8048 (p90) REVERT: F 471 GLN cc_start: 0.8307 (mp10) cc_final: 0.7981 (tm-30) REVERT: F 624 MET cc_start: 0.4248 (tmm) cc_final: 0.4024 (tpp) REVERT: H 13 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7469 (pttm) REVERT: H 187 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.8783 (tt) REVERT: H 226 MET cc_start: 0.9391 (tpp) cc_final: 0.8565 (tpp) REVERT: I 52 MET cc_start: 0.9531 (pmm) cc_final: 0.9183 (pmm) REVERT: I 96 ASP cc_start: 0.9079 (m-30) cc_final: 0.8743 (m-30) REVERT: I 120 PHE cc_start: 0.9707 (t80) cc_final: 0.9284 (t80) REVERT: I 124 CYS cc_start: 0.9283 (m) cc_final: 0.9020 (m) REVERT: K 49 ARG cc_start: 0.8616 (ppt170) cc_final: 0.8329 (ppt170) REVERT: K 72 GLU cc_start: 0.9396 (OUTLIER) cc_final: 0.9175 (pm20) REVERT: K 97 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8251 (pt0) REVERT: K 113 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8479 (pptt) REVERT: K 120 PHE cc_start: 0.9483 (t80) cc_final: 0.9194 (t80) REVERT: K 130 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8891 (mm) REVERT: K 137 TYR cc_start: 0.8687 (m-80) cc_final: 0.8098 (m-80) outliers start: 53 outliers final: 30 residues processed: 167 average time/residue: 0.1504 time to fit residues: 38.1187 Evaluate side-chains 156 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 133 VAL 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 142 LEU Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 464 GLU 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 597 ILE Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 255 TYR Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain K residue 130 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 7 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 171 optimal weight: 7.9990 chunk 212 optimal weight: 20.0000 chunk 24 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 167 optimal weight: 0.0770 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 40 GLN ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 722 ASN ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.061043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.047209 restraints weight = 124500.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.048743 restraints weight = 72728.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.049723 restraints weight = 50494.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.050358 restraints weight = 39454.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.050777 restraints weight = 33397.439| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 18948 Z= 0.141 Angle : 0.629 10.414 25751 Z= 0.334 Chirality : 0.045 0.406 2849 Planarity : 0.003 0.048 3088 Dihedral : 16.360 179.162 3189 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.47 % Allowed : 15.21 % Favored : 82.32 % 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: -0.38 (0.18), residues: 2086 helix: 0.95 (0.17), residues: 928 sheet: -0.42 (0.29), residues: 339 loop : -1.57 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 711 TYR 0.016 0.001 TYR I 123 PHE 0.018 0.001 PHE I 16 TRP 0.031 0.002 TRP H 52 HIS 0.003 0.001 HIS I 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (18947) covalent geometry : angle 0.62923 / 0.33 (25749) SS BOND : bond 0.00434 / 0.23 ( 1) SS BOND : angle 1.21613 / 0.65 ( 2) hydrogen bonds : bond 0.03812 / 2.59 ( 846) hydrogen bonds : angle 4.93435 / 3.46 ( 2401) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 121 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 SER cc_start: 0.8727 (OUTLIER) cc_final: 0.7889 (m) REVERT: A 113 GLN cc_start: 0.9403 (OUTLIER) cc_final: 0.9074 (pt0) REVERT: B 201 THR cc_start: 0.9263 (OUTLIER) cc_final: 0.8977 (m) REVERT: C 122 LYS cc_start: 0.9487 (OUTLIER) cc_final: 0.9138 (ptmt) REVERT: E 40 MET cc_start: 0.8415 (mmp) cc_final: 0.8075 (mmp) REVERT: E 68 LYS cc_start: 0.7205 (tptt) cc_final: 0.6865 (mptt) REVERT: F 1 MET cc_start: 