Starting phenix.real_space_refine on Mon Jun 16 15:22:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v01_26925/06_2025/7v01_26925_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v01_26925/06_2025/7v01_26925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v01_26925/06_2025/7v01_26925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v01_26925/06_2025/7v01_26925.map" model { file = "/net/cci-nas-00/data/ceres_data/7v01_26925/06_2025/7v01_26925_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v01_26925/06_2025/7v01_26925_neut.cif" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.030 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.17, per 1000 atoms: 0.66 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: 4.79 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 6.00 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: 6.56 Time building geometry restraints manager: 5.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3874 1.33 - 1.45: 4726 1.45 - 1.57: 10139 1.57 - 1.70: 118 1.70 - 1.82: 90 Bond restraints: 18947 Sorted by residual: bond pdb=" C4 ATP F 802 " pdb=" C5 ATP F 802 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 6.99e+01 bond pdb=" C5 ATP F 802 " pdb=" C6 ATP F 802 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.71e+01 bond pdb=" C5 ATP F 802 " pdb=" N7 ATP F 802 " ideal model delta sigma weight residual 1.387 1.333 0.054 1.00e-02 1.00e+04 2.97e+01 bond pdb=" C4 ATP F 802 " pdb=" N9 ATP F 802 " ideal model delta sigma weight residual 1.374 1.330 0.044 1.00e-02 1.00e+04 1.97e+01 bond pdb=" C8 ATP F 802 " pdb=" N7 ATP F 802 " ideal model delta sigma weight residual 1.310 1.352 -0.042 1.00e-02 1.00e+04 1.76e+01 ... (remaining 18942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 25454 3.28 - 6.57: 264 6.57 - 9.85: 23 9.85 - 13.14: 3 13.14 - 16.42: 5 Bond angle restraints: 25749 Sorted by residual: angle pdb=" PB ATP F 802 " pdb=" O3B ATP F 802 " pdb=" PG ATP F 802 " ideal model delta sigma weight residual 139.87 123.45 16.42 1.00e+00 1.00e+00 2.70e+02 angle pdb=" PA ATP F 802 " pdb=" O3A ATP F 802 " pdb=" PB ATP F 802 " ideal model delta sigma weight residual 136.83 121.94 14.89 1.00e+00 1.00e+00 2.22e+02 angle pdb=" CA PHE F 540 " pdb=" CB PHE F 540 " pdb=" CG PHE F 540 " ideal model delta sigma weight residual 113.80 99.01 14.79 1.00e+00 1.00e+00 2.19e+02 angle pdb=" C4' A U 25 " pdb=" C3' A U 25 " pdb=" O3' A U 25 " ideal model delta sigma weight residual 113.00 97.76 15.24 1.50e+00 4.44e-01 1.03e+02 angle pdb=" O3' U U 28 " pdb=" C3' U U 28 " pdb=" C2' U U 28 " ideal model delta sigma weight residual 109.50 124.01 -14.51 1.50e+00 4.44e-01 9.36e+01 ... (remaining 25744 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 11156 35.78 - 71.55: 277 71.55 - 107.33: 33 107.33 - 143.10: 3 143.10 - 178.88: 4 Dihedral angle restraints: 11473 sinusoidal: 5268 harmonic: 6205 Sorted by residual: dihedral pdb=" O4' U U 17 " pdb=" C1' U U 17 " pdb=" N1 U U 17 " pdb=" C2 U U 17 " ideal model delta sinusoidal sigma weight residual -128.00 48.98 -176.98 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U U 10 " pdb=" C1' U U 10 " pdb=" N1 U U 10 " pdb=" C2 U U 10 " ideal model delta sinusoidal sigma weight residual 232.00 75.77 156.23 1 1.70e+01 3.46e-03 6.36e+01 dihedral pdb=" O4' C G 2 " pdb=" C1' C G 2 " pdb=" N1 C G 2 " pdb=" C2 C G 2 " ideal model delta sinusoidal sigma weight residual -128.00 7.04 -135.04 1 1.70e+01 3.46e-03 5.67e+01 ... (remaining 11470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2472 0.074 - 0.149: 337 0.149 - 0.223: 32 0.223 - 0.297: 6 0.297 - 0.371: 2 Chirality restraints: 2849 Sorted by residual: chirality pdb=" P G U 29 " pdb=" OP1 G U 29 " pdb=" OP2 G U 29 " pdb=" O5' G U 29 " both_signs ideal model delta sigma weight residual True 2.41 -2.78 -0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" C3' A U 25 " pdb=" C4' A U 25 " pdb=" O3' A U 25 " pdb=" C2' A U 25 " both_signs ideal model delta sigma weight residual False -2.48 -2.83 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" C1' G G 21 " pdb=" O4' G G 21 " pdb=" C2' G G 21 " pdb=" N9 G G 21 " both_signs ideal model delta sigma weight residual False 2.44 2.16 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 2846 not shown) Planarity restraints: 3088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 540 " -0.061 2.00e-02 2.50e+03 4.57e-02 3.65e+01 pdb=" CG PHE F 540 " 0.102 2.00e-02 2.50e+03 pdb=" CD1 PHE F 540 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE F 540 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE F 540 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE F 540 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE F 540 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY E 14 " 0.063 5.00e-02 4.00e+02 9.41e-02 1.42e+01 pdb=" N PRO E 15 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO E 15 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO E 15 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 43 " 0.059 5.00e-02 4.00e+02 8.68e-02 1.20e+01 pdb=" N PRO A 44 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 44 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 44 " 0.048 5.00e-02 4.00e+02 ... (remaining 3085 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 66 2.44 - 3.05: 