0.7277 (mmt) cc_final: 0.6915 (mmt) REVERT: F 160 MET cc_start: 0.9401 (tmm) cc_final: 0.8849 (ptm) REVERT: F 163 MET cc_start: 0.8792 (ptp) cc_final: 0.8045 (tpt) REVERT: F 463 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.8046 (p90) REVERT: F 471 GLN cc_start: 0.8289 (mp10) cc_final: 0.7937 (tm-30) REVERT: F 624 MET cc_start: 0.4358 (tmm) cc_final: 0.4157 (tpp) REVERT: H 13 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7485 (pttm) REVERT: H 187 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.8872 (tt) REVERT: H 226 MET cc_start: 0.9401 (tpp) cc_final: 0.8588 (tpp) REVERT: I 52 MET cc_start: 0.9553 (pmm) cc_final: 0.9309 (pmm) REVERT: I 96 ASP cc_start: 0.9110 (m-30) cc_final: 0.8788 (m-30) REVERT: I 120 PHE cc_start: 0.9689 (t80) cc_final: 0.9256 (t80) REVERT: I 124 CYS cc_start: 0.9287 (m) cc_final: 0.9020 (m) REVERT: K 49 ARG cc_start: 0.8650 (ppt170) cc_final: 0.8263 (ppt170) REVERT: K 72 GLU cc_start: 0.9389 (OUTLIER) cc_final: 0.9135 (pm20) REVERT: K 95 VAL cc_start: 0.8672 (t) cc_final: 0.8430 (m) REVERT: K 113 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8473 (pptt) REVERT: K 120 PHE cc_start: 0.9482 (t80) cc_final: 0.9229 (t80) REVERT: K 126 TYR cc_start: 0.8974 (t80) cc_final: 0.8611 (t80) REVERT: K 130 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8799 (mm) REVERT: K 137 TYR cc_start: 0.8743 (m-80) cc_final: 0.8109 (m-80) outliers start: 47 outliers final: 29 residues processed: 159 average time/residue: 0.1550 time to fit residues: 37.4152 Evaluate side-chains 156 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 40 GLN 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 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 464 GLU Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 567 TYR Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 255 TYR Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain K residue 130 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 118 optimal weight: 0.8980 chunk 210 optimal weight: 6.9990 chunk 153 optimal weight: 0.3980 chunk 137 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 173 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 40 GLN ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.061160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.047391 restraints weight = 125050.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.048899 restraints weight = 72725.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.049865 restraints weight = 50626.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.050486 restraints weight = 39651.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.050899 restraints weight = 33663.142| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18948 Z= 0.125 Angle : 0.627 11.261 25751 Z= 0.332 Chirality : 0.044 0.398 2849 Planarity : 0.003 0.049 3088 Dihedral : 16.309 179.234 3189 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.16 % Allowed : 15.95 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.18), residues: 2086 helix: 0.99 (0.17), residues: 929 sheet: -0.39 (0.29), residues: 342 loop : -1.55 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 78 TYR 0.027 0.001 TYR I 126 PHE 0.018 0.001 PHE I 16 TRP 0.030 0.002 TRP H 52 HIS 0.002 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (18947) covalent geometry : angle 0.62740 / 0.33 (25749) SS BOND : bond 0.00393 / 0.21 ( 1) SS BOND : angle 1.06213 / 0.57 ( 2) hydrogen bonds : bond 0.03721 / 2.53 ( 846) hydrogen bonds : angle 4.87942 / 3.41 ( 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 162 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 SER cc_start: 0.8706 (OUTLIER) cc_final: 0.7877 (m) REVERT: A 113 GLN cc_start: 0.9415 (OUTLIER) cc_final: 0.9083 (pt0) REVERT: B 201 THR cc_start: 0.9254 (OUTLIER) cc_final: 0.8976 (m) REVERT: C 122 LYS cc_start: 0.9483 (OUTLIER) cc_final: 0.9140 (ptmt) REVERT: E 40 MET cc_start: 0.8425 (mmp) cc_final: 0.8067 (mmp) REVERT: E 68 LYS cc_start: 0.7405 (tptt) cc_final: 0.7038 (mptt) REVERT: E 117 HIS cc_start: 0.7188 (t70) cc_final: 0.6687 (t70) REVERT: F 1 MET cc_start: 0.7275 (mmt) cc_final: 0.6926 (mmt) REVERT: F 8 MET cc_start: 0.8871 (ptp) cc_final: 0.8648 (ptp) REVERT: F 47 PHE cc_start: 0.8000 (m-80) cc_final: 0.7669 (m-80) REVERT: F 160 MET cc_start: 0.9403 (tmm) cc_final: 0.8846 (ptm) REVERT: F 163 MET cc_start: 0.8818 (ptp) cc_final: 0.8060 (tpt) REVERT: F 463 TYR cc_start: 0.8672 (OUTLIER) cc_final: 0.8066 (p90) REVERT: F 471 GLN cc_start: 0.8282 (mp10) cc_final: 0.8057 (pm20) REVERT: F 624 MET cc_start: 0.4411 (tmm) cc_final: 0.4182 (tpp) REVERT: H 13 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7531 (pttm) REVERT: H 226 MET cc_start: 0.9393 (tpp) cc_final: 0.8641 (tpp) REVERT: I 52 MET cc_start: 0.9581 (pmm) cc_final: 0.9265 (pmm) REVERT: I 85 PHE cc_start: 0.9669 (m-80) cc_final: 0.9458 (m-80) REVERT: I 96 ASP cc_start: 0.9107 (m-30) cc_final: 0.8783 (m-30) REVERT: I 120 PHE cc_start: 0.9683 (t80) cc_final: 0.9267 (t80) REVERT: I 124 CYS cc_start: 0.9269 (m) cc_final: 0.9013 (m) REVERT: I 130 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9176 (mm) REVERT: K 49 ARG cc_start: 0.8596 (ppt170) cc_final: 0.8258 (ppt170) REVERT: K 72 GLU cc_start: 0.9396 (OUTLIER) cc_final: 0.9142 (pm20) REVERT: K 95 VAL cc_start: 0.8670 (t) cc_final: 0.8430 (m) REVERT: K 113 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8488 (pptt) REVERT: K 126 TYR cc_start: 0.8934 (t80) cc_final: 0.8598 (t80) REVERT: K 130 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8805 (mm) REVERT: K 137 TYR cc_start: 0.8768 (m-80) cc_final: 0.8106 (m-10) outliers start: 41 outliers final: 26 residues processed: 153 average time/residue: 0.1399 time to fit residues: 33.1537 Evaluate side-chains 149 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 133 VAL 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 122 LYS Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 567 TYR Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain K residue 130 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 182 optimal weight: 7.9990 chunk 2 optimal weight: 0.0970 chunk 28 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 210 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 206 optimal weight: 0.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 161 GLN ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.060698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.046975 restraints weight = 123838.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.048460 restraints weight = 72241.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.049415 restraints weight = 50448.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.050053 restraints weight = 39449.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.050436 restraints weight = 33366.198| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18948 Z= 0.142 Angle : 0.640 11.549 25751 Z= 0.338 Chirality : 0.044 0.388 2849 Planarity : 0.003 0.050 3088 Dihedral : 16.231 179.310 3189 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.05 % Allowed : 16.21 % 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: -0.31 (0.18), residues: 2086 helix: 0.99 (0.17), residues: 927 sheet: -0.40 (0.29), residues: 342 loop : -1.50 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 78 TYR 0.018 0.001 TYR I 123 PHE 0.029 0.001 PHE K 120 TRP 0.028 0.002 TRP H 52 HIS 0.010 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (18947) covalent geometry : angle 0.63986 / 0.34 (25749) SS BOND : bond 0.00510 / 0.27 ( 1) SS BOND : angle 0.90902 / 0.48 ( 2) hydrogen bonds : bond 0.03726 / 2.53 ( 846) hydrogen bonds : angle 4.92291 / 3.44 ( 2401) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 113 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 SER cc_start: 0.8692 (OUTLIER) cc_final: 0.7871 (m) REVERT: A 113 GLN