12282 3.05 - 3.67: 27339 3.67 - 4.28: 40610 4.28 - 4.90: 65946 Nonbonded interactions: 146243 Sorted by model distance: nonbonded pdb=" ND2 ASN B 57 " pdb=" O2 C G 8 " model vdw 1.822 3.120 nonbonded pdb=" OG SER B 86 " pdb=" O2' G G 5 " model vdw 2.070 3.040 nonbonded pdb=" OH TYR B 2 " pdb=" OE1 GLN H 45 " model vdw 2.177 3.040 nonbonded pdb=" OG SER I 46 " pdb=" OP2 U U 9 " model vdw 2.182 3.040 nonbonded pdb=" O2' G U 21 " pdb=" O5' C U 22 " model vdw 2.211 3.040 ... (remaining 146238 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 21 \ 4)) selection = chain 'B' selection = (chain 'C' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 21 \ 4)) } ncs_group { reference = chain 'I' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.800 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 48.080 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 18948 Z= 0.315 Angle : 0.884 16.419 25751 Z= 0.535 Chirality : 0.052 0.371 2849 Planarity : 0.005 0.094 3088 Dihedral : 15.848 178.878 7482 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.47 % Allowed : 0.58 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (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 TRP 0.041 0.002 TRP F 339 HIS 0.007 0.001 HIS F 60 PHE 0.102 0.003 PHE F 540 TYR 0.055 0.002 TYR K 86 ARG 0.040 0.001 ARG C 78 Details of bonding type rmsd hydrogen bonds : bond 0.18529 ( 846) hydrogen bonds : angle 6.80632 ( 2401) SS BOND : bond 0.00160 ( 1) SS BOND : angle 1.98932 ( 2) covalent geometry : bond 0.00563 (18947) covalent geometry : angle 0.88403 (25749) *********************** 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 : 2.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 137 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6566 (ttm170) REVERT: E 119 MET cc_start: 0.7313 (tpp) cc_final: 0.6999 (tpp) REVERT: E 289 LEU cc_start: 0.7281 (mt) cc_final: 0.6794 (tt) REVERT: F 163 MET cc_start: 0.7443 (ptp) cc_final: 0.7050 (tpt) REVERT: F 588 LEU cc_start: 0.8293 (tp) cc_final: 0.8052 (tp) REVERT: F 697 MET cc_start: 0.7188 (mmm) cc_final: 0.6916 (mmm) REVERT: H 258 MET cc_start: -0.0037 (mmm) cc_final: -0.0583 (mmt) REVERT: I 43 LEU cc_start: 0.8394 (tp) cc_final: 0.8112 (tp) REVERT: I 58 LEU cc_start: 0.9499 (mt) cc_final: 0.9086 (mt) REVERT: I 81 LEU cc_start: 0.9526 (tp) cc_final: 0.9092 (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: 0.9117 (t80) REVERT: K 75 ILE cc_start: 0.9334 (mm) cc_final: 0.8728 (mm) REVERT: K 77 GLU cc_start: 0.9211 (mm-30) cc_final: 0.9007 (mm-30) REVERT: K 87 TYR cc_start: 0.8289 (t80) cc_final: 0.6884 (t80) REVERT: K 137 TYR cc_start: 0.7843 (m-10) cc_final: 0.7469 (m-10) outliers start: 9 outliers final: 2 residues processed: 383 average time/residue: 0.3973 time to fit residues: 213.0278 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 : 1.999 ------------------------------------------------------------------------------- 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 180 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 109 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 167 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 HIS ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 ASN E 54 ASN ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 GLN ** 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 549 ASN F 560 GLN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 71 ASN ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 69 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.064882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.049380 restraints weight = 118590.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.050906 restraints weight = 72501.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.051919 restraints weight = 52212.512| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18948 Z= 0.186 Angle : 0.757 13.569 25751 Z= 0.401 Chirality : 0.046 0.273 2849 Planarity : 0.004 0.067 3088 Dihedral : 17.091 177.730 3199 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.95 % Allowed : 9.79 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.18), residues: 2086 helix: 0.56 (0.17), residues: 948 sheet: -0.12 (0.29), residues: 309 loop : -1.72 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 339 HIS 0.007 0.001 HIS H 100 PHE 0.044 0.002 PHE I 85 TYR 0.028 0.002 TYR E 155 ARG 0.010 0.001 ARG I 49 Details of bonding type rmsd hydrogen bonds : bond 0.04912 ( 846) hydrogen bonds : angle 5.44216 ( 2401) SS BOND : bond 0.00202 ( 1) SS BOND : angle 1.44182 ( 2) covalent geometry : bond 0.00398 (18947) covalent geometry : angle 0.75714 (25749) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.9459 (pt0) cc_final: 0.9208 (pt0) REVERT: C 122 LYS cc_start: 0.9524 (OUTLIER) cc_final: 0.9187 (ptmt) REVERT: E 190 ARG cc_start: 0.8058 (mtm110) cc_final: 0.7266 (ttm110) REVERT: F 163 MET cc_start: 0.8607 (ptp) cc_final: 0.7842 (tpt) REVERT: F 257 MET cc_start: 0.9498 (mtm) cc_final: 0.9181 (mtm) REVERT: F 352 MET cc_start: 0.8801 (mmm) cc_final: 0.8241 (mmm) REVERT: F 624 MET cc_start: 0.4363 (tmm) cc_final: 0.3808 (tpp) REVERT: H 13 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7525 (pttm) REVERT: I 58 LEU cc_start: 0.9703 (mt) cc_final: 0.9446 (mt) REVERT: I 120 PHE cc_start: 0.9755 (t80) cc_final: 0.9452 (t80) REVERT: K 52 MET cc_start: 0.8667 (pmm) cc_final: 0.8368 (pmm) REVERT: K 58 LEU cc_start: 0.9623 (mm) cc_final: 0.9251 (pp) REVERT: K 113 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8397 (pptt) REVERT: K 126 TYR cc_start: 0.8707 (t80) cc_final: 0.8493 (t80) REVERT: K 137 TYR cc_start: 0.8258 (m-10) cc_final: 0.7605 (m-80) outliers start: 37 outliers final: 16 residues processed: 210 average time/residue: 0.3596 time to fit residues: 110.9115 Evaluate side-chains 154 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 499 TYR Chi-restraints excluded: chain F residue 558 SER Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 255 TYR Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 94 SER 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 201 optimal weight: 5.9990 chunk 171 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 206 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 HIS ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 HIS H 206 GLN ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 HIS ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.063752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.049447 restraints weight = 122470.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.051032 restraints weight = 72298.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.052037 restraints weight = 50764.134| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18948 Z= 0.161 Angle : 0.680 13.229 25751 Z= 0.358 Chirality : 0.044 0.267 2849 Planarity : 0.004 0.058 3088 Dihedral : 16.860 177.145 3191 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.26 % Allowed : 10.79 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.18), residues: 2086 helix: 0.68 (0.17), residues: 953 sheet: -0.11 (0.29), residues: 309 loop : -1.74 (0.19), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 339 HIS 0.012 0.001 HIS K 18 PHE 0.043 0.002 PHE F 693 TYR 0.023 0.001 TYR K 133 ARG 0.011 0.000 ARG K 49 Details of bonding type rmsd hydrogen bonds : bond 0.04403 ( 846) hydrogen bonds : angle 5.16083 ( 2401) SS BOND : bond 0.00396 ( 1) SS BOND : angle 1.21534 ( 2) covalent geometry : bond 0.00341 (18947) covalent geometry : angle 0.67959 (25749) *********************** 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 198 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 155 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.9432 (pt0) cc_final: 0.9198 (pt0) REVERT: C 97 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8766 (mm-40) REVERT: C 122 LYS cc_start: 0.9513 (OUTLIER) cc_final: 0.9205 (ptmt) REVERT: E 56 LEU cc_start: 0.8793 (tt) cc_final: 0.8454 (mt) REVERT: E 68 LYS cc_start: 0.7356 (tptt) cc_final: 0.7043 (mptt) REVERT: E 327 MET cc_start: 0.8322 (pmm) cc_final: 0.8094 (pmm) REVERT: F 41 LEU cc_start: 0.9079 (tp) cc_final: 0.8842 (tp) REVERT: F 160 MET cc_start: 0.9381 (tmm) cc_final: 0.8688 (ptm) REVERT: F 163 MET cc_start: 0.8646 (ptp) cc_final: 0.7825 (tpt) REVERT: F 257 MET cc_start: 0.9483 (OUTLIER) cc_final: 0.9054 (mtm) REVERT: F 352 MET cc_start: 0.8765 (mmm) cc_final: 0.7944 (mmm) REVERT: F 624 MET cc_start: 0.4526 (tmm) cc_final: 0.3962 (tpp) REVERT: H 226 MET cc_start: 0.9258 (tpp) cc_final: 0.8441 (tpp) REVERT: I 58 LEU cc_start: 0.9688 (mt) cc_final: 0.9364 (mt) REVERT: I 120 PHE cc_start: 0.9748 (t80) cc_final: 0.9376 (t80) REVERT: K 58 LEU cc_start: 0.9580 (mm) cc_final: 0.9196 (pp) REVERT: K 137 TYR cc_start: 0.8538 (m-10) cc_final: 0.8264 (m-80) outliers start: 43 outliers final: 23 residues processed: 190 average time/residue: 0.3570 time to fit residues: 99.3048 Evaluate side-chains 155 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS 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 E residue 178 ASP Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain F residue 279 ARG Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 499 TYR Chi-restraints excluded: chain F residue 558 SER Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 13 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 78 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 86 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 135 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 192 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 GLN ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 731 ASN H 17 HIS ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.060934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.047015 restraints weight = 127188.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.048516 restraints weight = 74896.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.049451 restraints weight = 52616.459| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 18948 Z= 0.241 Angle : 0.707 13.059 25751 Z= 0.373 Chirality : 0.045 0.299 2849 Planarity : 0.004 0.054 3088 Dihedral : 16.775 178.859 3189 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.47 % Allowed : 12.63 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.18), residues: 2086 helix: 0.72 (0.17), residues: 949 sheet: -0.47 (0.28), residues: 355 loop : -1.76 (0.20), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 339 HIS 0.015 0.001 HIS K 18 PHE 0.027 0.002 PHE I 85 TYR 0.017 0.002 TYR E 155 ARG 0.007 0.001 ARG K 91 Details of bonding type rmsd hydrogen bonds : bond 0.04163 ( 846) hydrogen bonds : angle 5.19759 ( 2401) SS BOND : bond 0.01048 ( 1) SS BOND : angle 1.06396 ( 2) covalent geometry : bond 0.00505 (18947) covalent geometry : angle 0.70716 (25749) *********************** 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 191 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 144 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.9418 (pt0) cc_final: 0.9141 (pt0) REVERT: C 97 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8738 (mm-40) REVERT: C 122 LYS cc_start: 0.9546 (OUTLIER) cc_final: 0.9166 (ptmt) REVERT: E 40 MET cc_start: 0.8446 (mmp) cc_final: 0.8170 (mmp) REVERT: E 68 LYS cc_start: 0.7310 (tptt) cc_final: 0.6925 (mptt) REVERT: E 125 ASN cc_start: 0.9182 (OUTLIER) cc_final: 0.8878 (t0) REVERT: E 289 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6781 (mm) REVERT: E 327 MET cc_start: 0.8481 (pmm) cc_final: 0.8263 (pmm) REVERT: F 1 MET cc_start: 0.7326 (mmt) cc_final: 0.6936 (mmt) REVERT: F 41 LEU cc_start: 0.9255 (tp) cc_final: 0.9029 (tp) REVERT: F 163 MET cc_start: 0.8817 (ptp) cc_final: 0.8043 (tpt) REVERT: F 257 MET cc_start: 0.9431 (OUTLIER) cc_final: 0.8961 (mtm) REVERT: F 352 MET cc_start: 0.8839 (mmm) cc_final: 0.7951 (mmm) REVERT: F 463 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.8225 (p90) REVERT: F 624 MET cc_start: 0.4729 (tmm) cc_final: 0.4311 (tpp) REVERT: H 51 ASP cc_start: 0.8670 (p0) cc_final: 0.8185 (p0) REVERT: H 187 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.8675 (tt) REVERT: H 226 MET cc_start: 0.9392 (tpp) cc_final: 0.8536 (tpp) REVERT: I 41 ASN cc_start: 0.9063 (m-40) cc_final: 0.8521 (m-40) REVERT: I 52 MET cc_start: 0.9559 (pmm) cc_final: 0.9304 (pmm) REVERT: I 96 ASP cc_start: 0.9401 (OUTLIER) cc_final: 0.9083 (m-30) REVERT: I 120 PHE cc_start: 0.9713 (t80) cc_final: 0.9284 (t80) REVERT: I 126 TYR cc_start: 0.9226 (t80) cc_final: 0.9004 (t80) REVERT: K 72 GLU cc_start: 0.9397 (OUTLIER) cc_final: 0.9083 (pm20) REVERT: K 137 TYR cc_start: 0.8739 (m-10) cc_final: 0.8299 (m-80) outliers start: 47 outliers final: 23 residues processed: 180 average time/residue: 0.3381 time to fit residues: 91.1127 Evaluate side-chains 152 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain F residue 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 187 LEU Chi-restraints excluded: chain H residue 255 TYR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 91 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 99 optimal weight: 0.0970 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN E 117 HIS E 196 ASN ** 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** ** I 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.061917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.047876 restraints weight = 123288.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.049428 restraints weight = 72408.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.050417 restraints weight = 50510.408| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18948 Z= 0.130 Angle : 0.629 12.919 25751 Z= 0.334 Chirality : 0.043 0.293 2849 Planarity : 0.003 0.053 3088 Dihedral : 16.638 179.102 3189 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.32 % Allowed : 13.47 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.18), residues: 2086 helix: 0.96 (0.17), residues: 944 sheet: -0.38 (0.28), residues: 356 loop : -1.58 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 52 HIS 0.004 0.001 HIS B 110 PHE 0.022 0.001 PHE I 85 TYR 0.017 0.001 TYR H 184 ARG 0.004 0.000 ARG K 91 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 846) hydrogen bonds : angle 4.92800 ( 2401) SS BOND : bond 0.00273 ( 1) SS BOND : angle 1.29443 ( 2) covalent geometry : bond 0.00269 (18947) covalent geometry : angle 0.62875 (25749) *********************** 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 186 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 142 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.9441 (pt0) cc_final: 0.9124 (pt0) REVERT: C 97 GLN cc_start: 0.8930 (mm-40) cc_final: 0.8633 (mm-40) REVERT: C 108 LYS cc_start: 0.9562 (OUTLIER) cc_final: 0.9355 (mtpp) REVERT: C 122 LYS cc_start: 0.9545 (OUTLIER) cc_final: 0.9187 (ptmt) REVERT: E 40 MET cc_start: 0.8479 (mmp) cc_final: 0.8184 (mmp) REVERT: E 68 LYS cc_start: 0.7396 (tptt) cc_final: 0.7024 (mptt) REVERT: E 125 ASN cc_start: 0.9103 (OUTLIER) cc_final: 0.8739 (t0) REVERT: E 289 LEU cc_start: 0.6889 (mm) cc_final: 0.6679 (tp) REVERT: F 1 MET cc_start: 0.7273 (mmt) cc_final: 0.6923 (mmt) REVERT: F 41 LEU cc_start: 0.9231 (tp) cc_final: 0.9002 (tp) REVERT: F 160 MET cc_start: 0.9406 (tmm) cc_final: 0.8825 (ptm) REVERT: F 163 MET cc_start: 0.8768 (ptp) cc_final: 0.7985 (tpt) REVERT: F 257 MET cc_start: 0.9439 (mtp) cc_final: 0.8951 (mtm) REVERT: F 352 MET cc_start: 0.8733 (mmm) cc_final: 0.7861 (mmm) REVERT: F 471 GLN cc_start: 0.8421 (mp10) cc_final: 0.8091 (tm-30) REVERT: F 624 MET cc_start: 0.4279 (tmm) cc_final: 0.3886 (tpp) REVERT: H 129 GLN cc_start: 0.8699 (mp10) cc_final: 0.8484 (mm-40) REVERT: H 226 MET cc_start: 0.9371 (tpp) cc_final: 0.8686 (tpp) REVERT: I 41 ASN cc_start: 0.9176 (m-40) cc_final: 0.8634 (m-40) REVERT: I 52 MET cc_start: 0.9567 (OUTLIER) cc_final: 0.9198 (pmm) REVERT: I 85 PHE cc_start: 0.9656 (m-80) cc_final: 0.9447 (m-80) REVERT: I 96 ASP cc_start: 0.9376 (OUTLIER) cc_final: 0.9050 (m-30) REVERT: I 120 PHE cc_start: 0.9692 (t80) cc_final: 0.9294 (t80) REVERT: I 124 CYS cc_start: 0.9452 (m) cc_final: 0.9203 (m) REVERT: I 126 TYR cc_start: 0.9177 (t80) cc_final: 0.8945 (t80) REVERT: I 130 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9125 (mm) REVERT: K 52 MET cc_start: 0.8800 (pmm) cc_final: 0.8358 (pmm) REVERT: K 72 GLU cc_start: 0.9408 (OUTLIER) cc_final: 0.8998 (pm20) REVERT: K 78 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9419 (mm) REVERT: K 120 PHE cc_start: 0.9506 (t80) cc_final: 0.9199 (t80) REVERT: K 137 TYR cc_start: 0.8787 (m-10) cc_final: 0.8227 (m-10) outliers start: 44 outliers final: 24 residues processed: 178 average time/residue: 0.3623 time to fit residues: 95.6405 Evaluate side-chains 157 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 567 TYR Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 255 TYR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 116 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 184 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 ASN ** F 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 71 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.059495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.045775 restraints weight = 129205.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.047262 restraints weight = 75704.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.048211 restraints weight = 52922.384| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 18948 Z= 0.236 Angle : 0.690 12.866 25751 Z= 0.367 Chirality : 0.044 0.310 2849 Planarity : 0.004 0.051 3088 Dihedral : 16.647 178.979 3189 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.21 % Allowed : 14.00 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.18), residues: 2086 helix: 0.88 (0.17), residues: 941 sheet: -0.53 (0.28), residues: 354 loop : -1.69 (0.20), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP H 52 HIS 0.004 0.001 HIS C 62 PHE 0.019 0.002 PHE I 85 TYR 0.017 0.001 TYR E 155 ARG 0.016 0.001 ARG F 711 Details of bonding type rmsd hydrogen bonds : bond 0.04047 ( 846) hydrogen bonds : angle 5.07913 ( 2401) SS BOND : bond 0.01144 ( 1) SS BOND : angle 1.01747 ( 2) covalent geometry : bond 0.00491 (18947) covalent geometry : angle 0.68955 (25749) *********************** 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 186 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 125 time to evaluate : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7127 (mmtm) REVERT: B 201 THR cc_start: 0.9276 (OUTLIER) cc_final: 0.8961 (m) REVERT: C 122 LYS cc_start: 0.9523 (OUTLIER) cc_final: 0.9189 (ptmt) REVERT: E 40 MET cc_start: 0.8422 (mmp) cc_final: 0.8163 (mmp) REVERT: E 68 LYS cc_start: 0.7351 (tptt) cc_final: 0.6935 (mptt) REVERT: E 117 HIS cc_start: 0.7023 (t70) cc_final: 0.6724 (t70) REVERT: E 289 LEU cc_start: 0.7229 (mm) cc_final: 0.6851 (mm) REVERT: F 1 MET cc_start: 0.7243 (mmt) cc_final: 0.6939 (mmt) REVERT: F 41 LEU cc_start: 0.9246 (tp) cc_final: 0.9018 (tp) REVERT: F 160 MET cc_start: 0.9407 (tmm) cc_final: 0.8818 (ptm) REVERT: F 163 MET cc_start: 0.8946 (ptp) cc_final: 0.8126 (tpt) REVERT: F 257 MET cc_start: 0.9408 (OUTLIER) cc_final: 0.8850 (mtm) REVERT: F 352 MET cc_start: 0.8672 (mmm) cc_final: 0.7808 (mmm) REVERT: F 463 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.8156 (p90) REVERT: F 471 GLN cc_start: 0.8400 (mp10) cc_final: 0.8137 (pm20) REVERT: F 624 MET cc_start: 0.4726 (tmm) cc_final: 0.4443 (tpp) REVERT: H 129 GLN cc_start: 0.8671 (mp10) cc_final: 0.8451 (mm-40) REVERT: H 187 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.8763 (tt) REVERT: H 226 MET cc_start: 0.9419 (tpp) cc_final: 0.8576 (tpp) REVERT: I 52 MET cc_start: 0.9598 (OUTLIER) cc_final: 0.9269 (pmm) REVERT: I 96 ASP cc_start: 0.9344 (OUTLIER) cc_final: 0.9018 (m-30) REVERT: K 72 GLU cc_start: 0.9410 (OUTLIER) cc_final: 0.9052 (pm20) REVERT: K 78 LEU cc_start: 0.9695 (OUTLIER) cc_final: 0.9397 (mm) REVERT: K 137 TYR cc_start: 0.8963 (m-10) cc_final: 0.8449 (m-10) outliers start: 61 outliers final: 33 residues processed: 174 average time/residue: 0.3453 time to fit residues: 89.3667 Evaluate side-chains 156 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 113 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 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 155 ASN Chi-restraints excluded: chain F residue 257 MET 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 486 ILE 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 13 LYS Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 255 TYR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 86 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 42 optimal weight: 0.5980 chunk 121 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 176 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 ASN F 165 HIS F 722 ASN ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.059710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.046151 restraints weight = 126753.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.047612 restraints weight = 73756.