cc_start: 0.9416 (OUTLIER) cc_final: 0.9030 (pt0) REVERT: B 201 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8968 (m) REVERT: C 122 LYS cc_start: 0.9486 (OUTLIER) cc_final: 0.9159 (ptmt) REVERT: E 40 MET cc_start: 0.8411 (mmp) cc_final: 0.8102 (mmp) REVERT: E 68 LYS cc_start: 0.7425 (tptt) cc_final: 0.7042 (mptt) REVERT: E 117 HIS cc_start: 0.7080 (t70) cc_final: 0.6588 (t70) REVERT: F 1 MET cc_start: 0.7230 (mmt) cc_final: 0.6870 (mmt) REVERT: F 47 PHE cc_start: 0.8001 (m-80) cc_final: 0.7662 (m-80) REVERT: F 160 MET cc_start: 0.9402 (tmm) cc_final: 0.8859 (ptm) REVERT: F 163 MET cc_start: 0.8843 (ptp) cc_final: 0.8047 (tpt) REVERT: F 452 MET cc_start: 0.9017 (tpp) cc_final: 0.8701 (tpp) REVERT: F 463 TYR cc_start: 0.8658 (OUTLIER) cc_final: 0.8025 (p90) REVERT: F 471 GLN cc_start: 0.8287 (mp10) cc_final: 0.8055 (pm20) REVERT: F 624 MET cc_start: 0.4552 (tmm) cc_final: 0.4349 (tpp) REVERT: H 13 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7513 (pttm) REVERT: H 187 LEU cc_start: 0.9437 (mt) cc_final: 0.9042 (tt) REVERT: H 226 MET cc_start: 0.9405 (tpp) cc_final: 0.8670 (tpp) REVERT: I 52 MET cc_start: 0.9555 (pmm) cc_final: 0.9275 (pmm) REVERT: I 96 ASP cc_start: 0.9105 (m-30) cc_final: 0.8777 (m-30) REVERT: I 120 PHE cc_start: 0.9660 (t80) cc_final: 0.9243 (t80) REVERT: I 124 CYS cc_start: 0.9270 (m) cc_final: 0.9012 (m) REVERT: K 49 ARG cc_start: 0.8654 (ppt170) cc_final: 0.8307 (ppt170) REVERT: K 72 GLU cc_start: 0.9377 (OUTLIER) cc_final: 0.9107 (pm20) REVERT: K 113 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8487 (pptt) REVERT: K 126 TYR cc_start: 0.9003 (t80) cc_final: 0.8662 (t80) REVERT: K 130 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8759 (mm) REVERT: K 137 TYR cc_start: 0.8816 (m-80) cc_final: 0.8169 (m-10) outliers start: 39 outliers final: 26 residues processed: 146 average time/residue: 0.1450 time to fit residues: 32.5432 Evaluate side-chains 145 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 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 F residue 262 ILE Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 567 TYR Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain K residue 130 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 72 optimal weight: 0.8980 chunk 94 optimal weight: 0.4980 chunk 163 optimal weight: 8.9990 chunk 88 optimal weight: 0.8980 chunk 202 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 206 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.060723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.047146 restraints weight = 123786.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.048580 restraints weight = 71802.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.049533 restraints weight = 49911.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.050166 restraints weight = 39026.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.050573 restraints weight = 32968.938| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18948 Z= 0.133 Angle : 0.637 14.017 25751 Z= 0.335 Chirality : 0.044 0.371 2849 Planarity : 0.003 0.051 3088 Dihedral : 16.133 179.278 3189 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.16 % Allowed : 16.42 % 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: -0.29 (0.18), residues: 2086 helix: 1.00 (0.17), residues: 933 sheet: -0.37 (0.29), residues: 342 loop : -1.52 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 78 TYR 0.015 0.001 TYR H 184 PHE 0.068 0.001 PHE K 120 TRP 0.027 0.002 TRP H 52 HIS 0.002 0.001 HIS I 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (18947) covalent geometry : angle 0.63719 / 0.33 (25749) SS BOND : bond 0.00421 / 0.22 ( 1) SS BOND : angle 0.86035 / 0.46 ( 2) hydrogen bonds : bond 0.03642 / 2.47 ( 846) hydrogen bonds : angle 4.86521 / 3.40 ( 2401) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3404.88 seconds wall clock time: 60 minutes 1.83 seconds (3601.83 seconds total)