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.048550 restraints weight = 51506.508| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18948 Z= 0.173 Angle : 0.644 12.772 25751 Z= 0.343 Chirality : 0.043 0.315 2849 Planarity : 0.003 0.049 3088 Dihedral : 16.531 178.973 3189 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.21 % Allowed : 14.00 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.18), residues: 2086 helix: 0.97 (0.17), residues: 944 sheet: -0.39 (0.29), residues: 342 loop : -1.65 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 52 HIS 0.002 0.001 HIS A 72 PHE 0.018 0.001 PHE I 16 TYR 0.026 0.001 TYR E 78 ARG 0.006 0.000 ARG K 91 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 846) hydrogen bonds : angle 4.99085 ( 2401) SS BOND : bond 0.00666 ( 1) SS BOND : angle 1.25958 ( 2) covalent geometry : bond 0.00362 (18947) covalent geometry : angle 0.64382 (25749) *********************** 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 187 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 126 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.8970 (m) REVERT: C 122 LYS cc_start: 0.9517 (OUTLIER) cc_final: 0.9177 (ptmt) REVERT: E 40 MET cc_start: 0.8386 (mmp) cc_final: 0.8118 (mmp) REVERT: E 68 LYS cc_start: 0.7540 (tptt) cc_final: 0.7101 (mptt) REVERT: E 117 HIS cc_start: 0.7258 (t70) cc_final: 0.6747 (t70) REVERT: E 125 ASN cc_start: 0.9214 (OUTLIER) cc_final: 0.8981 (t0) REVERT: E 289 LEU cc_start: 0.6533 (mm) cc_final: 0.6311 (tp) REVERT: F 1 MET cc_start: 0.7078 (mmt) cc_final: 0.6751 (mmt) REVERT: F 163 MET cc_start: 0.8922 (ptp) cc_final: 0.8197 (tpt) REVERT: F 257 MET cc_start: 0.9405 (OUTLIER) cc_final: 0.8887 (mtm) REVERT: F 352 MET cc_start: 0.8648 (mmm) cc_final: 0.7811 (mmm) REVERT: F 463 TYR cc_start: 0.8766 (OUTLIER) cc_final: 0.8147 (p90) REVERT: F 471 GLN cc_start: 0.8330 (mp10) cc_final: 0.8026 (pm20) REVERT: F 624 MET cc_start: 0.4865 (tmm) cc_final: 0.4653 (tpp) REVERT: H 187 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.8881 (tt) REVERT: H 226 MET cc_start: 0.9386 (tpp) cc_final: 0.8599 (tpp) REVERT: I 52 MET cc_start: 0.9575 (OUTLIER) cc_final: 0.9251 (pmm) REVERT: I 96 ASP cc_start: 0.9371 (OUTLIER) cc_final: 0.9043 (m-30) REVERT: I 126 TYR cc_start: 0.9253 (t80) cc_final: 0.9053 (t80) REVERT: K 72 GLU cc_start: 0.9345 (OUTLIER) cc_final: 0.8899 (pm20) REVERT: K 78 LEU cc_start: 0.9719 (OUTLIER) cc_final: 0.9443 (mm) REVERT: K 87 TYR cc_start: 0.8799 (t80) cc_final: 0.8423 (t80) REVERT: K 126 TYR cc_start: 0.9005 (t80) cc_final: 0.8730 (t80) REVERT: K 137 TYR cc_start: 0.9026 (m-10) cc_final: 0.8529 (m-10) outliers start: 61 outliers final: 33 residues processed: 175 average time/residue: 0.3331 time to fit residues: 88.1789 Evaluate side-chains 159 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 116 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 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 125 ASN Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 257 MET 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 486 ILE Chi-restraints excluded: chain F residue 540 PHE Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 567 TYR Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 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 99 HIS Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 255 TYR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 94 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 62 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 ASN ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 ASN H 129 GLN ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.057443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.044182 restraints weight = 128845.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.045587 restraints weight = 74883.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.046481 restraints weight = 52248.270| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.6038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 18948 Z= 0.285 Angle : 0.758 12.701 25751 Z= 0.400 Chirality : 0.046 0.339 2849 Planarity : 0.004 0.048 3088 Dihedral : 16.745 179.688 3189 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.00 % Allowed : 15.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.18), residues: 2086 helix: 0.71 (0.17), residues: 944 sheet: -0.65 (0.28), residues: 347 loop : -1.85 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 52 HIS 0.006 0.001 HIS C 72 PHE 0.017 0.002 PHE E 243 TYR 0.031 0.002 TYR E 78 ARG 0.006 0.001 ARG E 190 Details of bonding type rmsd hydrogen bonds : bond 0.04281 ( 846) hydrogen bonds : angle 5.27803 ( 2401) SS BOND : bond 0.01554 ( 1) SS BOND : angle 1.58554 ( 2) covalent geometry : bond 0.00592 (18947) covalent geometry : angle 0.75817 (25749) *********************** 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 173 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 116 time to evaluate : 2.106 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: B 201 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.8942 (m) REVERT: C 122 LYS cc_start: 0.9532 (OUTLIER) cc_final: 0.9217 (ptmt) REVERT: E 40 MET cc_start: 0.8381 (mmp) cc_final: 0.8120 (mmp) REVERT: E 68 LYS cc_start: 0.7419 (tptt) cc_final: 0.6963 (mptt) REVERT: E 117 HIS cc_start: 0.7212 (t70) cc_final: 0.6613 (t70) REVERT: E 289 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6996 (mm) REVERT: F 1 MET cc_start: 0.7004 (mmt) cc_final: 0.6671 (mmt) REVERT: F 160 MET cc_start: 0.9474 (tmm) cc_final: 0.8911 (ptm) REVERT: F 163 MET cc_start: 0.9097 (ptp) cc_final: 0.8423 (tpt) REVERT: F 257 MET cc_start: 0.9446 (OUTLIER) cc_final: 0.8779 (mtm) REVERT: F 352 MET cc_start: 0.8656 (mmm) cc_final: 0.7763 (mmm) REVERT: F 463 TYR cc_start: 0.8863 (OUTLIER) cc_final: 0.8200 (p90) REVERT: H 226 MET cc_start: 0.9422 (tpp) cc_final: 0.8615 (tpp) REVERT: I 52 MET cc_start: 0.9569 (OUTLIER) cc_final: 0.9259 (pmm) REVERT: I 96 ASP cc_start: 0.9323 (OUTLIER) cc_final: 0.9003 (m-30) REVERT: K 49 ARG cc_start: 0.8870 (ppt170) cc_final: 0.8551 (ppt170) REVERT: K 72 GLU cc_start: 0.9369 (OUTLIER) cc_final: 0.8962 (pm20) REVERT: K 87 TYR cc_start: 0.8832 (t80) cc_final: 0.8448 (t80) REVERT: K 137 TYR cc_start: 0.9139 (m-10) cc_final: 0.8732 (m-10) outliers start: 57 outliers final: 42 residues processed: 159 average time/residue: 0.3432 time to fit residues: 83.4811 Evaluate side-chains 159 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 109 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 110 HIS 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 91 ILE Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain F residue 155 ASN Chi-restraints excluded: chain F residue 257 MET 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 486 ILE Chi-restraints excluded: chain F residue 540 PHE Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 558 SER Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 255 TYR Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain I residue 16 PHE Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain K residue 14 MET Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 94 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 88 optimal weight: 1.9990 chunk 205 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 196 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 ASN ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.059073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.045655 restraints weight = 127428.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.047091 restraints weight = 73328.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.048039 restraints weight = 50899.150| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.6107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18948 Z= 0.139 Angle : 0.662 12.488 25751 Z= 0.348 Chirality : 0.044 0.325 2849 Planarity : 0.004 0.117 3088 Dihedral : 16.572 179.981 3189 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.16 % Allowed : 16.32 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.18), residues: 2086 helix: 0.91 (0.17), residues: 946 sheet: -0.56 (0.29), residues: 333 loop : -1.67 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 52 HIS 0.006 0.001 HIS F 165 PHE 0.029 0.001 PHE F 47 TYR 0.048 0.001 TYR I 126 ARG 0.017 0.001 ARG E 319 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 846) hydrogen bonds : angle 4.98982 ( 2401) SS BOND : bond 0.00425 ( 1) SS BOND : angle 1.37524 ( 2) covalent geometry : bond 0.00290 (18947) covalent geometry : angle 0.66177 (25749) *********************** 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 164 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 2.319 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: C 122 LYS cc_start: 0.9527 (OUTLIER) cc_final: 0.9199 (ptmt) REVERT: E 68 LYS cc_start: 0.7582 (tptt) cc_final: 0.7111 (mptt) REVERT: E 125 ASN cc_start: 0.9205 (OUTLIER) cc_final: 0.8904 (t0) REVERT: E 289 LEU cc_start: 0.6861 (mm) cc_final: 0.6568 (mm) REVERT: F 160 MET cc_start: 0.9478 (tmm) cc_final: 0.8877 (ptm) REVERT: F 163 MET cc_start: 0.9068 (ptp) cc_final: 0.8241 (tpt) REVERT: F 257 MET cc_start: 0.9419 (OUTLIER) cc_final: 0.8811 (mtm) REVERT: F 296 LEU cc_start: 0.9899 (OUTLIER) cc_final: 0.9623 (mt) REVERT: F 352 MET cc_start: 0.8676 (mmm) cc_final: 0.7899 (mmm) REVERT: F 463 TYR cc_start: 0.8893 (OUTLIER) cc_final: 0.8218 (p90) REVERT: H 226 MET cc_start: 0.9388 (tpp) cc_final: 0.8605 (tpp) REVERT: I 52 MET cc_start: 0.9524 (OUTLIER) cc_final: 0.9164 (pmm) REVERT: I 96 ASP cc_start: 0.9332 (OUTLIER) cc_final: 0.9003 (m-30) REVERT: K 26 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8802 (pptt) REVERT: K 49 ARG cc_start: 0.8855 (ppt170) cc_final: 0.8508 (ppt170) REVERT: K 72 GLU cc_start: 0.9315 (OUTLIER) cc_final: 0.8863 (pm20) REVERT: K 87 TYR cc_start: 0.8836 (t80) cc_final: 0.8561 (t80) REVERT: K 126 TYR cc_start: 0.9054 (t80) cc_final: 0.8807 (t80) REVERT: K 137 TYR cc_start: 0.9083 (m-10) cc_final: 0.8682 (m-10) outliers start: 41 outliers final: 28 residues processed: 154 average time/residue: 0.3328 time to fit residues: 77.9368 Evaluate side-chains 149 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 110 HIS 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 125 ASN Chi-restraints excluded: chain F residue 257 MET 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 486 ILE Chi-restraints excluded: chain F residue 540 PHE Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 567 TYR Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 53 optimal weight: 0.9990 chunk 182 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 152 optimal weight: 9.9990 chunk 159 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 156 optimal weight: 0.4980 chunk 95 optimal weight: 6.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.057808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.044586 restraints weight = 130388.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.045969 restraints weight = 75005.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.046884 restraints weight = 52278.791| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.6340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18948 Z= 0.226 Angle : 0.713 12.768 25751 Z= 0.374 Chirality : 0.045 0.318 2849 Planarity : 0.004 0.074 3088 Dihedral : 16.535 179.731 3189 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.11 % Allowed : 16.63 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.18), residues: 2086 helix: 0.87 (0.17), residues: 945 sheet: -0.57 (0.29), residues: 336 loop : -1.73 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 52 HIS 0.005 0.001 HIS K 18 PHE 0.036 0.002 PHE K 120 TYR 0.044 0.002 TYR I 126 ARG 0.013 0.001 ARG E 319 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 846) hydrogen bonds : angle 5.11072 ( 2401) SS BOND : bond 0.01085 ( 1) SS BOND : angle 1.67308 ( 2) covalent geometry : bond 0.00476 (18947) covalent geometry : angle 0.71335 (25749) ********************** 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: 40 poor density : 112 time to evaluate : 2.174 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: B 201 THR cc_start: 0.9232 (OUTLIER) cc_final: 0.8951 (m) REVERT: C 122 LYS cc_start: 0.9534 (OUTLIER) cc_final: 0.9199 (ptmt) REVERT: E 68 LYS cc_start: 0.7488 (tptt) cc_final: 0.7003 (mptt) REVERT: E 117 HIS cc_start: 0.7161 (t70) cc_final: 0.6693 (t70) REVERT: E 289 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6540 (mm) REVERT: F 8 MET cc_start: 0.9012 (ptp) cc_final: 0.8762 (mpp) REVERT: F 160 MET cc_start: 0.9492 (tmm) cc_final: 0.9234 (ttt) REVERT: F 163 MET cc_start: 0.9130 (ptp) cc_final: 0.8443 (tpt) REVERT: F 257 MET cc_start: 0.9416 (OUTLIER) cc_final: 0.8705 (mtm) REVERT: F 296 LEU cc_start: 0.9901 (OUTLIER) cc_final: 0.9613 (mt) REVERT: F 352 MET cc_start: 0.8603 (mmm) cc_final: 0.7745 (mmm) REVERT: F 463 TYR cc_start: 0.8896 (OUTLIER) cc_final: 0.8205 (p90) REVERT: F 624 MET cc_start: 0.6909 (OUTLIER) cc_final: 0.4651 (mpp) REVERT: H 226 MET cc_start: 0.9395 (tpp) cc_final: 0.8560 (tpp) REVERT: I 52 MET cc_start: 0.9542 (OUTLIER) cc_final: 0.9209 (pmm) REVERT: I 96 ASP cc_start: 0.9329 (OUTLIER) cc_final: 0.9000 (m-30) REVERT: K 49 ARG cc_start: 0.8890 (ppt170) cc_final: 0.8544 (ppt170) REVERT: K 72 GLU cc_start: 0.9317 (OUTLIER) cc_final: 0.8891 (pm20) REVERT: K 78 LEU cc_start: 0.9718 (OUTLIER) cc_final: 0.9444 (mm) REVERT: K 87 TYR cc_start: 0.8865 (t80) cc_final: 0.8551 (t80) REVERT: K 120 PHE cc_start: 0.9423 (t80) cc_final: 0.9212 (t80) REVERT: K 137 TYR cc_start: 0.9100 (m-10) cc_final: 0.8689 (m-10) outliers start: 40 outliers final: 29 residues processed: 140 average time/residue: 0.3804 time to fit residues: 81.0757 Evaluate side-chains 151 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain F residue 257 MET 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 486 ILE Chi-restraints excluded: chain F residue 540 PHE Chi-restraints excluded: chain F residue 551 ILE 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 F residue 624 MET Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 14 THR 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 99 HIS Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain I residue 16 PHE Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 43 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 184 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 0.0170 chunk 186 optimal weight: 0.7980 chunk 48 optimal weight: 0.0980 chunk 61 optimal weight: 0.9980 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.059377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.045966 restraints weight = 124756.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.047432 restraints weight = 72254.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.048381 restraints weight = 50099.591| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.6385 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= 0.127 Angle : 0.664 12.837 25751 Z= 0.344 Chirality : 0.044 0.318 2849 Planarity : 0.004 0.058 3088 Dihedral : 16.366 179.402 3189 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.00 % Allowed : 16.74 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.18), residues: 2086 helix: 1.01 (0.17), residues: 943 sheet: -0.47 (0.30), residues: 331 loop : -1.54 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 52 HIS 0.004 0.001 HIS F 165 PHE 0.035 0.001 PHE K 120 TYR 0.042 0.001 TYR I 126 ARG 0.012 0.000 ARG E 319 Details of bonding type rmsd hydrogen bonds : bond 0.03569 ( 846) hydrogen bonds : angle 4.86273 ( 2401) SS BOND : bond 0.00350 ( 1) SS BOND : angle 1.30243 ( 2) covalent geometry : bond 0.00269 (18947) covalent geometry : angle 0.66419 (25749) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6425.23 seconds wall clock time: 113 minutes 9.37 seconds (6789.37 seconds total)